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Shigeyuki Yokoyama

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Yukuhiko Asada; Akio Ebihara; Tetsuya Ishikawa; Eri Kaminuma; Norio Kobayashi; Yoshihiro Agari; Seiki Kuramitsu; Yoshinori Matsuura; Hisashi Mizutani; Hisashi Naitow; Koro Nishikata; Sayoko Shimoyama; Akeo Shinkai; Michihiro Sugahara; Tomoyuki Tanaka; Tetsuro Toyoda; Shigeyuki Yokoyama; Naoki Kunishima
Integrated database of information from structural genomics experiments.
Michiko Kimoto; Ken-Ichiro Matsunaga; Rie Yamashige; Shigeyuki Yokoyama; Ichiro Hirao
Generation of high-affinity DNA aptamers using an expanded genetic alphabet.
Tomonari Muramatsu; Wataru Nishii; Mikako Shirouzu; Takaho Terada; Yong-Tae Kim; Shigeyuki Yokoyama
Autoprocessing mechanism of severe acute respiratory syndrome coronavirus 3C-like protease (SARS-CoV 3CL(pro) ) from its polyproteins.

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All Publications

2013: Yukuhiko Asada; Akio Ebihara; Tetsuya Ishikawa; Eri Kaminuma; Norio Kobayashi; Yoshihiro Agari; Seiki Kuramitsu; Yoshinori Matsuura; Hisashi Mizutani; Hisashi Naitow; Koro Nishikata; Sayoko Shimoyama; Akeo Shinkai; Michihiro Sugahara; Tomoyuki Tanaka; Tetsuro Toyoda; Shigeyuki Yokoyama; Naoki Kunishima
Integrated database of information from structural genomics experiments.
Acta crystallographica. Section D, Biological crystallography 2013;69(Pt 5):914-9.
2013: Michiko Kimoto; Ken-Ichiro Matsunaga; Rie Yamashige; Shigeyuki Yokoyama; Ichiro Hirao
Generation of high-affinity DNA aptamers using an expanded genetic alphabet.
Nature biotechnology 2013;31(5):453-7.
2013: Tomonari Muramatsu; Wataru Nishii; Mikako Shirouzu; Takaho Terada; Yong-Tae Kim; Shigeyuki Yokoyama
Autoprocessing mechanism of severe acute respiratory syndrome coronavirus 3C-like protease (SARS-CoV 3CL(pro) ) from its polyproteins.
The FEBS journal 2013;280(9):2002-13.
2013: Kazuhiko Yamasaki; Takanori Kigawa; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama
DNA-binding domains of plant-specific transcription factors: structure, function, and evolution.
Trends in plant science 2013;18(5):267-76.
2013: Yoriko Saito; Mikako Shirouzu; Leonard D Shultz; Akiko Sone; Nahoko Suzuki; Shinsuke Takagi; Akiko Tanaka; Satoshi Tanaka; Shuichi Taniguchi; Yuri Tomabechi; Mariko Tomizawa-Murasawa; Naoyuki Uchida; Motoaki Wakiyama; Shigeyuki Yokoyama; Hitomi Yuki; Yuki Aoki; Takehiro Fukami; Toshio Goto; Noriko Handa; Yoshinobu Hashizume; Teruki Honma; Hiroshi Kajita; Akiko Kaneko; Mitsuo Kuratani; Junko Mikuni; Yuho Najima; Ikuko Ogahara; Osamu Ohara; Fumihiko Ishikawa
A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo.
Science translational medicine 2013;5(181):181ra52.
2013: Yuzuru Itoh; Shun-ichi Sekine; Dieter Söll; Shiro Suetsugu; Markus J Bröcker; Gifty Hammond; Shigeyuki Yokoyama
Decameric SelA•tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation.
Science (New York, N.Y.) 2013;340(6128):75-8.
2013: Hideaki Niwa; Noboru Ohsawa; Mikako Shirouzu; Yuri Tomabechi; Mitsutoshi Toyama; Takashi Umehara; Noriko Handa; Tomoya Hirano; Keiko Honda; Hiroyuki Kagechika; Shigeyuki Yokoyama
Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives.
Acta crystallographica. Section D, Biological crystallography 2013;69(Pt 4):595-602.
2013: Aribam Swarmistha Devi; Akio Ebihara; Thirumananseri Kumarevel; Seiki Kuramitsu; Shigeyuki Yokoyama; Karthe Ponnuraj
Crystal structure of type I 3-dehydroquinate dehydratase of Aquifex aeolicus suggests closing of active site flap is not essential for enzyme action.
Biochemical and biophysical research communications 2013;432(2):350-4.
2013: Yuko Murayama; Shun-ichi Sekine; Shigeyuki Yokoyama
Crystallization and preliminary X-ray crystallographic analyses of Thermus thermophilus backtracked RNA polymerase.
Acta crystallographica. Section F, Structural biology and crystallization communications 2013;69(Pt 2):174-7.
2013: Preethi Ragunathan; Shigeyuki Yokoyama; Thirumananseri Kumarevel; Seiki Kuramitsu; Gokul Raghunath; Karthe Ponnuraj
Crystallization, characterization and preliminary X-ray crystallographic analysis of GK2848, a putative carbonic anhydrase of Geobacillus kaustophilus.
Acta crystallographica. Section F, Structural biology and crystallization communications 2013;69(Pt 2):162-4.
2013: Keiko Tsuganezawa; Rei Utata; Shigeyuki Yokoyama; Shigenao Taruya; Masaaki Aoki; Morio Endoh; Yoshinobu Hashizume; Teruki Honma; Takuma Kasai; Miki Kato; Takanori Kigawa; Hirotatsu Kojima; Masumi Mori; Tetsuo Nagano; Yukari Nakagawa; Naoko Ogawa; Takayoshi Okabe; Fumio Takahashi; Akiko Tanaka
A fluorescent-based high-throughput screening assay for small molecules that inhibit the interaction of MdmX with p53.
Journal of biomolecular screening 2013;18(2):191-8.
2013: Satoshi Arai; Yoshiko Ishizuka-Katsura; So Iwata; Yoshimi Kakinuma; Kenji Mizutani; Noboru Ohsawa; Shinya Saijo; Mikako Shirouzu; Kano Suzuki; Takaho Terada; Ichiro Yamato; Shigeyuki Yokoyama; Takeshi Murata
Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures.
Nature 2013;493(7434):703-7.
2013: Aya Komori; Jacobus Johannes Marion Meyer; Tomoko Nishizawa; Hikaru Seki; Hideaki Shimizu; Munenori Suzuki; Shigeyuki Yokoyama; Toshiya Muranaka
Comparative functional analysis of CYP71AV1 natural variants reveals an important residue for the successive oxidation of amorpha-4,11-diene.
FEBS letters 2013;587(3):278-84.
2013: S Yoshikawa; Lieping Chen; T Fujimoto; N Handa; S Kawa; T Kobayashi; Mutsuko Kukimoto-Niino; Z-J Liu; L Parker; S Sano; M Sato; K Semba; Mikako Shirouzu; T Tanaka; Takaho Terada; Y Terazawa; Motoaki Wakiyama; B-C Wang; Tadashi Yamamoto; Shigeyuki Yokoyama
Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor.
Oncogene 2013;32(1):27-38.
2013: Kenji Fukui; Atsuhiro Shimada; Shigeyuki Yokoyama; Yoshitaka Bessho; Seiki Kuramitsu
Thermostable Mismatch-Recognizing Protein MutS Suppresses Nonspecific Amplification during Polymerase Chain Reaction (PCR).
International journal of molecular sciences 2013;14(3):6436-53.
2013: Suhaila Rahman; Shinya Saijo; Mikako Shirouzu; Takaho Terada; Ichiro Yamato; Shigeyuki Yokoyama; Yoshiko Ishizuka-Katsura; So Iwata; Kenji Mizutani; Noboru Ohsawa; Takeshi Murata
Biochemical and biophysical properties of interactions between subunits of the peripheral stalk region of human V-ATPase.
PloS one 2013;8(2):e55704.
2013: Tatsuo Yanagisawa; Ryohei Ishii; Tomomi Sumida; Shigeyuki Yokoyama
A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site.
Acta crystallographica. Section D, Biological crystallography 2013;69(Pt 1):5-15.
2012: Kazutaka Murayama; Ryogo Akasaka; Miyuki Kato-Murayama; Takaho Terada; Shigeyuki Yokoyama; Mikako Shirouzu
Structure of the Rho-specific guanine nucleotide-exchange factor Xpln.
Acta crystallographica. Section F, Structural biology and crystallization communications 2012;68(Pt 12):1455-9.
2012: Fahu He; Takanori Kigawa; Naohiro Kobayashi; Kanako Kuwasako; Mikako Shirouzu; Mari Takahashi; Takaho Terada; Kengo Tsuda; Satoru Watanabe; Shigeyuki Yokoyama; Peter Güntert; Yutaka Muto
Structural insight into the interaction of ADP-ribose with the PARP WWE domains.
FEBS letters 2012;586(21):3858-64.
2012: Akio Kawahara-Kobayashi; Yuhei Araiso; Shun Asami; Naoshi Dohmae; Ryuichiro Ishitani; Takanori Kigawa; Atsushi Kohda; Akiko Masuda; Takayoshi Matsuda; Osamu Nureki; Yoko Sakai; Masahiko Uchiyama; Shigeyuki Yokoyama; Daisuke Kiga
Simplification of the genetic code: restricted diversity of genetically encoded amino acids.
Nucleic acids research 2012;40(20):10576-84.
2012: Kazutaka Murayama; Kazunari Arima; Toshiaki Hosaka; Miyuki Kato-Murayama; Ami Sotokawauchi; Shigeyuki Yokoyama; Mikako Shirouzu
Crystal structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L.
Journal of molecular biology 2012;423(3):386-96.
2012: Miki Hara-Yokoyama; Satoru Harumiya; Noritaka Hashii; Nobumasa Hino; Yoshio Hirabayashi; Yoko Hiruta; Satsuki Itoh; Yoko Kaitsu; Takeshi Kasama; Toshiaki Katada; Nana Kawasaki; Mutsuko Kukimoto-Niino; Tomoko Matsumoto; Chiemi Mishima-Tsumagari; Katarzyna A Podyma-Inoue; Kensaku Sakamoto; Mikako Shirouzu; Kiyoshi Takatsu; Hiroshi Takayanagi; Kazue Terasawa; Naoko Utsunomiya-Tate; Motoaki Wakiyama; Shigeyuki Yokoyama; Masaki Yanagishita
Tetrameric interaction of the ectoenzyme CD38 on the cell surface enables its catalytic and raft-association activities.
Structure (London, England : 1993) 2012;20(9):1585-95.
2012: Yuzuru Itoh; Shun-ichi Sekine; Shigeyuki Yokoyama
Crystallization and preliminary X-ray crystallographic analysis of Aquifex aeolicus SelA, a bacterial selenocysteine synthase.
Acta crystallographica. Section F, Structural biology and crystallization communications 2012;68(Pt 9):1128-33.
2012: Motoaki Wakiyama; Yoko Kaitsu; Reiko Muramatsu; Koji Takimoto; Shigeyuki Yokoyama
Tethering of proteins to RNAs using the bovine immunodeficiency virus-Tat peptide and BIV-TAR RNA.
Analytical biochemistry 2012;427(2):130-2.
2012: Alexander A Tokmakov; Mitsutoshi Toyama; Yasuo Fukami; Atsushi Kurotani; Mikako Shirouzu; Tetsuo Takagi; Shigeyuki Yokoyama
Multiple post-translational modifications affect heterologous protein synthesis.
The Journal of biological chemistry 2012;287(32):27106-16.
2012: Lorien J Parker; Mikako Shirouzu; Noriko Handa; Teruki Honma; Tetsuo Nagano; Naoko Ogawa; Yuri Tomabechi; Keiko Tsuganezawa; Hisami Watanabe; Shigeyuki Yokoyama; Hitomi Yuki; Akiko Tanaka
Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor.
Acta crystallographica. Section F, Structural biology and crystallization communications 2012;68(Pt 8):860-6.
2012: Naohiro Kobayashi; Steve Mading; John L Markley; Eiichi Nakatani; Naoya Tochio; Eldon L Ulrich; Shigeyuki Yokoyama; Hideo Akutsu; Yoko Harano; Takanori Kigawa; Toshimichi Fujiwara
An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database.
Journal of biomolecular NMR 2012;53(4):311-20.
2012: Tomohiro Sato; Mikako Shirouzu; Akiko Tanaka; Yumiko Terazawa; Keiko Tsuganezawa; Motoaki Wakiyama; Hisami Watanabe; Shigeyuki Yokoyama; Seiko Yoshikawa; Hitomi Yuki; Hirotatsu Kojima; Mutsuko Kukimoto-Niino; Junko Mikuni; Tetsuo Nagano; Takayoshi Okabe; Takako Fujimoto; Teruki Honma
Identification of novel drug-resistant EGFR mutant inhibitors by in silico screening using comprehensive assessments of protein structures.
Bioorganic & medicinal chemistry 2012;20(12):3756-67.
2012: Hirofumi Nakano; Takayoshi Okabe; Lorien Parker; Nae Saito; Yukio Tada; Akiko Tanaka; Keiko Tsuganezawa; Shigeyuki Yokoyama; Masanao Abe; Hirotatsu Kojima; Tetsuo Nagano
Rational evolution of a novel type of potent and selective proviral integration site in Moloney murine leukemia virus kinase 1 (PIM1) inhibitor from a screening-hit compound.
Journal of medicinal chemistry 2012;55(11):5151-64.
2012: Yuzuru Itoh; Shun Ichi Sekine; Shigeyuki Yokoyama
Crystallization and preliminary X-ray crystallographic analysis of bacterial tRNA(Sec) in complex with seryl-tRNA synthetase.
Acta crystallographica. Section F, Structural biology and crystallization communications 2012;68(Pt 6):678-82.
2012: Seisuke Kusano; Noboru Ohsawa; Kensaku Sakamoto; Mikako Shirouzu; Satoshi Takaki; Kiyoshi Takatsu; Miki Hara-Yokoyama; Nobumasa Hino; Masashi Ikutani; Mutsuko Kukimoto-Niino; Shigeyuki Yokoyama
Structural basis of interleukin-5 dimer recognition by its α receptor.
Protein science : a publication of the Protein Society 2012;21(6):850-64.
2012: Yosuke Harada; Tomoya Katakai; Tatsuo Kinashi; Mutsuko Kukimoto-Niino; Akihiko Nishikimi; Tomoko Nishizaki; Markus Pieczyk; Fumiyuki Sanematsu; Mikako Shirouzu; Jens V Stein; Yoshihiko Tanaka; Masao Terasawa; Takehito Uruno; Shigeyuki Yokoyama; Xuefeng Duan; Katsuyoshi Habiro; Kyoko Hanawa-Suetsugu; Yoshinori Fukui
DOCK8 is a Cdc42 activator critical for interstitial dendritic cell migration during immune responses.
Blood 2012;119(19):4451-61.
2012: Kazumasa Ohtake; Nobumasa Hino; Takahito Mukai; Aya Sato; Shigeyuki Yokoyama; Kensaku Sakamoto
Efficient decoding of the UAG triplet as a full-fledged sense codon enhances the growth of a prfA-deficient strain of Escherichia coli.
Journal of bacteriology 2012;194(10):2606-13.
2012: Ramya Sundaresan; Shigeyuki Yokoyama; Thirumananseri Kumarevel; Seiki Kuramitsu; Preethi Ragunathan; Karthe Ponnuraj
The structure of putative N-acetyl glutamate kinase from Thermus thermophilus reveals an intermediate active site conformation of the enzyme.
Biochemical and biophysical research communications 2012;420(3):692-7.
2012: Tomomi Sumida; Makoto Ito; Keith A Stubbs; Shigeyuki Yokoyama
Gaining insight into the inhibition of glycoside hydrolase family 20 exo-β-N-acetylhexosaminidases using a structural approach.
Organic & biomolecular chemistry 2012;10(13):2607-12.
2012: Masatoshi Wakamori; Takashi Umehara; Shigeyuki Yokoyama
A tandem insertion vector for large-scale preparation of nucleosomal DNA.
Analytical biochemistry 2012;423(1):184-6.
2012: Tatsuo Yanagisawa; Nobumasa Hino; Fumie Iraha; Takahito Mukai; Kensaku Sakamoto; Shigeyuki Yokoyama
Wide-range protein photo-crosslinking achieved by a genetically encoded N(ε)-(benzyloxycarbonyl)lysine derivative with a diazirinyl moiety.
Molecular bioSystems 2012;8(4):1131-5.
2012: Keiko Tsuganezawa; Hisami Watanabe; Shigeyuki Yokoyama; Hitomi Yuki; Shigenao Taruya; Yuri Tomabechi; Noriko Handa; Teruki Honma; Daisuke Kamei; Hirotatsu Kojima; Masumi Mori; Tetsuo Nagano; Yukari Nakagawa; Naoko Ogawa; Takayoshi Okabe; Lorien Parker; Akiko Tanaka
A novel Pim-1 kinase inhibitor targeting residues that bind the substrate peptide.
Journal of molecular biology 2012;417(3):240-52.
2012: Kazuhiko Yamasaki; Tomoko Yamasaki; Makoto Inoue; Takanori Kigawa; Motoaki Seki; Kazuo Shinozaki; Satoru Watanabe; Shigeyuki Yokoyama
Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor.
The Journal of biological chemistry 2012;287(10):7683-91.
2012: Fahu He; Makoto Inoue; Takanori Kigawa; Naohiro Kobayashi; Kanako Kuwasako; Mikako Shirouzu; Mari Takahashi; Takaho Terada; Kengo Tsuda; Shigeyuki Yokoyama; Peter Güntert; Yutaka Muto
Solution structure of the splicing factor motif of the human Prp18 protein.
Proteins 2012;80(3):968-74.
2012: Loro L Kujjo; Hitoshi Kurumizaka; Ricardo J G Pereira; Thomas Baumann; Zeki Beyhan; Cagri Camsari; Jose B Cibelli; Marcelo D Goissis; Wataru Kagawa; Ramon Rodriguez; Reg Ronningen; Pablo Ross; George W Smith; Shigeyuki Yokoyama; Gloria I Perez
RAD51 plays a crucial role in halting cell death program induced by ionizing radiation in bovine oocytes.
Biology of reproduction 2012;86(3):76.
2012: Rie Yamashige; Shigeyuki Yokoyama; Michiko Kimoto; Tsuneo Mitsui; Akira Sato; Yusuke Takezawa; Ichiro Hirao
Highly specific unnatural base pair systems as a third base pair for PCR amplification.
Nucleic acids research 2012;40(6):2793-806.
2012: Kyoko Hanawa-Suetsugu; Takuhiro Ito; Tomoya Katakai; Takanori Kigawa; Tatsuo Kinashi; Daisuke Kohda; Seizo Koshiba; Mutsuko Kukimoto-Niino; Chiemi Mishima-Tsumagari; Akihiko Nishikimi; Noboru Ohsawa; Shun-ichi Sekine; Mikako Shirouzu; Takaho Terada; Naoya Tochio; Takehito Uruno; Ryogo Akasaka; Yoshinori Fukui; Shigeyuki Yokoyama
Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(9):3305-10.
2012: Seisuke Kusano; Noboru Ohsawa; Ken-ichi Okuda; Kensaku Sakamoto; Takayuki Shindo; Mikako Shirouzu; Nobumasa Hino; Mutsuko Kukimoto-Niino; Shigeyuki Yokoyama
Structural basis for extracellular interactions between calcitonin receptor-like receptor and receptor activity-modifying protein 2 for adrenomedullin-specific binding.
Protein science : a publication of the Protein Society 2012;21(2):199-210.
2012: Masao Terasawa; Takehito Uruno; Shigeyuki Yokoyama; Mutsuko Kukimoto-Niino; Sayako Mori; Akihiko Nishikimi; Fumiyuki Sanematsu; Yoshihiko Tanaka; Yoshinori Fukui
Dimerization of DOCK2 is essential for DOCK2-mediated Rac activation and lymphocyte migration.
PloS one 2012;7(9):e46277.
2012: Michiko Kimoto; Rie Yamashige; Shigeyuki Yokoyama; Ichiro Hirao
PCR amplification and transcription for site-specific labeling of large RNA molecules by a two-unnatural-base-pair system.
Journal of nucleic acids 2012;2012():230943.
2012: Nobumasa Hino; Kensaku Sakamoto; Shigeyuki Yokoyama
Site-specific incorporation of unnatural amino acids into proteins in mammalian cells.
Methods in molecular biology (Clifton, N.J.) 2012;794():215-28.
2011: Motoaki Wakiyama; Mariko Ikeda; Yoko Kaitsu; Reiko Muramatsu; Shigeyuki Yokoyama
Inducible protein expression in Drosophila Schneider 2 cells using the lac operator-repressor system.
Biotechnology letters 2011;33(12):2361-6.
2011: Bum-Ho Bin; Toshiyuki Fukada; Shintaro Hojyo; Toshiaki Hosaka; Tomohiro Miyai; Keigo Nishida; Wakana Ohashi; Satoru Yamasaki; Shigeyuki Yokoyama; Toshio Hirano
Biochemical characterization of human ZIP13 protein: a homo-dimerized zinc transporter involved in the spondylocheiro dysplastic Ehlers-Danlos syndrome.
The Journal of biological chemistry 2011;286(46):40255-65.
2011: Daisuke Takaya; Hideaki Umeyama; Yoshiaki Watanabe; Atsuya Yamashita; Ryoichi Arai; Nobuyuki Enomoto; Junko Gomi; Teruki Honma; Masahiko Ito; Kazue Kamijo; Shinya Maekawa; Takehisa Matsumoto; Naoya Sakamoto; Shigeyuki Yokoyama
A new method for induced fit docking (GENIUS) and its application to virtual screening of novel HCV NS3-4A protease inhibitors.
Bioorganic & medicinal chemistry 2011;19(22):6892-905.
2011: Rie Yamashige; Shigeyuki Yokoyama; Michiko Kimoto; Tsuneo Mitsui; Ichiro Hirao
Monitoring the site-specific incorporation of dual fluorophore-quencher base analogues for target DNA detection by an unnatural base pair system.
Organic & biomolecular chemistry 2011;9(21):7504-9.
2011: Takuhiro Ito; Shigeyuki Yokoyama
[Structural basis of the glutaminyl-tRNA synthesis in bacteria].
Seikagaku. The Journal of Japanese Biochemical Society 2011;83(11):1047-50.
2011: Toru Sengoku; Shigeyuki Yokoyama
Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6A.
Genes & development 2011;25(21):2266-77.
2011: Takashi Kikukawa; So Young Kim; Tomomi Kimura-Someya; Seiji Miyauchi; Kazumi Shimono; Mikako Shirouzu; Jun Tamogami; Shigeyuki Yokoyama; Kwang-Hwan Jung; Naoki Kamo
Photochemistry of Acetabularia rhodopsin II from a marine plant, Acetabularia acetabulum.
Biochemistry 2011;50(41):8888-98.
2011: Ella Czarina Morishita; Kazutaka Murayama; Mikako Shirouzu; Takaho Terada; Yuri Tomabechi; Tetsu Akiyama; Noriko Handa; Tomoatsu Hayashi; Yoshiko Ishizuka-Katsura; Miyuki Kato-Murayama; Shigeyuki Yokoyama
Crystal structures of the armadillo repeat domain of adenomatous polyposis coli and its complex with the tyrosine-rich domain of Sam68.
Structure (London, England : 1993) 2011;19(10):1496-508.
2011: Makoto Nagano; Mikako Shirouzu; Takuya Shuo; Naoya Tochio; Tadashi Tomizawa; Satoru Watanabe; Shigeyuki Yokoyama; Toshifumi Akizawa; Noriko Handa; Takushi Harada; Fumiaki Hayashi; Daisuke Hoshino; Takanori Kigawa; Seizo Koshiba; Naohiko Koshikawa; Motoharu Seiki
ZF21 protein, a regulator of the disassembly of focal adhesions and cancer metastasis, contains a novel noncanonical pleckstrin homology domain.
The Journal of biological chemistry 2011;286(36):31598-609.
2011: Takashi Wada; Masakatsu Hato; Kwang-Hwan Jung; Naoki Kamo; Takashi Kikukawa; So Young Kim; Tomomi Kimura-Someya; Seiji Miyauchi; Kazumi Shimono; Naoko Shinya; Mikako Shirouzu; Jun Tamogami; Shigeyuki Yokoyama
Crystal structure of the eukaryotic light-driven proton-pumping rhodopsin, Acetabularia rhodopsin II, from marine alga.
Journal of molecular biology 2011;411(5):986-98.
2011: Mutsuko Kukimoto-Niino; Tomokazu Matsusue; Naomi Ohbayashi; Ikuya Shiromizu; Mikako Shirouzu; Takaho Terada; Alexander Tokmakov; Takako Fujimoto; Sumiko Gomi; Masaki Kawamoto; Shigeyuki Yokoyama
Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4.
Acta crystallographica. Section D, Biological crystallography 2011;67(Pt 9):763-73.
2011: Haruhiko Ehara; Shun-ichi Sekine; Shigeyuki Yokoyama
Crystal structure of the C17/25 subcomplex from Schizosaccharomyces pombe RNA polymerase III.
Protein science : a publication of the Protein Society 2011;20(9):1558-65.
2011: Takahito Mukai; Kazumasa Ohtake; Jiro Adachi; Akiko Hayashi; Nobumasa Hino; Takatsugu Kobayashi; Aya Sato; Mikako Shirouzu; Takashi Umehara; Minoru Wakamori; Tatsuo Yanagisawa; Shigeyuki Yokoyama; Kensaku Sakamoto
Genetic-code evolution for protein synthesis with non-natural amino acids.
Biochemical and biophysical research communications 2011;411(4):757-61.
2011: Akihiko Arakawa; Noriko Handa; Mikako Shirouzu; Shigeyuki Yokoyama
Biochemical and structural studies on the high affinity of Hsp70 for ADP.
Protein science : a publication of the Protein Society 2011;20(8):1367-79.
2011: Suhaila Rahman; Shinya Saijo; Mikako Shirouzu; Takaho Terada; Mitsutoshi Toyama; Ichiro Yamato; Shigeyuki Yokoyama; Satoshi Arai; Keiko Honda; Mio Inoue; Yoshiko Ishizuka-Katsura; So Iwata; Noboru Ohsawa; Takeshi Murata
Expression, purification and characterization of isoforms of peripheral stalk subunits of human V-ATPase.
Protein expression and purification 2011;78(2):181-8.
2011: Yumiko Terazawa; Motoaki Wakiyama; Shigeyuki Yokoyama
pCMV-Leu2/pUCA-Neo, a vector set for screening Schizosaccharomyces pombe transformants expressing heterologous proteins.
Analytical biochemistry 2011;414(2):306-8.
2011: Aya Kitamura; Madoka Nishimoto; Toru Sengoku; Shigeyuki Yokoyama; Yoshitaka Bessho
Crystal structure of the bifunctional tRNA modification enzyme MnmC from Escherichia coli.
Protein science : a publication of the Protein Society 2011;20(7):1105-13.
2011: Mitsuo Kuratani; Akeo Shinkai; Takaho Terada; Ryogo Akasaka; Yoshitaka Bessho; Kyoko Higashijima; Takuma Kasai; Takanori Kigawa; Shigeyuki Yokoyama
Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP.
Proteins 2011;79(7):2065-75.
2011: Mutsuko Kukimoto-Niino; Suni Lee; Yasuhiko Minokoshi; Noboru Ohsawa; Miki Okada-Iwabu; Mikako Shirouzu; Atsushi Suzuki; Tetsuo Takagi; Takaho Terada; Yuri Tomabechi; Toshimasa Yamauchi; Masato Iwabu; Takashi Kadowaki; Seiko Yoshikawa; Shigeyuki Yokoyama
Crystal structure of the Ca²⁺/calmodulin-dependent protein kinase kinase in complex with the inhibitor STO-609.
The Journal of biological chemistry 2011;286(25):22570-9.
2011: Nicole Hajicek; Mutsuko Kukimoto-Niino; Chiemi Mishima-Tsumagari; Christina R Chow; Mikako Shirouzu; Takaho Terada; Maulik Patel; Shigeyuki Yokoyama; Tohru Kozasa
Identification of critical residues in G(alpha)13 for stimulation of p115RhoGEF activity and the structure of the G(alpha)13-p115RhoGEF regulator of G protein signaling homology (RH) domain complex.
The Journal of biological chemistry 2011;286(23):20625-36.
2011: Noriko Handa; Tetsuo Takagi; Shinya Saijo; Seiichiro Kishishita; Daisuke Takaya; Mitsutoshi Toyama; Takaho Terada; Mikako Shirouzu; Atsushi Suzuki; Suni Lee; Toshimasa Yamauchi; Miki Okada-Iwabu; Masato Iwabu; Takashi Kadowaki; Yasuhiko Minokoshi; Shigeyuki Yokoyama
Structural basis for compound C inhibition of the human AMP-activated protein kinase α2 subunit kinase domain.
Acta crystallographica. Section D, Biological crystallography 2011;67(Pt 5):480-7.
2011: Taiko Kim To; Jong-Myong Kim; Akihiro Matsui; Yukio Kurihara; Taeko Morosawa; Junko Ishida; Maho Tanaka; Takaho Endo; Tetsuji Kakutani; Tetsuro Toyoda; Hiroshi Kimura; Shigeyuki Yokoyama; Kazuo Shinozaki; Motoaki Seki
Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1.
PLoS genetics 2011;7(4):e1002055.
2011: Taiko Kim To; Kentaro Nakaminami; Jong-Myong Kim; Taeko Morosawa; Junko Ishida; Maho Tanaka; Shigeyuki Yokoyama; Kazuo Shinozaki; Motoaki Seki
Arabidopsis HDA6 is required for freezing tolerance.
Biochemical and biophysical research communications 2011;406(3):414-9.
2011: Kengo Tsuda; Tatsuhiko Someya; Kanako Kuwasako; Mari Takahashi; Fahu He; Satoru Unzai; Makoto Inoue; Takushi Harada; Satoru Watanabe; Takaho Terada; Naohiro Kobayashi; Mikako Shirouzu; Takanori Kigawa; Akiko Tanaka; Sumio Sugano; Peter Güntert; Shigeyuki Yokoyama; Yutaka Muto
Structural basis for the dual RNA-recognition modes of human Tra2-β RRM.
Nucleic acids research 2011;39(4):1538-53.
2011: Nobumasa Hino; Masaaki Oyama; Aya Sato; Takahito Mukai; Fumie Iraha; Akiko Hayashi; Hiroko Kozuka-Hata; Tadashi Yamamoto; Shigeyuki Yokoyama; Kensaku Sakamoto
Genetic incorporation of a photo-crosslinkable amino acid reveals novel protein complexes with GRB2 in mammalian cells.
Journal of molecular biology 2011;406(2):343-53.
2011: Akiko Hayashi; Nobumasa Hino; Takatsugu Kobayashi; Ryoichi Arai; Mikako Shirouzu; Shigeyuki Yokoyama; Kensaku Sakamoto
Dissecting cell signaling pathways with genetically encoded 3-iodo-L-tyrosine.
Chembiochem : a European journal of chemical biology 2011;12(3):387-9.
2011: Daisuke Morishita; Miho Takami; Seiko Yoshikawa; Ryohei Katayama; Shigeo Sato; Mutsuko Kukimoto-Niino; Takashi Umehara; Mikako Shirouzu; Kazuhisa Sekimizu; Shigeyuki Yokoyama; Naoya Fujita
Cell-permeable carboxyl-terminal p27(Kip1) peptide exhibits anti-tumor activity by inhibiting Pim-1 kinase.
The Journal of biological chemistry 2011;286(4):2681-8.
2011: Shin Sato; Takashi Umehara; Nobumasa Hino; Shinya Mimasu; Kensaku Sakamoto; Aya Sato; Shigeyuki Yokoyama
Crystallographic study of a site-specifically cross-linked protein complex with a genetically incorporated photoreactive amino acid.
Biochemistry 2011;50(2):250-7.
2011: Shankar Prasad Kanaujia; Jeyaraman Jeyakanthan; Akeo Shinkai; Seiki Kuramitsu; Shigeyuki Yokoyama; Kanagaraj Sekar
Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms.
Acta crystallographica. Section F, Structural biology and crystallization communications 2011;67(Pt 1):2-16.
2011: Seisuke Yamashita; Takashi Nagata; Masahito Kawazoe; Chie Takemoto; Takanori Kigawa; Peter Güntert; Naohiro Kobayashi; Takaho Terada; Mikako Shirouzu; Motoaki Wakiyama; Yutaka Muto; Shigeyuki Yokoyama
Structures of the first and second double-stranded RNA-binding domains of human TAR RNA-binding protein.
Protein science : a publication of the Protein Society 2011;20(1):118-30.
2010: Shunsuke Tagami; Shun-Ichi Sekine; Thirumananseri Kumarevel; Nobumasa Hino; Yuko Murayama; Syunsuke Kamegamori; Masaki Yamamoto; Kensaku Sakamoto; Shigeyuki Yokoyama
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.
Nature 2010;468(7326):978-82.
2010: Gota Kawai; Shigeyuki Yokoyama
Professor Tatsuo Miyazawa: from molecular structure to biological function.
Journal of biochemistry 2010;148(6):631-8.
2010: Yasushi Hikida; Mitsuo Kuratani; Yoshitaka Bessho; Shun-ichi Sekine; Shigeyuki Yokoyama
Structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase.
Acta crystallographica. Section D, Biological crystallography 2010;66(Pt 12):1301-7.
2010: Alexander K Goroncy; Kazutaka Murayama; Mikako Shirouzu; Seiki Kuramitsu; Takanori Kigawa; Shigeyuki Yokoyama
NMR and X-ray structures of the putative sterol carrier protein 2 from Thermus thermophilus HB8 show conformational changes.
Journal of structural and functional genomics 2010;11(4):247-56.
2010: Takahito Mukai; Akiko Hayashi; Fumie Iraha; Aya Sato; Kazumasa Ohtake; Shigeyuki Yokoyama; Kensaku Sakamoto
Codon reassignment in the Escherichia coli genetic code.
Nucleic acids research 2010;38(22):8188-95.
2010: Michiko Kimoto; Tsuneo Mitsui; Rie Yamashige; Akira Sato; Shigeyuki Yokoyama; Ichiro Hirao
A new unnatural base pair system between fluorophore and quencher base analogues for nucleic acid-based imaging technology.
Journal of the American Chemical Society 2010;132(43):15418-26.
2010: Masatoshi Wakamori; Takashi Umehara; Shigeyuki Yokoyama
A series of bacterial co-expression vectors with rare-cutter recognition sequences.
Protein expression and purification 2010;74(1):88-98.
2010: Takuhiro Ito; Shigeyuki Yokoyama
Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions.
Nature 2010;467(7315):612-6.
2010: Takashi Umehara; Yoshihiro Nakamura; Minoru Wakamori; Keiko Ozato; Shigeyuki Yokoyama; Balasundaram Padmanabhan
Structural implications for K5/K12-di-acetylated histone H4 recognition by the second bromodomain of BRD2.
FEBS letters 2010;584(18):3901-8.
2010: Tomoyuki Tanaka; Hideaki Niwa; Katsuhide Yutani; Seiki Kuramitsu; Shigeyuki Yokoyama; Thirumananseri Kumarevel
Crystal structure of TTHA0061, an uncharacterized protein from Thermus thermophilus HB8, reveals a novel fold.
Biochemical and biophysical research communications 2010;400(2):258-64.
2010: Fahu He; Takashi Umehara; Kohei Saito; Takushi Harada; Satoru Watanabe; Takashi Yabuki; Takanori Kigawa; Mari Takahashi; Kanako Kuwasako; Kengo Tsuda; Takayoshi Matsuda; Masaaki Aoki; Eiko Seki; Naohiro Kobayashi; Peter Güntert; Shigeyuki Yokoyama; Yutaka Muto
Structural insight into the zinc finger CW domain as a histone modification reader.
Structure (London, England : 1993) 2010;18(9):1127-39.
2010: Tomomi Sumida; Tatsuo Yanagisawa; Ryohei Ishii; Shigeyuki Yokoyama
Crystallization and preliminary X-ray crystallographic study of GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, in complex with translation elongation factor P.
Acta crystallographica. Section F, Structural biology and crystallization communications 2010;66(Pt 9):1115-8.
2010: Tatsuo Yanagisawa; Tomomi Sumida; Ryohei Ishii; Chie Takemoto; Shigeyuki Yokoyama
A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.
Nature structural & molecular biology 2010;17(9):1136-43.
2010: Mitsuo Kuratani; Masashi Hirano; Sakurako Goto-Ito; Yuzuru Itoh; Yasushi Hikida; Madoka Nishimoto; Shun-ichi Sekine; Yoshitaka Bessho; Takuhiro Ito; Henri Grosjean; Shigeyuki Yokoyama
Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin.
Journal of molecular biology 2010;401(3):323-33.
2010: Shiho Chiba; Yuzuru Itoh; Shun-ichi Sekine; Shigeyuki Yokoyama
Structural basis for the major role of O-phosphoseryl-tRNA kinase in the UGA-specific encoding of selenocysteine.
Molecular cell 2010;39(3):410-20.
2010: Naoya Tochio; Takashi Umehara; Yoshiko Munemasa; Toru Suzuki; Shin Sato; Kengo Tsuda; Seizo Koshiba; Takanori Kigawa; Ryozo Nagai; Shigeyuki Yokoyama
Solution structure of histone chaperone ANP32B: interaction with core histones H3-H4 through its acidic concave domain.
Journal of molecular biology 2010;401(1):97-114.
2010: Shinya Mimasu; Naoki Umezawa; Shin Sato; Tsunehiko Higuchi; Takashi Umehara; Shigeyuki Yokoyama
Structurally designed trans-2-phenylcyclopropylamine derivatives potently inhibit histone demethylase LSD1/KDM1 .
Biochemistry 2010;49(30):6494-503.
2010: Koichiro Kodama; Hiroshi Nakayama; Kensaku Sakamoto; Seketsu Fukuzawa; Takanori Kigawa; Takashi Yabuki; Makoto Kitabatake; Koji Takio; Shigeyuki Yokoyama
Site-specific incorporation of 4-iodo-L-phenylalanine through opal suppression.
Journal of biochemistry 2010;148(2):179-87.
2010: Shankar Prasad Kanaujia; Jeyaraman Jeyakanthan; Noriko Nakagawa; Sathyaramya Balasubramaniam; Akeo Shinkai; Seiki Kuramitsu; Shigeyuki Yokoyama; Kanagaraj Sekar
Structures of apo and GTP-bound molybdenum cofactor biosynthesis protein MoaC from Thermus thermophilus HB8.
Acta crystallographica. Section D, Biological crystallography 2010;66(Pt 7):821-33.
2010: Takuhiro Ito; Noriko Kiyasu; Risa Matsunaga; Seizo Takahashi; Shigeyuki Yokoyama
Structure of nondiscriminating glutamyl-tRNA synthetase from Thermotoga maritima.
Acta crystallographica. Section D, Biological crystallography 2010;66(Pt 7):813-20.
2010: Yasushi Hikida; Michiko Kimoto; Shigeyuki Yokoyama; Ichiro Hirao
Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis.
Nature protocols 2010;5(7):1312-23.
2010: Alexander K Goroncy; Seizo Koshiba; Naoya Tochio; Tadashi Tomizawa; Makoto Inoue; Akiko Tanaka; Sumio Sugano; Takanori Kigawa; Shigeyuki Yokoyama
Solution structure of the C-terminal DUF1000 domain of the human thioredoxin-like 1 protein.
Proteins 2010;78(9):2176-80.
2010: Satoshi Mikami; Tominari Kobayashi; Kodai Machida; Mamiko Masutani; Shigeyuki Yokoyama; Hiroaki Imataka
N-terminally truncated GADD34 proteins are convenient translation enhancers in a human cell-derived in vitro protein synthesis system.
Biotechnology letters 2010;32(7):897-902.
2010: Junko Mikuni; Miki Kato; Shigenao Taruya; Keiko Tsuganezawa; Masumi Mori; Naoko Ogawa; Teruki Honma; Shigeyuki Yokoyama; Hirotatsu Kojima; Takayoshi Okabe; Tetsuo Nagano; Akiko Tanaka
A fluorescence correlation spectroscopy-based assay for fragment screening of slowly inhibiting protein-peptide interaction inhibitors.
Analytical biochemistry 2010;402(1):26-31.
2010: Seizo Koshiba; Hua Li; Yoko Motoda; Tadashi Tomizawa; Takuma Kasai; Naoya Tochio; Takashi Yabuki; Takushi Harada; Satoru Watanabe; Akiko Tanaka; Mikako Shirouzu; Takanori Kigawa; Tadashi Yamamoto; Shigeyuki Yokoyama
Structural basis for the recognition of nucleophosmin-anaplastic lymphoma kinase oncoprotein by the phosphotyrosine binding domain of Suc1-associated neurotrophic factor-induced tyrosine-phosphorylated target-2.
Journal of structural and functional genomics 2010;11(2):125-41.
2010: Alexander K Goroncy; Seizo Koshiba; Naoya Tochio; Tadashi Tomizawa; Makoto Inoue; Makato Inoue; Satoru Watanabe; Takushi Harada; Akiko Tanaka; Osamu Ohara; Takanori Kigawa; Shigeyuki Yokoyama
The NMR solution structures of the five constituent cold-shock domains (CSD) of the human UNR (upstream of N-ras) protein.
Journal of structural and functional genomics 2010;11(2):181-8.
2010: Fumie Iraha; Kenji Oki; Takatsugu Kobayashi; Satoshi Ohno; Takashi Yokogawa; Kazuya Nishikawa; Shigeyuki Yokoyama; Kensaku Sakamoto
Functional replacement of the endogenous tyrosyl-tRNA synthetase-tRNATyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion.
Nucleic acids research 2010;38(11):3682-91.
2010: Motoaki Wakiyama; Yoko Kaitsu; Tomoko Matsumoto; Shigeyuki Yokoyama
Coupled transcription and translation from polymerase chain reaction-amplified DNA in Drosophila Schneider 2 cell-free system.
Analytical biochemistry 2010;400(1):142-4.
2010: Michiko Kimoto; Tsuneo Mitsui; Shigeyuki Yokoyama; Ichiro Hirao
A unique fluorescent base analogue for the expansion of the genetic alphabet.
Journal of the American Chemical Society 2010;132(14):4988-9.
2010: Atsushi Kurotani; Tetsuo Takagi; Mitsutoshi Toyama; Mikako Shirouzu; Shigeyuki Yokoyama; Yasuo Fukami; Alexander A Tokmakov
Comprehensive bioinformatics analysis of cell-free protein synthesis: identification of multiple protein properties that correlate with successful expression.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2010;24(4):1095-104.
2010: Jeyaraman Jeyakanthan; Randy M Drevland; Dasara Raju Gayathri; devadasan velmurugan; Akeo Shinkai; Seiki Kuramitsu; Shigeyuki Yokoyama; David E Graham
Substrate specificity determinants of the methanogen homoaconitase enzyme: structure and function of the small subunit.
Biochemistry 2010;49(12):2687-96.
2010: Atsushi Shimada; Kazunori Takano; Mikako Shirouzu; Kyoko Hanawa-Suetsugu; Takaho Terada; Kiminori Toyooka; Takashi Umehara; Masaki Yamamoto; Shigeyuki Yokoyama; Shiro Suetsugu
Mapping of the basic amino-acid residues responsible for tubulation and cellular protrusion by the EFC/F-BAR domain of pacsin2/Syndapin II.
FEBS letters 2010;584(6):1111-8.
2010: Akihiko Arakawa; Noriko Handa; Noboru Ohsawa; Meiri Shida; Takanori Kigawa; Fumiaki Hayashi; Mikako Shirouzu; Shigeyuki Yokoyama
The C-terminal BAG domain of BAG5 induces conformational changes of the Hsp70 nucleotide-binding domain for ADP-ATP exchange.
Structure (London, England : 1993) 2010;18(3):309-19.
2010: Takashi Umehara; Yoshihiro Nakamura; Moon Kyoo Jang; Kazumi Nakano; Akiko Tanaka; Keiko Ozato; Balasundaram Padmanabhan; Shigeyuki Yokoyama
Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain.
The Journal of biological chemistry 2010;285(10):7610-8.
2010: Meiri Shida; Akihiko Arakawa; Ryohei Ishii; Seiichiro Kishishita; Tetsuo Takagi; Mutsuko Kukimoto-Niino; Sumio Sugano; Akiko Tanaka; Mikako Shirouzu; Shigeyuki Yokoyama
Direct inter-subdomain interactions switch between the closed and open forms of the Hsp70 nucleotide-binding domain in the nucleotide-free state.
Acta crystallographica. Section D, Biological crystallography 2010;66(Pt 3):223-32.
2010: Takahito Mukai; Motoaki Wakiyama; Kensaku Sakamoto; Shigeyuki Yokoyama
Genetic encoding of non-natural amino acids in Drosophila melanogaster Schneider 2 cells.
Protein science : a publication of the Protein Society 2010;19(3):440-8.
2010: Jeyaraman Jeyakanthan; Subbiah Thamotharan; Santosh Panjikar; Yoshiaki Kitamura; Noriko Nakagawa; Akeo Shinkai; Seiki Kuramitsu; Shigeyuki Yokoyama
Expression, purification and X-ray analysis of 1,3-propanediol dehydrogenase (Aq_1145) from Aquifex aeolicus VF5.
Acta crystallographica. Section F, Structural biology and crystallization communications 2010;66(Pt 2):184-6.
2010: Kavyashree Manjunath; Jeyaraman Jeyakanthan; Noriko Nakagawa; Akeo Shinkai; Masato Yoshimura; Seiki Kuramitsu; Shigeyuki Yokoyama; Kanagaraj Sekar
Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of the putative SAICAR synthetase (PH0239) from Pyrococcus horikoshii OT3.
Acta crystallographica. Section F, Structural biology and crystallization communications 2010;66(Pt 2):180-3.
2010: Jeyaraman Jeyakanthan; Shankar Prasad Kanaujia; Yuya Nishida; Noriko Nakagawa; Surendran Praveen; Akeo Shinkai; Seiki Kuramitsu; Shigeyuki Yokoyama; Kanagaraj Sekar
Free and ATP-bound structures of Ap4A hydrolase from Aquifex aeolicus V5.
Acta crystallographica. Section D, Biological crystallography 2010;66(Pt 2):116-24.
2010: Eisuke Chikayama; Atsushi Kurotani; Takanori Tanaka; Takashi Yabuki; Satoshi Miyazaki; Shigeyuki Yokoyama; Yutaka Kuroda
Mathematical model for empirically optimizing large scale production of soluble protein domains.
BMC bioinformatics 2010;11():113.
2010: Shunsuke Tagami; Shun-ichi Sekine; Thirumananseri Kumarevel; Masaki Yamamoto; Shigeyuki Yokoyama
Crystallization and preliminary X-ray crystallographic analysis of Thermus thermophilus transcription elongation complex bound to Gfh1.
Acta crystallographica. Section F, Structural biology and crystallization communications 2010;66(Pt 1):64-8.
2010: Tomohiro Sato; Teruki Honma; Shigeyuki Yokoyama
Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening.
Journal of chemical information and modeling 2010;50(1):170-85.
2010: Motoaki Wakiyama; Shigeyuki Yokoyama
MicroRNA-mediated mRNA deadenylation and repression of protein synthesis in a mammalian cell-free system.
Progress in molecular and subcellular biology 2010;50():85-97.
2009: Satoshi Arai; Ichiro Yamato; Asuka Shiokawa; Shinya Saijo; Yoshimi Kakinuma; Yoshiko Ishizuka-Katsura; Mitsutoshi Toyama; Takaho Terada; Mikako Shirouzu; Shigeyuki Yokoyama; So Iwata; Takeshi Murata
Reconstitution in vitro of the catalytic portion (NtpA3-B3-D-G complex) of Enterococcus hirae V-type Na+-ATPase.
Biochemical and biophysical research communications 2009;390(3):698-702.
2009: Kazutaka Murayama; Sanae Nakayama; Miyuki Kato-Murayama; Ryogo Akasaka; Naomi Ohbayashi; Yuki Kamewari-Hayami; Takaho Terada; Mikako Shirouzu; Tatsuya Tsurumi; Shigeyuki Yokoyama
Crystal structure of epstein-barr virus DNA polymerase processivity factor BMRF1.
The Journal of biological chemistry 2009;284(51):35896-905.
2009: Balasundaram Padmanabhan; Yoshitaka Bessho; Akio Ebihara; Svetlana V Antonyuk; Mark J Ellis; Richard W Strange; Seiki Kuramitsu; Nobuhisa Watanabe; S Samar Hasnain; Shigeyuki Yokoyama
Structure of putative 4-amino-4-deoxychorismate lyase from Thermus thermophilus HB8.
Acta crystallographica. Section F, Structural biology and crystallization communications 2009;65(Pt 12):1234-9.
2009: Ali D Malay; Yoshitaka Bessho; Mark J Ellis; Svetlana V Antonyuk; Richard W Strange; S Samar Hasnain; Akeo Shinkai; Balasundaram Padmanabhan; Shigeyuki Yokoyama
Structure of glyceraldehyde-3-phosphate dehydrogenase from the archaeal hyperthermophile Methanocaldococcus jannaschii.
Acta crystallographica. Section F, Structural biology and crystallization communications 2009;65(Pt 12):1227-33.
2009: Balasundaram Padmanabhan; Richard W Strange; Svetlana V Antonyuk; Mark J Ellis; S Samar Hasnain; Hitoshi Iino; Yoshihiro Agari; Yoshitaka Bessho; Shigeyuki Yokoyama
Structure of dihydrodipicolinate synthase from Methanocaldococcus jannaschii.
Acta crystallographica. Section F, Structural biology and crystallization communications 2009;65(Pt 12):1222-6.
2009: Ai Takemoto; Kazuhiro Maeshima; Tsuyoshi Ikehara; Kazumitsu Yamaguchi; Akiko Murayama; Shihoko Imamura; Naoko Imamoto; Shigeyuki Yokoyama; Tatsuya Hirano; Yoshinori Watanabe; Fumio Hanaoka; Junn Yanagisawa; Keiji Kimura
The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A.
Nature structural & molecular biology 2009;16(12):1302-8.
2009: Masaaki Aoki; Takayoshi Matsuda; Yasuko Tomo; Yukako Miyata; Makoto Inoue; Takanori Kigawa; Shigeyuki Yokoyama
Automated system for high-throughput protein production using the dialysis cell-free method.
Protein expression and purification 2009;68(2):128-36.
2009: Ryoichi Arai; Kazutaka Murayama; Tomomi Uchikubo-Kamo; Madoka Nishimoto; Mitsutoshi Toyama; Seiki Kuramitsu; Takaho Terada; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8.
Journal of structural biology 2009;168(3):575-81.
2009: Thirumananseri Kumarevel; Tomoyuki Tanaka; Akeo Shinkai; Shigeyuki Yokoyama
Crystal structure of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8.
Proteins 2009;77(3):747-51.
2009: Thirumananseri Kumarevel; Tomoyuki Tanaka; Yoshitaka Bessho; Akeo Shinkai; Shigeyuki Yokoyama
Crystal structure of hydrogenase maturating endopeptidase HycI from Escherichia coli.
Biochemical and biophysical research communications 2009;389(2):310-4.
2009: Alexander K Goroncy; Seizo Koshiba; Naoya Tochio; Tadashi Tomizawa; Manami Sato; Makato Inoue; Satoru Watanabe; Yoshihide Hayashizaki; Akiko Tanaka; Takanori Kigawa; Shigeyuki Yokoyama
NMR solution structures of actin depolymerizing factor homology domains.
Protein science : a publication of the Protein Society 2009;18(11):2384-92.
2009: Fahu He; Kohei Saito; Naohiro Kobayashi; Takushi Harada; Satoru Watanabe; Takanori Kigawa; Peter Güntert; Osamu Ohara; Akiko Tanaka; Satoru Unzai; Yutaka Muto; Shigeyuki Yokoyama
Structural and functional characterization of the NHR1 domain of the Drosophila neuralized E3 ligase in the notch signaling pathway.
Journal of molecular biology 2009;393(2):478-95.
2009: Takuya B Hiyama; Takuhiro Ito; Hiroaki Imataka; Shigeyuki Yokoyama
Crystal structure of the alpha subunit of human translation initiation factor 2B.
Journal of molecular biology 2009;392(4):937-51.
2009: Jeyaraman Jeyakanthan; Subbiah Thamotharan; devadasan velmurugan; Vaijayanthimala Surya Narayna Rao; Shanthi Nagarajan; Akeo Shinkai; Seiki Kuramitsu; Shigeyuki Yokoyama
New structural insights and molecular-modelling studies of 4-methyl-5-beta-hydroxyethylthiazole kinase from Pyrococcus horikoshii OT3 (PhThiK).
Acta crystallographica. Section F, Structural biology and crystallization communications 2009;65(Pt 10):978-86.
2009: Sakurako Goto-Ito; Takuhiro Ito; Mitsuo Kuratani; Yoshitaka Bessho; Shigeyuki Yokoyama
Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation.
Nature structural & molecular biology 2009;16(10):1109-15.
2009: Kazumi Shimono; Mie Goto; Takashi Kikukawa; Seiji Miyauchi; Mikako Shirouzu; Naoki Kamo; Shigeyuki Yokoyama
Production of functional bacteriorhodopsin by an Escherichia coli cell-free protein synthesis system supplemented with steroid detergent and lipid.
Protein science : a publication of the Protein Society 2009;18(10):2160-71.
2009: Yuzuru Itoh; Shiho Chiba; Shun-Ichi Sekine; Shigeyuki Yokoyama
Crystal structure of human selenocysteine tRNA.
Nucleic acids research 2009;37(18):6259-68.
2009: Tomomi Sumida; Ryohei Ishii; Tatsuo Yanagisawa; Shigeyuki Yokoyama; Makoto Ito
Molecular cloning and crystal structural analysis of a novel beta-N-acetylhexosaminidase from Paenibacillus sp. TS12 capable of degrading glycosphingolipids.
Journal of molecular biology 2009;392(1):87-99.
2009: Toshiaki Hosaka; Kazutaka Murayama; Miyuki Kato-Murayama; Akiko Urushibata; Ryogo Akasaka; Takaho Terada; Mikako Shirouzu; Seiki Kuramitsu; Shigeyuki Yokoyama
Structure of the putative thioesterase protein TTHA1846 from Thermus thermophilus HB8 complexed with coenzyme A and a zinc ion.
Acta crystallographica. Section D, Biological crystallography 2009;65(Pt 8):767-76.
2009: Kengo Tsuda; Kanako Kuwasako; Mari Takahashi; Tatsuhiko Someya; Makoto Inoue; Takaho Terada; Naohiro Kobayashi; Mikako Shirouzu; Takanori Kigawa; Akiko Tanaka; Sumio Sugano; Peter Güntert; Yutaka Muto; Shigeyuki Yokoyama
Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3.
Nucleic acids research 2009;37(15):5151-66.
2009: Thirumananseri Kumarevel; Tomoyuki Tanaka; Takashi Umehara; Shigeyuki Yokoyama
ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.
Nucleic acids research 2009;37(14):4723-35.
2009: Koji Takimoto; Motoaki Wakiyama; Shigeyuki Yokoyama
Mammalian GW182 contains multiple Argonaute-binding sites and functions in microRNA-mediated translational repression.
RNA (New York, N.Y.) 2009;15(6):1078-89.
2009: Masahiro Naganuma; Shun-ichi Sekine; Ryuya Fukunaga; Shigeyuki Yokoyama
Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(21):8489-94.
2009: Keiko Sakamoto; Yoshihiro Agari; Kazuko Agari; Shigeyuki Yokoyama; Seiki Kuramitsu; Akeo Shinkai
X-ray crystal structure of a CRISPR-associated RAMP module [corrected] Cmr5 protein [corrected] from Thermus thermophilus HB8.
Proteins 2009;75(2):528-32.
2009: Kazuki Kurimoto; Kanako Kuwasako; Alan Sandercock; Satoru Unzai; Carol V Robinson; Yutaka Muto; Shigeyuki Yokoyama
AU-rich RNA-binding induces changes in the quaternary structure of AUH.
Proteins 2009;75(2):360-72.
2009: Toshiyuki Kawashima; Ying Chun Bao; Yukinori Minoshima; Yasushi Nomura; Tomonori Hatori; Tetsuya Hori; Tatsuo Fukagawa; Toshiyuki Fukada; Noriko Takahashi; Tetsuya Nosaka; Makoto Inoue; Tomohiro Sato; Mutsuko Kukimoto-Niino; Mikako Shirouzu; Shigeyuki Yokoyama; Toshio Kitamura
A Rac GTPase-activating protein, MgcRacGAP, is a nuclear localizing signal-containing nuclear chaperone in the activation of STAT transcription factors.
Molecular and cellular biology 2009;29(7):1796-813.
2009: Hongfei Wang; Chie Takemoto; Ryogo Akasaka; Tomomi Uchikubo-Kamo; Seiichiro Kishishita; Kazutaka Murayama; Takaho Terada; Lirong Chen; Zhi-Jie Liu; Bi-Cheng Wang; Sumio Sugano; Akiko Tanaka; Makoto Inoue; Takanori Kigawa; Mikako Shirouzu; Shigeyuki Yokoyama
Novel dimerization mode of the human Bcl-2 family protein Bak, a mitochondrial apoptosis regulator.
Journal of structural biology 2009;166(1):32-7.
2009: Kensaku Sakamoto; Kazutaka Murayama; Kenji Oki; Fumie Iraha; Miyuki Kato-Murayama; Masahiro Takahashi; Kazumasa Ohtake; Takatsugu Kobayashi; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography.
Structure (London, England : 1993) 2009;17(3):335-44.
2009: Masayo Harada; Hirotaka Murakami; Akihiko Okawa; Noriaki Okimoto; Shuichi Hiraoka; Taka Nakahara; Ryogo Akasaka; Yo-Ichi Shiraishi; Noriyuki Futatsugi; Yoko Mizutani-Koseki; Atsushi Kuroiwa; Mikako Shirouzu; Shigeyuki Yokoyama; Makoto Taiji; Sachiko Iseki; David M Ornitz; Haruhiko Koseki
FGF9 monomer-dimer equilibrium regulates extracellular matrix affinity and tissue diffusion.
Nature genetics 2009;41(3):289-98.
2009: Alexander A Tokmakov; Yumiko Terazawa; Mariko Ikeda; Mikako Shirouzu; Yasuo Fukami; Shigeyuki Yokoyama
Comparative expression analysis of multiple PDK genes in Xenopus laevis during oogenesis, maturation, fertilization, and early embryogenesis.
Gene expression patterns : GEP 2009;9(3):158-65.
2009: Takatsugu Kobayashi; Tatsuo Yanagisawa; Kensaku Sakamoto; Shigeyuki Yokoyama
Recognition of non-alpha-amino substrates by pyrrolysyl-tRNA synthetase.
Journal of molecular biology 2009;385(5):1352-60.
2009: Yuzuru Itoh; Shun-ichi Sekine; Eiko Matsumoto; Ryogo Akasaka; Chie Takemoto; Mikako Shirouzu; Shigeyuki Yokoyama
Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs.
Journal of molecular biology 2009;385(5):1456-69.
2009: Jeyaraman Jeyakanthan; Katsumi Takada; Masahide Sawano; Kyoko Ogasahara; Hisashi Mizutani; Naoki Kunishima; Shigeyuki Yokoyama; Katsuhide Yutani
Crystal Structural and Functional Analysis of the Putative Dipeptidase from Pyrococcus horikoshii OT3.
Journal of biophysics (Hindawi Publishing Corporation : Online) 2009;2009():434038.
2009: Yuki Haraguchi; Kanako Kuwasako; Yutaka Muto; Yoshitaka Bessho; Madoka Nishimoto; Shigeyuki Yokoyama; Akio Kanai; Gota Kawai; Taiichi Sakamoto
Characterization of RNA aptamers against SRP19 protein having sequences different from SRP RNA.
Nucleic acids symposium series (2004) 2009;(53):265-6.
2009: Michiko Kimoto; Akira Sato; Rie Kawai; Shigeyuki Yokoyama; Ichiro Hirao
Site-specific incorporation of functional components into RNA by transcription using unnatural base pair systems.
Nucleic acids symposium series (2004) 2009;(53):73-4.
2009: Fahu He; Weirong Dang; Chikage Abe; Kengo Tsuda; Makoto Inoue; Satoru Watanabe; Naohiro Kobayashi; Takanori Kigawa; Takayoshi Matsuda; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takushi Harada; Yuri Tomabechi; Takaho Terada; Mikako Shirouzu; Akiko Tanaka; Peter Güntert; Yutaka Muto; Shigeyuki Yokoyama
Solution structure of the RNA binding domain in the human muscleblind-like protein 2.
Protein science : a publication of the Protein Society 2009;18(1):80-91.
2008: Kazutaka Murayama; Miyuki Kato-Murayama; Chiemi Mishima; Ryogo Akasaka; Mikako Shirouzu; Yasuhisa Fukui; Shigeyuki Yokoyama
Crystal structure of the Bruton's tyrosine kinase PH domain with phosphatidylinositol.
Biochemical and biophysical research communications 2008;377(1):23-8.
2008: Tatsuo Yanagisawa; Ryohei Ishii; Ryuya Fukunaga; Takatsugu Kobayashi; Kensaku Sakamoto; Shigeyuki Yokoyama
Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification.
Chemistry & biology 2008;15(11):1187-97.
2008: Madoka Nishimoto; Kyoko Higashijima; Mikako Shirouzu; Henri Grosjean; Yoshitaka Bessho; Shigeyuki Yokoyama
Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii.
Journal of molecular biology 2008;383(4):871-84.
2008: Seisuke Kusano; Mutsuko Kukimoto-Niino; Ryogo Akasaka; Mitsutoshi Toyama; Takaho Terada; Mikako Shirouzu; Takayuki Shindo; Shigeyuki Yokoyama
Crystal structure of the human receptor activity-modifying protein 1 extracellular domain.
Protein science : a publication of the Protein Society 2008;17(11):1907-14.
2008: Keiko Sakamoto; Yoshihiro Agari; Shigeyuki Yokoyama; Seiki Kuramitsu; Akeo Shinkai
Functional identification of an anti-sigmaE factor from Thermus thermophilus HB8.
Gene 2008;423(2):153-9.
2008: Preethi Ragunathan; Thirumananseri Kumarevel; Yoshihiro Agari; Akeo Shinkai; Seiki Kuramitsu; Shigeyuki Yokoyama; Karthe Ponnuraj
Crystal structure of ST2348, a CBS domain protein, from hyperthermophilic archaeon Sulfolobus tokodaii.
Biochemical and biophysical research communications 2008;375(1):124-8.
2008: Mutsuko Kukimoto-Niino; Ayako Sakamoto; Eiko Kanno; Kyoko Hanawa-Suetsugu; Takaho Terada; Mikako Shirouzu; Mitsunori Fukuda; Shigeyuki Yokoyama
Structural basis for the exclusive specificity of Slac2-a/melanophilin for the Rab27 GTPases.
Structure (London, England : 1993) 2008;16(10):1478-90.
2008: Jeyaraman Jeyakanthan; Sarani Rangarajan; P Mridula; Shankar Prasad Kanaujia; Yoshitsugu Shiro; Seiki Kuramitsu; Shigeyuki Yokoyama; Kanagaraj Sekar
Observation of a calcium-binding site in the gamma-class carbonic anhydrase from Pyrococcus horikoshii.
Acta crystallographica. Section D, Biological crystallography 2008;64(Pt 10):1012-9.
2008: Naoyuki Sarai; Wataru Kagawa; Norie Fujikawa; Kengo Saito; Juri Hikiba; Kozo Tanaka; Kiyoshi Miyagawa; Hitoshi Kurumizaka; Shigeyuki Yokoyama
Biochemical analysis of the N-terminal domain of human RAD54B.
Nucleic acids research 2008;36(17):5441-50.
2008: Yoshihiro Agari; Aiko Kashihara; Shigeyuki Yokoyama; Seiki Kuramitsu; Akeo Shinkai
Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator.
Molecular microbiology 2008;70(1):60-75.
2008: Kenji Oki; Kensaku Sakamoto; Takatsugu Kobayashi; Hiroshi M Sasaki; Shigeyuki Yokoyama
Transplantation of a tyrosine editing domain into a tyrosyl-tRNA synthetase variant enhances its specificity for a tyrosine analog.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(36):13298-303.
2008: Sakurako Goto-Ito; Takuhiro Ito; Ryohei Ishii; Yutaka Muto; Yoshitaka Bessho; Shigeyuki Yokoyama
Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.
Proteins 2008;72(4):1274-89.
2008: Asako Minagawa; Ryohei Ishii; Hiroaki Takaku; Shigeyuki Yokoyama; Masayuki Nashimoto
The flexible arm of tRNase Z is not essential for pre-tRNA binding but affects cleavage site selection.
Journal of molecular biology 2008;381(2):289-99.
2008: Thirumananseri Kumarevel; Noboru Nakano; Karthe Ponnuraj; Subash C B Gopinath; Keiko Sakamoto; Akeo Shinkai; PARMOD KUMAR; Shigeyuki Yokoyama
Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector L-glutamine: implications of effector binding in molecular association and DNA binding.
Nucleic acids research 2008;36(14):4808-20.
2008: Takashi Nagata; Sakura Suzuki; Ryuta Endo; Mikako Shirouzu; Takaho Terada; Makoto Inoue; Takanori Kigawa; Naohiro Kobayashi; Peter Güntert; Akiko Tanaka; Yoshihide Hayashizaki; Yutaka Muto; Shigeyuki Yokoyama
The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.
Nucleic acids research 2008;36(14):4754-67.
2008: Ryuya Fukunaga; Yoko Harada; Ichiro Hirao; Shigeyuki Yokoyama
Phosphoserine aminoacylation of tRNA bearing an unnatural base anticodon.
Biochemical and biophysical research communications 2008;372(3):480-5.
2008: Noriko Handa; Eiichi Mizohata; Seiichiro Kishishita; Mitsutoshi Toyama; Satoshi Morita; Tomomi Uchikubo-Kamo; Ryogo Akasaka; Kenji Omori; Jun Kotera; Takaho Terada; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of the GAF-B domain from human phosphodiesterase 10A complexed with its ligand, cAMP.
The Journal of biological chemistry 2008;283(28):19657-64.
2008: Misaki Yamamoto; Satoru Unzai; Shinya Saijo; Kazuki Ito; Kenji Mizutani; Chiyo Suno-Ikeda; Yukako Yabuki-Miyata; Takaho Terada; Mitsutoshi Toyama; Mikako Shirouzu; Takuya Kobayashi; Yoshimi Kakinuma; Ichiro Yamato; Shigeyuki Yokoyama; So Iwata; Takeshi Murata
Interaction and stoichiometry of the peripheral stalk subunits NtpE and NtpF and the N-terminal hydrophilic domain of NtpI of Enterococcus hirae V-ATPase.
The Journal of biological chemistry 2008;283(28):19422-31.
2008: Yuzuru Itoh; Shun-ichi Sekine; Chizu Kuroishi; Takaho Terada; Mikako Shirouzu; Seiki Kuramitsu; Shigeyuki Yokoyama
Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii.
RNA biology 2008;5(3):169-77.
2008: Kanako Kuwasako; Mari Takahashi; Naoya Tochio; Chikage Abe; Kengo Tsuda; Makoto Inoue; Takaho Terada; Mikako Shirouzu; Naohiro Kobayashi; Takanori Kigawa; Seiichi Taguchi; Akiko Tanaka; Yoshihide Hayashizaki; Peter Güntert; Yutaka Muto; Shigeyuki Yokoyama
Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode.
Biochemistry 2008;47(24):6437-50.
2008: Masumi Mori; Naoko Ogawa; Kunihiro Tanikawa; Sanae Dodo; Sotaro Shibayama; Shigeyuki Yokoyama; Akiko Tanaka
Contribution of structural biology to clinically validated target proteins.
Drug discovery today 2008;13(11-12):469-72.
2008: Hitoshi Iino; Hisashi Naitow; Yuki Nakamura; Noriko Nakagawa; Yoshihiro Agari; Mayumi Kanagawa; Akio Ebihara; Akeo Shinkai; Mitsuaki Sugahara; Masashi Miyano; Nobuo Kamiya; Shigeyuki Yokoyama; Ken Hirotsu; Seiki Kuramitsu
Crystallization screening test for the whole-cell project on Thermus thermophilus HB8.
Acta crystallographica. Section F, Structural biology and crystallization communications 2008;64(Pt 6):487-91.
2008: Akio Ebihara; Miho Manzoku; Hitoshi Iino; Mayumi Kanagawa; Akeo Shinkai; Shigeyuki Yokoyama; Seiki Kuramitsu
Crystal structure of uncharacterized protein TTHA1756 from Thermus thermophilus HB8: Structural variety in UPF0150 family proteins.
Proteins 2008;71(4):2097-101.
2008: Kanako Kuwasako; Naoshi Dohmae; Mio Inoue; Mikako Shirouzu; Seiichi Taguchi; Peter Güntert; Bertrand Séraphin; Yutaka Muto; Shigeyuki Yokoyama
Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses.
Proteins 2008;71(4):1617-36.
2008: Thirumananseri Kumarevel; Keiko Sakamoto; Subash C B Gopinath; Akeo Shinkai; PARMOD KUMAR; Shigeyuki Yokoyama
Crystal structure of an archaeal specific DNA-binding protein (Ape10b2) from Aeropyrum pernix K1.
Proteins 2008;71(3):1156-62.
2008: Tatsuo Yanagisawa; Ryohei Ishii; Ryuya Fukunaga; Takatsugu Kobayashi; Kensaku Sakamoto; Shigeyuki Yokoyama
Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase.
Journal of molecular biology 2008;378(3):634-52.
2008: Balasundaram Padmanabhan; Kit I Tong; Akira Kobayashi; Masayuki Yamamoto; Shigeyuki Yokoyama
Structural insights into the similar modes of Nrf2 transcription factor recognition by the cytoplasmic repressor Keap1.
Journal of synchrotron radiation 2008;15(Pt 3):273-6.
2008: Balasundaram Padmanabhan; Yoshihiro Nakamura; Shigeyuki Yokoyama
Structural analysis of the complex of Keap1 with a prothymosin alpha peptide.
Acta crystallographica. Section F, Structural biology and crystallization communications 2008;64(Pt 4):233-8.
2008: Seiichiro Kishishita; Katsumi Shimizu; Kazutaka Murayama; Takaho Terada; Mikako Shirouzu; Shigeyuki Yokoyama; Naoki Kunishima
Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2.
Acta crystallographica. Section D, Biological crystallography 2008;64(Pt 4):397-406.
2008: Shogo Ozaki; Hironori Kawakami; Kenta Nakamura; Norie Fujikawa; Wataru Kagawa; Sam-Yong Park; Shigeyuki Yokoyama; Hitoshi Kurumizaka; Tsutomu Katayama
A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin.
The Journal of biological chemistry 2008;283(13):8351-62.
2008: Mitsuhiro Nishimura; Tatsuya Kaminishi; Chie Takemoto; Masahito Kawazoe; Takuya Yoshida; Akiko Tanaka; Sumio Sugano; Mikako Shirouzu; Tadayasu Ohkubo; Shigeyuki Yokoyama; Yuji Kobayashi
Crystal structure of human ribosomal protein L10 core domain reveals eukaryote-specific motifs in addition to the conserved fold.
Journal of molecular biology 2008;377(2):421-30.
2008: Kazuhiko Yamasaki; Takanori Kigawa; Makoto Inoue; Satoru Watanabe; Masaru Tateno; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama
Structures and evolutionary origins of plant-specific transcription factor DNA-binding domains.
Plant physiology and biochemistry : PPB / Société française de physiologie végétale 2008;46(3):394-401.
2008: Yoshihiro Agari; Shinya Sato; Taisuke Wakamatsu; Yoshitaka Bessho; Akio Ebihara; Shigeyuki Yokoyama; Seiki Kuramitsu; Akeo Shinkai
X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7.
Proteins 2008;70(3):1108-11.
2008: Sarani Rangarajan; Jeyaraman Jeyakanthan; Palappetty Mridula; Keiko Sakamoto; Yoshiaki Kitamura; Yoshihiro Agari; Akeo Shinkai; Akio Ebihara; Seiki Kuramitsu; Shigeyuki Yokoyama; Kanagaraj Sekar
Crystallization and preliminary crystallographic studies of L30e, a ribosomal protein from Methanocaldococcus jannaschii (MJ1044).
Acta crystallographica. Section F, Structural biology and crystallization communications 2008;64(Pt 2):102-4.
2008: Shinya Mimasu; Toru Sengoku; Seketsu Fukuzawa; Takashi Umehara; Shigeyuki Yokoyama
Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A.
Biochemical and biophysical research communications 2008;366(1):15-22.
2008: Mitsuo Kuratani; Yoshitaka Bessho; Madoka Nishimoto; Henri Grosjean; Shigeyuki Yokoyama
Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA.
Journal of molecular biology 2008;375(4):1064-75.
2008: Masahide Sawano; Hitoshi Yamamoto; Kyoko Ogasahara; Shun-ichi Kidokoro; Shizue Katoh; Takayuki Ohnuma; Etsuko Katoh; Shigeyuki Yokoyama; Katsuhide Yutani
Thermodynamic basis for the stabilities of three CutA1s from Pyrococcus horikoshii,Thermus thermophilus, and Oryza sativa, with unusually high denaturation temperatures.
Biochemistry 2008;47(2):721-30.
2008: Michiko Kimoto; Rie Kawai; Tsuneo Mitsui; Shigeyuki Yokoyama; Ichiro Hirao
Efficient PCR amplification by an unnatural base pair system.
Nucleic acids symposium series (2004) 2008;(52):469-70.
2008: Michiko Kimoto; Rie Kawai; Tsuneo Mitsui; Shigeyuki Yokoyama; Ichiro Hirao
Sequences around the unnatural base pair in DNA templates for efficient replication.
Nucleic acids symposium series (2004) 2008;(52):457-8.
2008: Miki Hara-Yokoyama; Tomoko Kimura; Hiroaki Kaku; Motoaki Wakiyama; Yoko Kaitsu; Mio Inoue; Seisuke Kusano; Mikako Shirouzu; Shigeyuki Yokoyama; Toshiaki Katada; Yoshio Hirabayashi; Kiyoshi Takatsu; Masaki Yanagishita
Alteration of enzymatic properties of cell-surface antigen CD38 by agonistic anti-CD38 antibodies that prolong B cell survival and induce activation.
International immunopharmacology 2008;8(1):59-70.
2008: Thirumananseri Kumarevel; Tomoyuki Tanaka; Megumi Nishio; Subash C B Gopinath; Koji Takio; Akeo Shinkai; PARMOD KUMAR; Shigeyuki Yokoyama
Crystal structure of the MarR family regulatory protein, ST1710, from Sulfolobus tokodaii strain 7.
Journal of structural biology 2008;161(1):9-17.
2007: Shaun K Olsen; Naruhisa Ota; Seiichiro Kishishita; Mutsuko Kukimoto-Niino; Kazutaka Murayama; Hidemi Uchiyama; Mitsutoshi Toyama; Takaho Terada; Mikako Shirouzu; Osami Kanagawa; Shigeyuki Yokoyama
Crystal Structure of the interleukin-15.interleukin-15 receptor alpha complex: insights into trans and cis presentation.
The Journal of biological chemistry 2007;282(51):37191-204.
2007: Ichiro Hirao; Tsuneo Mitsui; Michiko Kimoto; Shigeyuki Yokoyama
An efficient unnatural base pair for PCR amplification.
Journal of the American Chemical Society 2007;129(50):15549-55.
2007: Yoshihiro Kawasaki; Mina Sagara; Y Shibata; Mikako Shirouzu; Shigeyuki Yokoyama; Tetsu Akiyama
Identification and characterization of Asef2, a guanine-nucleotide exchange factor specific for Rac1 and Cdc42.
Oncogene 2007;26(55):7620-267.
2007: Takashi Yabuki; Yoko Motoda; Kazuharu Hanada; Emi Nunokawa; Miyuki Saito; Eiko Seki; Makoto Inoue; Takanori Kigawa; Shigeyuki Yokoyama
A robust two-step PCR method of template DNA production for high-throughput cell-free protein synthesis.
Journal of structural and functional genomics 2007;8(4):173-91.
2007: Yong Xie; Chie Takemoto; Seiichiro Kishishita; Tomomi Uchikubo-Kamo; Kazutaka Murayama; Lirong Chen; Zhi Jie Liu; Bi-Cheng Wang; Miho Manzoku; Akio Ebihara; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Structure of the minimized alpha/beta-hydrolase fold protein from Thermus thermophilus HB8.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 12):993-7.
2007: Noriko Handa; Seiichiro Kishishita; Satoshi Morita; Ryogo Akasaka; Zhongmin Jin; John Chrzas; Lirong Chen; Zhi-Jie Liu; Bi-Cheng Wang; Sumio Sugano; Akiko Tanaka; Takaho Terada; Mikako Shirouzu; Shigeyuki Yokoyama
Structure of the human Tim44 C-terminal domain in complex with pentaethylene glycol: ligand-bound form.
Acta crystallographica. Section D, Biological crystallography 2007;63(Pt 12):1225-34.
2007: Mitsuo Kuratani; Yuka Yoshikawa; Yoshitaka Bessho; Kyoko Higashijima; Takeshi Ishii; Rie Shibata; Seizo Takahashi; Katsuhide Yutani; Shigeyuki Yokoyama
Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine.
Structure (London, England : 1993) 2007;15(12):1642-53.
2007: Akeo Shinkai; Naomi Ohbayashi; Takaho Terada; Mikako Shirouzu; Seiki Kuramitsu; Shigeyuki Yokoyama
Identification of promoters recognized by RNA polymerase-sigmaE holoenzyme from Thermus thermophilus HB8.
Journal of bacteriology 2007;189(23):8758-64.
2007: Partha Datta; Daniel N Wilson; Masahito Kawazoe; Neil K Swami; Tatsuya Kaminishi; Manjuli R Sharma; Timothy M Booth; Chie Takemoto; Paola Fucini; Shigeyuki Yokoyama; Rajendra K Agrawal
Structural aspects of RbfA action during small ribosomal subunit assembly.
Molecular cell 2007;28(3):434-45.
2007: Noboru Nakano; Thirumananseri Kumarevel; Emiko Matsunaga; Akeo Shinkai; Seiki Kuramitsu; Shigeyuki Yokoyama
Purification, crystallization and preliminary X-ray crystallographic analysis of ST1022, a putative member of the Lrp/AsnC family of transcriptional regulators isolated from Sulfolobus tokodaii strain 7.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 11):964-6.
2007: Mitsuhiro Nishimura; Tatsuya Kaminishi; Masahito Kawazoe; Mikako Shirouzu; Chie Takemoto; Shigeyuki Yokoyama; Akiko Tanaka; Sumio Sugano; Takuya Yoshida; Tadayasu Ohkubo; Yuji Kobayashi
Purification, crystallization and preliminary X-ray diffraction study of human ribosomal protein L10 core domain.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 11):950-2.
2007: Michiko Kimoto; Kei Moriyama; Shigeyuki Yokoyama; Ichiro Hirao
Cytostatic evaluations of nucleoside analogs related to unnatural base pairs for a genetic expansion system.
Bioorganic & medicinal chemistry letters 2007;17(20):5582-5.
2007: Akeo Shinkai; Shun-Ichi Sekine; Akiko Urushibata; Takaho Terada; Mikako Shirouzu; Shigeyuki Yokoyama
The putative DNA-binding protein Sto12a from the thermoacidophilic archaeon Sulfolobus tokodaii contains intrachain and interchain disulfide bonds.
Journal of molecular biology 2007;372(5):1293-304.
2007: Sakurako Goto-Ito; Ryohei Ishii; Takuhiro Ito; Rie Shibata; Emiko Fusatomi; Shun-ichi Sekine; Yoshitaka Bessho; Shigeyuki Yokoyama
Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis.
Acta crystallographica. Section D, Biological crystallography 2007;63(Pt 10):1059-68.
2007: Naohiro Kobayashi; Junji Iwahara; Seizo Koshiba; Tadashi Tomizawa; Naoya Tochio; Peter Güntert; Takanori Kigawa; Shigeyuki Yokoyama
KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies.
Journal of biomolecular NMR 2007;39(1):31-52.
2007: Sakura Suzuki; Ayako Tatsuguchi; Eiko Matsumoto; Masahito Kawazoe; Tatsuya Kaminishi; Mikako Shirouzu; Yutaka Muto; Chie Takemoto; Shigeyuki Yokoyama
Structural characterization of the ribosome maturation protein, RimM.
Journal of bacteriology 2007;189(17):6397-406.
2007: Kenji Keyamura; Norie Fujikawa; Takuma Ishida; Shogo Ozaki; Masayuki Su'etsugu; Kazuyuki Fujimitsu; Wataru Kagawa; Shigeyuki Yokoyama; Hitoshi Kurumizaka; Tsutomu Katayama
The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP DnaA-specific initiation complexes.
Genes & development 2007;21(16):2083-99.
2007: Yoshihiro Nakamura; Takashi Umehara; Akiko Tanaka; Masami Horikoshi; Balasundaram Padmanabhan; Shigeyuki Yokoyama
Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome.
Biochemical and biophysical research communications 2007;359(3):503-9.
2007: Ryohei Ishii; Asako Minagawa; Hiroshi Takaku; Masamichi Takagi; Masayuki Nashimoto; Shigeyuki Yokoyama
The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 8):637-41.
2007: Fahu He; Takashi Umehara; Kengo Tsuda; Makoto Inoue; Takanori Kigawa; Takayoshi Matsuda; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takaho Terada; Mikako Shirouzu; Akiko Tanaka; Sumio Sugano; Yutaka Muto; Shigeyuki Yokoyama
Solution structure of the zinc finger HIT domain in protein FON.
Protein science : a publication of the Protein Society 2007;16(8):1577-87.
2007: Yukiko Doi-Katayama; Fumiaki Hayashi; Makoto Inoue; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Takanori Kigawa; Mayumi Yoshida; Mikako Shirouzu; Takaho Terada; Yoshihide Hayashizaki; Shigeyuki Yokoyama; Hiroshi Hirota
Solution structure of the general transcription factor 2I domain in mouse TFII-I protein.
Protein science : a publication of the Protein Society 2007;16(8):1788-92.
2007: Mamiko Masutani; Nahum Sonenberg; Shigeyuki Yokoyama; Hiroaki Imataka
Reconstitution reveals the functional core of mammalian eIF3.
The EMBO journal 2007;26(14):3373-83.
2007: Takashi Umehara; Masatoshi Wakamori; Akiko Tanaka; Balasundaram Padmanabhan; Shigeyuki Yokoyama
Purification, crystallization and preliminary X-ray diffraction of the C-terminal bromodomain from human BRD2.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 7):613-5.
2007: Ryuya Fukunaga; Shigeyuki Yokoyama
Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus.
Journal of molecular biology 2007;370(1):128-41.
2007: Yoshihiro Nakamura; Takashi Umehara; Hiroaki Hamana; Yoshihide Hayashizaki; Makoto Inoue; Takanori Kigawa; Mikako Shirouzu; Takaho Terada; Akiko Tanaka; Balasundaram Padmanabhan; Shigeyuki Yokoyama
Crystal structure analysis of the PHD domain of the transcription co-activator Pygopus.
Journal of molecular biology 2007;370(1):80-92.
2007: Eiji Inagaki; Noriyasu Ohshima; Keiko Sakamoto; Nigar D Babayeva; Hiroaki Kato; Shigeyuki Yokoyama; Tahir Tahirov
New insights into the binding mode of coenzymes: structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase complexed with NADP+.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 6):462-5.
2007: Tominari Kobayashi; Satoshi Mikami; Shigeyuki Yokoyama; Hiroaki Imataka
An improved cell-free system for picornavirus synthesis.
Journal of virological methods 2007;142(1-2):182-8.
2007: Misao Yoneyama; Naoya Tochio; Takashi Umehara; Seizo Koshiba; Makoto Inoue; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Satoru Watanabe; Yasuko Tomo; Yuji Nishimura; Takushi Harada; Takaho Terada; Mikako Shirouzu; Yoshihide Hayashizaki; Osamu Ohara; Akiko Tanaka; Takanori Kigawa; Shigeyuki Yokoyama
Structural and functional differences of SWIRM domain subtypes.
Journal of molecular biology 2007;369(1):222-38.
2007: Atsushi Shimada; Hideaki Niwa; Kenichi Tsujita; Shiro Suetsugu; Koji Nitta; Kyoko Hanawa-Suetsugu; Ryogo Akasaka; Yuri Nishino; Mitsutoshi Toyama; Lirong Chen; Zhi-Jie Liu; Bi-Cheng Wang; Masaki Yamamoto; Takaho Terada; Atsuo Miyazawa; Akiko Tanaka; Sumio Sugano; Mikako Shirouzu; Kuniaki Nagayama; Tadaomi Takenawa; Shigeyuki Yokoyama
Curved EFC/F-BAR-domain dimers are joined end to end into a filament for membrane invagination in endocytosis.
Cell 2007;129(4):761-72.
2007: Yoshitaka Bessho; Rie Shibata; Shun-ichi Sekine; Kazutaka Murayama; Kyoko Higashijima; Chie Hori-Takemoto; Mikako Shirouzu; Seiki Kuramitsu; Shigeyuki Yokoyama
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(20):8293-8.
2007: Ryoichi Arai; Kaori Ito; Tetsuo Ohnishi; Hisako Ohba; Ryogo Akasaka; Yoshitaka Bessho; Kyoko Hanawa-Suetsugu; Takeo Yoshikawa; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of human myo-inositol monophosphatase 2, the product of the putative susceptibility gene for bipolar disorder, schizophrenia, and febrile seizures.
Proteins 2007;67(3):732-42.
2007: Shankar Prasad Kanaujia; Chellamuthu Vasuki Ranjani; Jeyaraman Jeyakanthan; Masami Nishida; Yoshiaki Kitamura; Seiki Baba; Akio Ebihara; Nobutaka Shimizu; Noriko Nakagawa; Akeo Shinkai; Masaki Yamamoto; Seiki Kuramitsu; Yoshitsugu Shiro; Kanagaraj Sekar; Shigeyuki Yokoyama
Preliminary X-ray crystallographic study of glucose dehydrogenase from Thermus thermophilus HB8.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 5):446-8.
2007: Ryuya Fukunaga; Shigeyuki Yokoyama
The C-terminal domain of the archaeal leucyl-tRNA synthetase prevents misediting of isoleucyl-tRNA(Ile).
Biochemistry 2007;46(17):4985-96.
2007: Akeo Shinkai; Satoshi Kira; Noriko Nakagawa; Aiko Kashihara; Seiki Kuramitsu; Shigeyuki Yokoyama
Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8.
Journal of bacteriology 2007;189(10):3891-901.
2007: Shankar Prasad Kanaujia; Chellamuthu Vasuki Ranjani; Jeyaraman Jeyakanthan; Miwa Ohmori; Kazuko Agari; Yoshiaki Kitamura; Seiki Baba; Akio Ebihara; Akeo Shinkai; Seiki Kuramitsu; Yoshitsugu Shiro; Kanagaraj Sekar; Shigeyuki Yokoyama
Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of molybdopterin synthase from Thermus thermophilus HB8.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 4):324-6.
2007: Ryuya Fukunaga; Shigeyuki Yokoyama
Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.
Nature structural & molecular biology 2007;14(4):272-9.
2007: Kazuma Takada; Chie Takemoto; Masahito Kawazoe; Takayuki Konno; Kyoko Hanawa-Suetsugu; SungGa Lee; Mikako Shirouzu; Shigeyuki Yokoyama; Akira Muto; Hyouta Himeno
In vitro trans-translation of Thermus thermophilus: ribosomal protein S1 is not required for the early stage of trans-translation.
RNA (New York, N.Y.) 2007;13(4):503-10.
2007: Rie Shibata; Yoshitaka Bessho; Akeo Shinkai; Madoka Nishimoto; Emiko Fusatomi; Takaho Terada; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure and RNA-binding analysis of the archaeal transcription factor NusA.
Biochemical and biophysical research communications 2007;355(1):122-8.
2007: Sean connell; Chie Takemoto; Daniel N Wilson; Hongfei Wang; Kazutaka Murayama; Takaho Terada; Mikako Shirouzu; Maximilian Rost; Martin Schüler; Jan Giesebrecht; Marylena Dabrowski; Thorsten Mielke; Paola Fucini; Shigeyuki Yokoyama; Christian M T Spahn
Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
Molecular cell 2007;25(5):751-64.
2007: Hyouta Himeno; Daisuke Kurita; Kazuma Takada; Takayuki Konno; Kyoko Hanawa-Suetsugu; Chie Takemoto; Masahito Kawazoe; Shigeyuki Yokoyama; Nobukazu Nameki; Gota Kawai; Akira Muto
[Molecular mechanism of trans-translation].
Seikagaku. The Journal of Japanese Biochemical Society 2007;79(3):213-21.
2007: Tatsuya Kaminishi; Daniel N Wilson; Chie Takemoto; Jörg M Harms; Masahito Kawazoe; Frank Schluenzen; Kyoko Hanawa-Suetsugu; Mikako Shirouzu; Paola Fucini; Shigeyuki Yokoyama
A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction.
Structure (London, England : 1993) 2007;15(3):289-97.
2007: Ryuya Fukunaga; Shigeyuki Yokoyama
Crystallization and preliminary X-ray crystallographic study of alanyl-tRNA synthetase from the archaeon Archaeoglobus fulgidus.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 3):224-8.
2007: Yoshihiro Nakamura; Takashi Umehara; Akiko Tanaka; Masami Horikoshi; Balasundaram Padmanabhan; Shigeyuki Yokoyama
Purification, crystallization and preliminary X-ray diffraction analysis of the non-ATPase subunit Nas6 in complex with the ATPase subunit Rpt3 of the 26S proteasome from Saccharomyces cerevisiae.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 3):190-2.
2007: Nobuo Okazaki; Maki Kumei; Miho Manzoku; Seiki Kuramitsu; Mikako Shirouzu; Akeo Shinkai; Shigeyuki Yokoyama
Structure of a UPF0150-family protein from Thermus thermophilus HB8.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 3):173-7.
2007: Ryuya Fukunaga; Shigeyuki Yokoyama
Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii.
Acta crystallographica. Section D, Biological crystallography 2007;63(Pt 3):390-400.
2007: Seiko Yoshikawa; Ryoichi Arai; Yukiko Kinoshita; Tomomi Uchikubo-Kamo; Taisuke Wakamatsu; Ryogo Akasaka; Ryoji Masui; Takaho Terada; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate.
Acta crystallographica. Section D, Biological crystallography 2007;63(Pt 3):357-65.
2007: Xuesong Dong; Miyuki Kato-Murayama; Tomonari Muramatsu; Hirotada Mori; Mikako Shirouzu; Yoshitaka Bessho; Shigeyuki Yokoyama
The crystal structure of leucyl/phenylalanyl-tRNA-protein transferase from Escherichia coli.
Protein science : a publication of the Protein Society 2007;16(3):528-34.
2007: Takayoshi Matsuda; Seizo Koshiba; Naoya Tochio; Eiko Seki; Noriyuki Iwasaki; Takashi Yabuki; Makoto Inoue; Shigeyuki Yokoyama; Takanori Kigawa
Improving cell-free protein synthesis for stable-isotope labeling.
Journal of biomolecular NMR 2007;37(3):225-9.
2007: Gloria I Perez; Beth M Acton; Andrea Jurisicova; Guy Perkins; A White; J Brown; Alexander M Trbovich; Mee-Ran Kim; R Fissore; J Xu; A Ahmady; S G D'Estaing; H Li; Wataru Kagawa; Hitoshi Kurumizaka; Shigeyuki Yokoyama; H Okada; Tak W Mak; M H Ellisman; Robert Casper; Jonathan L Tilly
Genetic variance modifies apoptosis susceptibility in mature oocytes via alterations in DNA repair capacity and mitochondrial ultrastructure.
Cell death and differentiation 2007;14(3):524-33.
2007: Kazutaka Murayama; Mikako Shirouzu; Yoshihiro Kawasaki; Miyuki Kato-Murayama; Kyoko Hanawa-Suetsugu; Ayako Sakamoto; Yasuhiro Katsura; Atsushi Suenaga; Mitsutoshi Toyama; Takaho Terada; Makoto Taiji; Tetsu Akiyama; Shigeyuki Yokoyama
Crystal structure of the rac activator, Asef, reveals its autoinhibitory mechanism.
The Journal of biological chemistry 2007;282(7):4238-42.
2007: Yoshihiro Nakamura; Takashi Umehara; Kazumi Nakano; Moon Kyoo Jang; Mikako Shirouzu; Satoshi Morita; Hiroko Uda-Tochio; Hiroaki Hamana; Takaho Terada; Naruhiko Adachi; Takehisa Matsumoto; Akiko Tanaka; Masami Horikoshi; Keiko Ozato; Balasundaram Padmanabhan; Shigeyuki Yokoyama
Crystal structure of the human BRD2 bromodomain: insights into dimerization and recognition of acetylated histone H4.
The Journal of biological chemistry 2007;282(6):4193-201.
2007: Satoshi Ohnishi; Peter Güntert; Seizo Koshiba; Tadashi Tomizawa; Ryogo Akasaka; Naoya Tochio; Manami Sato; Makoto Inoue; Takushi Harada; Satoru Watanabe; Akiko Tanaka; Mikako Shirouzu; Takanori Kigawa; Shigeyuki Yokoyama
Solution structure of an atypical WW domain in a novel beta-clam-like dimeric form.
FEBS letters 2007;581(3):462-8.
2007: Naoei Yoshitani; Kazuki Saito; Wakana Saikawa; Miwako Asanuma; Shigeyuki Yokoyama; Hiroshi Hirota
NTA-mediated protein capturing strategy in screening experiments for small organic molecules by surface plasmon resonance.
Proteomics 2007;7(4):494-9.
2007: Yoshihiro Nakamura; Kazumi Nakano; Takashi Umehara; Mayumi Kimura; Yoshihide Hayashizaki; Akiko Tanaka; Masami Horikoshi; Balasundaram Padmanabhan; Shigeyuki Yokoyama
Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome.
Structure (London, England : 1993) 2007;15(2):179-89.
2007: Shankar Prasad Kanaujia; Chellamuthu Vasuki Ranjani; Jeyaraman Jeyakanthan; Seiki Baba; Chizu Kuroishi; Akio Ebihara; Akeo Shinkai; Seiki Kuramitsu; Yoshitsugu Shiro; Kanagaraj Sekar; Shigeyuki Yokoyama
Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of DHNA synthetase from Geobacillus kaustophilus.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 2):103-5.
2007: Hiroaki Tanaka; Takashi Umehara; Koji Inaka; Sachiko Takahashi; Rie Shibata; Yoshitaka Bessho; Masaru Sato; Shigeru Sugiyama; Emiko Fusatomi; Takaho Terada; Mikako Shirouzu; Satoshi Sano; Moritoshi Motohara; Tomoyuki Kobayashi; Tetsuo Tanaka; Akiko Tanaka; Shigeyuki Yokoyama
Crystallization of the archaeal transcription termination factor NusA: a significant decrease in twinning under microgravity conditions.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 2):69-73.
2007: Naoyuki Kondo; Noriko Nakagawa; Akio Ebihara; Lirong Chen; Zhi-Jie Liu; Bi-Cheng Wang; Shigeyuki Yokoyama; Seiki Kuramitsu; Ryoji Masui
Structure of dNTP-inducible dNTP triphosphohydrolase: insight into broad specificity for dNTPs and triphosphohydrolase-type hydrolysis.
Acta crystallographica. Section D, Biological crystallography 2007;63(Pt 2):230-9.
2007: Koichiro Kodama; Seketsu Fukuzawa; Hiroshi Nakayama; Kensaku Sakamoto; Takanori Kigawa; Takashi Yabuki; Natsuko Matsuda; Mikako Shirouzu; Koji Takio; Shigeyuki Yokoyama; Kazuo Tachibana
Site-specific functionalization of proteins by organopalladium reactions.
Chembiochem : a European journal of chemical biology 2007;8(2):232-8.
2007: Kazuma Takada; Chie Takemoto; Masahito Kawazoe; Mikako Shirouzu; Shigeyuki Yokoyama; Akira Muto; Hyouta Himeno
Thermus thermophilus tmRNA and trans-translation.
Nucleic acids symposium series (2004) 2007;(51):369-70.
2007: Ichiro Hirao; Tsuneo Mitsui; Michiko Kimoto; Shigeyuki Yokoyama
Development of an unnatural base pair for efficient PCR amplification.
Nucleic acids symposium series (2004) 2007;(51):9-10.
2007: Michiko Kimoto; Tsuneo Mitsui; Yoko Harada; Akira Sato; Shigeyuki Yokoyama; Ichiro Hirao
Fluorescent probing for RNA molecules by an unnatural base-pair system.
Nucleic acids research 2007;35(16):5360-9.
2007: Shankar Prasad Kanaujia; Chellamuthu Vasuki Ranjani; Jeyaraman Jeyakanthan; Seiki Baba; Lirong Chen; Zhi-Jie Liu; Bi-Cheng Wang; Masami Nishida; Akio Ebihara; Akeo Shinkai; Seiki Kuramitsu; Yoshitsugu Shiro; Kanagaraj Sekar; Shigeyuki Yokoyama
Crystallization and preliminary crystallographic analysis of molybdenum-cofactor biosynthesis protein C from Thermus thermophilus.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 1):27-9.
2006: Satoshi Mikami; Tominari Kobayashi; Shigeyuki Yokoyama; Hiroaki Imataka
A hybridoma-based in vitro translation system that efficiently synthesizes glycoproteins.
Journal of biotechnology 2006;127(1):65-78.
2006: Takuya B Hiyama; Min Zhao; Yu Kitago; Min Yao; Shun-ichi Sekine; Takaho Terada; Chizu Kuroishi; Zhi-Jie Liu; John P Rose; Seiki Kuramitsu; Mikako Shirouzu; Nobuhisa Watanabe; Shigeyuki Yokoyama; Isao Tanaka; Bi-Cheng Wang
Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins.
Journal of structural and functional genomics 2006;7(3-4):119-29.
2006: Shun-ichi Sekine; Mika Shichiri; Stéphane Bernier; Robert Chênevert; Jacques Lapointe; Shigeyuki Yokoyama
Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase.
Structure (London, England : 1993) 2006;14(12):1791-9.
2006: Noriko Handa; Mutsuko Kukimoto-Niino; Ryogo Akasaka; Kazutaka Murayama; Takaho Terada; Makoto Inoue; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Emi Nunokawa; Akiko Tanaka; Yoshihide Hayashizaki; Takanori Kigawa; Mikako Shirouzu; Shigeyuki Yokoyama
Structure of the UNC5H2 death domain.
Acta crystallographica. Section D, Biological crystallography 2006;62(Pt 12):1502-9.
2006: Shiro Suetsugu; Kazutaka Murayama; Ayako Sakamoto; Kyoko Hanawa-Suetsugu; Azusa Seto; Tsukasa Oikawa; Chiemi Mishima; Mikako Shirouzu; Tadaomi Takenawa; Shigeyuki Yokoyama
The RAC binding domain/IRSp53-MIM homology domain of IRSp53 induces RAC-dependent membrane deformation.
The Journal of biological chemistry 2006;281(46):35347-58.
2006: Naoya Tochio; Seizo Koshiba; Naohiro Kobayashi; Makoto Inoue; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Yasuko Tomo; Yoko Motoda; Atsuo Kobayashi; Akiko Tanaka; Yoshihide Hayashizaki; Takaho Terada; Mikako Shirouzu; Takanori Kigawa; Shigeyuki Yokoyama
Solution structure of the kinase-associated domain 1 of mouse microtubule-associated protein/microtubule affinity-regulating kinase 3.
Protein science : a publication of the Protein Society 2006;15(11):2534-43.
2006: Mutsuko Kukimoto-Niino; Tetsuo Takagi; Ryogo Akasaka; Kazutaka Murayama; Tomomi Uchikubo-Kamo; Takaho Terada; Makoto Inoue; Satoru Watanabe; Akiko Tanaka; Yoshihide Hayashizaki; Takanori Kigawa; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of the RUN domain of the RAP2-interacting protein x.
The Journal of biological chemistry 2006;281(42):31843-53.
2006: Noriko Handa; Mutsuko Kukimoto-Niino; Ryogo Akasaka; Seiichiro Kishishita; Kazutaka Murayama; Takaho Terada; Makoto Inoue; Takanori Kigawa; Shingo Kose; Naoko Imamoto; Akiko Tanaka; Yoshihide Hayashizaki; Mikako Shirouzu; Shigeyuki Yokoyama
The crystal structure of mouse Nup35 reveals atypical RNP motifs and novel homodimerization of the RRM domain.
Journal of molecular biology 2006;363(1):114-24.
2006: Noriko Morikubo; Yoriyuki Fukuda; Kazumasa Ohtake; Naoko Shinya; Daisuke Kiga; Kensaku Sakamoto; Miwako Asanuma; Hiroshi Hirota; Shigeyuki Yokoyama; Tsutomu Hoshino
Cation-pi interaction in the polyolefin cyclization cascade uncovered by incorporating unnatural amino acids into the catalytic sites of squalene cyclase.
Journal of the American Chemical Society 2006;128(40):13184-94.
2006: Hiroshi M Sasaki; Shun-ichi Sekine; Toru Sengoku; Ryuya Fukunaga; Motoyuki Hattori; Yukiko Utsunomiya; Chizu Kuroishi; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(40):14744-9.
2006: Frank Schluenzen; Chie Takemoto; Daniel N Wilson; Tatsuya Kaminishi; Jörg M Harms; Kyoko Hanawa-Suetsugu; Witold Szaflarski; Masahito Kawazoe; Mikako Shirouzu; Mikako Shirouzo; Knud H Nierhaus; Shigeyuki Yokoyama; Paola Fucini
The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation.
Nature structural & molecular biology 2006;13(10):871-8.
2006: Koichiro Kodama; Seketsu Fukuzawa; Kensaku Sakamoto; Hiroshi Nakayama; Takanori Kigawa; Takashi Yabuki; Natsuko Matsuda; Mikako Shirouzu; Koji Takio; Kazuo Tachibana; Shigeyuki Yokoyama
A new protein engineering approach combining chemistry and biology, part I; site-specific incorporation of 4-iodo-L-phenylalanine in vitro by using misacylated suppressor tRNAPhe.
Chembiochem : a European journal of chemical biology 2006;7(10):1577-81.
2006: Alexander A Tokmakov; Yumiko Terazawa; Mariko Ikeda; Mikako Shirouzu; Shigeyuki Yokoyama
Coupled transcription-and-translation in Xenopus oocyte and egg extracts.
Journal of biotechnology 2006;125(4):557-64.
2006: Hiromi Okumura; Junko Nakazawa; Keiko Tsuganezawa; Takeo Usui; Hiroyuki Osada; Takehisa Matsumoto; Akiko Tanaka; Shigeyuki Yokoyama
Phenothiazine and carbazole-related compounds inhibit mitotic kinesin Eg5 and trigger apoptosis in transformed culture cells.
Toxicology letters 2006;166(1):44-52.
2006: Eiji Inagaki; Noriyasu Ohshima; Hitomi Takahashi; Chizu Kuroishi; Shigeyuki Yokoyama; Tahir Tahirov
Crystal structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase.
Journal of molecular biology 2006;362(3):490-501.
2006: Noboru Nakano; Nobuo Okazaki; Shinya Satoh; Koji Takio; Seiki Kuramitsu; Akeo Shinkai; Shigeyuki Yokoyama
Structure of the stand-alone RAM-domain protein from Thermus thermophilus HB8.
Acta crystallographica. Section F, Structural biology and crystallization communications 2006;62(Pt 9):855-60.
2006: Ichiro Hirao; Michiko Kimoto; Tsuneo Mitsui; Tsuyoshi Fujiwara; Rie Kawai; Akira Sato; Yoko Harada; Shigeyuki Yokoyama
An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA.
Nature methods 2006;3(9):729-35.
2006: Tomoyuki Tanaka; Masahide Sawano; Kyoko Ogasahara; Yasushi Sakaguchi; Bagautdin Bagautdinov; Etsuko Katoh; Chizu Kuroishi; Akeo Shinkai; Shigeyuki Yokoyama; Katsuhide Yutani
Hyper-thermostability of CutA1 protein, with a denaturation temperature of nearly 150 degrees C.
FEBS letters 2006;580(17):4224-30.
2006: Wataru Iwasaki; Shun-ichi Sekine; Chizu Kuroishi; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase.
Journal of molecular biology 2006;360(2):329-42.
2006: Xuesong Dong; Yoshitaka Bessho; Rie Shibata; Madoka Nishimoto; Mikako Shirouzu; Seiki Kuramitsu; Shigeyuki Yokoyama
Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8.
RNA biology 2006;3(3):115-22.
2006: Motoyuki Hattori; Eiichi Mizohata; Ayako Tatsuguchi; Rie Shibata; Seiichiro Kishishita; Kazutaka Murayama; Takaho Terada; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of the single-domain rhodanese homologue TTHA0613 from Thermus thermophilus HB8.
Proteins 2006;64(1):284-7.
2006: Asako Minagawa; Hiroshi Takaku; Hirotaka S Shibata; Ryohei Ishii; Masamichi Takagi; Shigeyuki Yokoyama; Masayuki Nashimoto
Substrate recognition ability differs among various prokaryotic tRNase Zs.
Biochemical and biophysical research communications 2006;345(1):385-93.
2006: Ryuya Fukunaga; Shigeyuki Yokoyama
Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase.
Journal of molecular biology 2006;359(4):901-12.
2006: Takayoshi Matsuda; Takanori Kigawa; Seizo Koshiba; Makoto Inoue; Masaaki Aoki; Kazuhiko Yamasaki; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama
Cell-free synthesis of zinc-binding proteins.
Journal of structural and functional genomics 2006;7(2):93-100.
2006: Motoaki Wakiyama; Yoko Kaitsu; Shigeyuki Yokoyama
Cell-free translation system from Drosophila S2 cells that recapitulates RNAi.
Biochemical and biophysical research communications 2006;343(4):1067-71.
2006: Kaori Ito; Ryoichi Arai; Emiko Fusatomi; Tomomi Kamo-Uchikubo; Shin-Ichi Kawaguchi; Ryogo Akasaka; Takaho Terada; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 A resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD.
Protein science : a publication of the Protein Society 2006;15(5):1187-92.
2006: Toshiyuki Hamada; Yoko Ito; Takamasa Abe; Fumiaki Hayashi; Peter Güntert; Makoto Inoue; Takanori Kigawa; Takaho Terada; Mikako Shirouzu; Mayumi Yoshida; Akiko Tanaka; Sumio Sugano; Shigeyuki Yokoyama; Hiroshi Hirota
Solution structure of the antifreeze-like domain of human sialic acid synthase.
Protein science : a publication of the Protein Society 2006;15(5):1010-6.
2006: Toru Sengoku; Osamu Nureki; Akira Nakamura; Satoru Kobayashi; Shigeyuki Yokoyama
Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.
Cell 2006;125(2):287-300.
2006: Kazuhiko Yamasaki; Takanori Kigawa; Makoto Inoue; Tomoko Yamasaki; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Yasuko Tomo; Takaho Terada; Mikako Shirouzu; Akiko Tanaka; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama
An Arabidopsis SBP-domain fragment with a disrupted C-terminal zinc-binding site retains its tertiary structure.
FEBS letters 2006;580(8):2109-16.
2006: Ryoichi Arai; Seiko Yoshikawa; Kazutaka Murayama; Yuzuru Imai; Ryosuke Takahashi; Mikako Shirouzu; Shigeyuki Yokoyama
Structure of human ubiquitin-conjugating enzyme E2 G2 (UBE2G2/UBC7).
Acta crystallographica. Section F, Structural biology and crystallization communications 2006;62(Pt 4):330-4.
2006: Takayuki Hondoh; Atsushi Kato; Shigeyuki Yokoyama; Yutaka Kuroda
Computer-aided NMR assay for detecting natively folded structural domains.
Protein science : a publication of the Protein Society 2006;15(4):871-83.
2006: Satoshi Mikami; Mamiko Masutani; Nahum Sonenberg; Shigeyuki Yokoyama; Hiroaki Imataka
An efficient mammalian cell-free translation system supplemented with translation factors.
Protein expression and purification 2006;46(2):348-57.
2006: Alexander A Tokmakov; Eiko Matsumoto; Mikako Shirouzu; Shigeyuki Yokoyama
Coupled cytoplasmic transcription-and-translation--a method of choice for heterologous gene expression in Xenopus oocytes.
Journal of biotechnology 2006;122(1):5-15.
2006: Balasundaram Padmanabhan; Kit I Tong; Tsutomu Ohta; Yoshihiro Nakamura; Maria Scharlock; Makiko Ohtsuji; MOON-IL KANG; Akira Kobayashi; Shigeyuki Yokoyama; Masayuki Yamamoto
Structural basis for defects of Keap1 activity provoked by its point mutations in lung cancer.
Molecular cell 2006;21(5):689-700.
2006: Rima Enomoto; Takashi Kinebuchi; Makoto Sato; Hideshi Yagi; Hitoshi Kurumizaka; Shigeyuki Yokoyama
Stimulation of DNA strand exchange by the human TBPIP/Hop2-Mnd1 complex.
The Journal of biological chemistry 2006;281(9):5575-81.
2006: Namthip Chumpolkulwong; Kensaku Sakamoto; Akiko Hayashi; Fumie Iraha; Naoko Shinya; Natsuko Matsuda; Daisuke Kiga; Akiko Urushibata; Mikako Shirouzu; Kenji Oki; Takanori Kigawa; Shigeyuki Yokoyama
Translation of 'rare' codons in a cell-free protein synthesis system from Escherichia coli.
Journal of structural and functional genomics 2006;7(1):31-6.
2006: Naoya Tochio; Takashi Umehara; Seizo Koshiba; Makoto Inoue; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Satoru Watanabe; Yasuko Tomo; Masaru Hanada; Masaomi Ikari; Miyuki Sato; Takaho Terada; Takahiro Nagase; Osamu Ohara; Mikako Shirouzu; Akiko Tanaka; Takanori Kigawa; Shigeyuki Yokoyama
Solution structure of the SWIRM domain of human histone demethylase LSD1.
Structure (London, England : 1993) 2006;14(3):457-68.
2006: Eiji Inagaki; Keiko Sakamoto; Naomi Obayashi; Takaho Terada; Mikako Shirouzu; Yoshitaka Bessho; Chizu Kuroishi; Seiki Kuramitsu; Akeo Shinkai; Shigeyuki Yokoyama
Expression, purification, crystallization and preliminary X-ray diffraction analysis of galactokinase from Pyrococcus horikoshii.
Acta crystallographica. Section F, Structural biology and crystallization communications 2006;62(Pt 2):169-71.
2006: Ryoichi Arai; Mutsuko Kukimoto-Niino; Chizu Kuroishi; Yoshitaka Bessho; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3.
Protein science : a publication of the Protein Society 2006;15(2):373-7.
2006: Mitsuo Kuratani; Hiroaki Sakai; Masahiro Takahashi; Tatsuo Yanagisawa; Takatsugu Kobayashi; Kazutaka Murayama; Lirong Chen; Zhi-Jie Liu; Bi-Cheng Wang; Chizu Kuroishi; Seiki Kuramitsu; Takaho Terada; Yoshitaka Bessho; Mikako Shirouzu; Shun-ichi Sekine; Shigeyuki Yokoyama
Crystal structures of tyrosyl-tRNA synthetases from Archaea.
Journal of molecular biology 2006;355(3):395-408.
2006: Nobumasa Hino; Akiko Hayashi; Kensaku Sakamoto; Shigeyuki Yokoyama
Site-specific incorporation of non-natural amino acids into proteins in mammalian cells with an expanded genetic code.
Nature protocols 2006;1(6):2957-62.
2006: Ichiro Hirao; Michiko Kimoto; Tsuneo Mitsui; Tsuyoshi Fujiwara; Rie Kawai; Akira Sato; Yoko Harada; Shigeyuki Yokoyama
An unnatural base pair system for in vitro replication and transcription.
Nucleic acids symposium series (2004) 2006;(50):33-4.
2006: Naoyuki Sarai; Wataru Kagawa; Takashi Kinebuchi; Ako Kagawa; Kozo Tanaka; Kiyoshi Miyagawa; Shukuko Ikawa; Takehiko Shibata; Hitoshi Kurumizaka; Shigeyuki Yokoyama
Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein.
Nucleic acids research 2006;34(16):4429-37.
2006: Asako Minagawa; Hiroshi Takaku; Ryohei Ishii; Masamichi Takagi; Shigeyuki Yokoyama; Masayuki Nashimoto
Identification by Mn2+ rescue of two residues essential for the proton transfer of tRNase Z catalysis.
Nucleic acids research 2006;34(13):3811-8.
2006: Satoshi Miyazaki; Yutaka Kuroda; Shigeyuki Yokoyama
Identification of putative domain linkers by a neural network - application to a large sequence database.
BMC bioinformatics 2006;7():323.
2006: Ken Komiya; Kensaku Sakamoto; Atsushi Kameda; Masahito Yamamoto; Azuma Ohuchi; Daisuke Kiga; Shigeyuki Yokoyama; Masami Hagiya
DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing.
Bio Systems 2006;83(1):18-25.
2006: Koichiro Kodama; Seketsu Fukuzawa; Hiroshi Nakayama; Takanori Kigawa; Kensaku Sakamoto; Takashi Yabuki; Natsuko Matsuda; Mikako Shirouzu; Koji Takio; Kazuo Tachibana; Shigeyuki Yokoyama
Regioselective carbon-carbon bond formation in proteins with palladium catalysis; new protein chemistry by organometallic chemistry.
Chembiochem : a European journal of chemical biology 2006;7(1):134-9.
2006: Takanori Tanaka; Shigeyuki Yokoyama; Yutaka Kuroda
Improvement of domain linker prediction by incorporating loop-length-dependent characteristics.
Biopolymers 2006;84(2):161-8.
2005: Yoshinori Tanaka; Hiroaki Tachiwana; Kinya Yoda; Hiroshi Masumoto; Tsuneko Okazaki; Hitoshi Kurumizaka; Shigeyuki Yokoyama
Human centromere protein B induces translational positioning of nucleosomes on alpha-satellite sequences.
The Journal of biological chemistry 2005;280(50):41609-18.
2005: Rie Kawai; Michiko Kimoto; Shuji Ikeda; Tsuneo Mitsui; Masayuki Endo; Shigeyuki Yokoyama; Ichiro Hirao
Site-specific fluorescent labeling of RNA molecules by specific transcription using unnatural base pairs.
Journal of the American Chemical Society 2005;127(49):17286-95.
2005: Balasundaram Padmanabhan; Kazuhiro Kataoka; Takashi Umehara; Naruhiko Adachi; Shigeyuki Yokoyama; Masami Horikoshi
Structural similarity between histone chaperone Cia1p/Asf1p and DNA-binding protein NF-kappaB.
Journal of biochemistry 2005;138(6):821-9.
2005: Nobukazu Nameki; Tatsuhiko Someya; Satoshi Okano; Reiko Suemasa; Michiko Kimoto; Kyoko Hanawa-Suetsugu; Takaho Terada; Mikako Shirouzu; Ichiro Hirao; Hiroshi Takaku; Hyouta Himeno; Akira Muto; Seiki Kuramitsu; Shigeyuki Yokoyama; Gota Kawai
Interaction analysis between tmRNA and SmpB from Thermus thermophilus.
Journal of biochemistry 2005;138(6):729-39.
2005: Motoyuki Hattori; Eiichi Mizohata; Miho Manzoku; Yoshitaka Bessho; Kazutaka Murayama; Takaho Terada; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8.
Proteins 2005;61(4):1117-20.
2005: Eiichi Mizohata; Hiroaki Sakai; Emiko Fusatomi; Takaho Terada; Kazutaka Murayama; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon Aeropyrum pernix K1.
Journal of molecular biology 2005;354(2):317-29.
2005: Takashi Umehara; Yumi Otta; Keiko Tsuganezawa; Takehisa Matsumoto; Akiko Tanaka; Masami Horikoshi; Balasundaram Padmanabhan; Shigeyuki Yokoyama
Purification, crystallization and preliminary X-ray diffraction analysis of the histone chaperone cia1 from fission yeast.
Acta crystallographica. Section F, Structural biology and crystallization communications 2005;61(Pt 11):971-3.
2005: Augen A Pioszak; Kazutaka Murayama; Noriko Nakagawa; Akio Ebihara; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Structures of a putative RNA 5-methyluridine methyltransferase, Thermus thermophilus TTHA1280, and its complex with S-adenosyl-L-homocysteine.
Acta crystallographica. Section F, Structural biology and crystallization communications 2005;61(Pt 10):867-74.
2005: Ryuya Fukunaga; Shigeyuki Yokoyama
Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator-base recognition.
Nature structural & molecular biology 2005;12(10):915-22.
2005: Michael Tukalo; Anna Yaremchuk; Ryuya Fukunaga; Shigeyuki Yokoyama; Stephen Cusack
The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation.
Nature structural & molecular biology 2005;12(10):923-30.
2005: Neratur K Lokanath; Noriyasu Ohshima; Koji Takio; Ikuya Shiromizu; Chizu Kuroishi; Nobuo Okazaki; Seiki Kuramitsu; Shigeyuki Yokoyama; Masashi Miyano; Naoki Kunishima
Crystal structure of novel NADP-dependent 3-hydroxyisobutyrate dehydrogenase from Thermus thermophilus HB8.
Journal of molecular biology 2005;352(4):905-17.
2005: Naoki Kunishima; Yukuhiko Asada; Mayumi Sugahara; Jun Ishijima; Yuichi Nodake; Mitsuaki Sugahara; Masashi Miyano; Seiki Kuramitsu; Shigeyuki Yokoyama; Michihiro Sugahara
A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAI.
Journal of molecular biology 2005;352(1):212-28.
2005: Yoko Tanaka; Noriko Nakagawa; Seiki Kuramitsu; Shigeyuki Yokoyama; Ryoji Masui
Novel reaction mechanism of GTP cyclohydrolase I. High-resolution X-ray crystallography of Thermus thermophilus HB8 enzyme complexed with a transition state analogue, the 8-oxoguanine derivative.
Journal of biochemistry 2005;138(3):263-75.
2005: Ryuya Fukunaga; Shigeyuki Yokoyama
Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain.
The Journal of biological chemistry 2005;280(33):29937-45.
2005: Takashi Kinebuchi; Wataru Kagawa; Hitoshi Kurumizaka; Shigeyuki Yokoyama
Role of the N-terminal domain of the human DMC1 protein in octamer formation and DNA binding.
The Journal of biological chemistry 2005;280(31):28382-7.
2005: Hua Li; Makoto Inoue; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Emi Nunokawa; Yoko Motoda; Atsuo Kobayashi; Takaho Terada; Mikako Shirouzu; Seizo Koshiba; Yi-Jan Lin; Peter Güntert; Harukazu Suzuki; Yoshihide Hayashizaki; Takanori Kigawa; Shigeyuki Yokoyama
Solution structure of the mouse enhancer of rudimentary protein reveals a novel fold.
Journal of biomolecular NMR 2005;32(4):329-34.
2005: Ryoichi Arai; Mutsuko Kukimoto-Niino; Hiroko Uda-Tochio; Satoshi Morita; Tomomi Uchikubo-Kamo; Ryogo Akasaka; Yuuka Etou; Yoshihide Hayashizaki; Takanori Kigawa; Takaho Terada; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 Angstroms resolution.
Protein science : a publication of the Protein Society 2005;14(7):1888-93.
2005: Tsuneo Mitsui; Michiko Kimoto; Yoko Harada; Shigeyuki Yokoyama; Ichiro Hirao
An efficient unnatural base pair for a base-pair-expanded transcription system.
Journal of the American Chemical Society 2005;127(24):8652-8.
2005: Motoaki Wakiyama; Tomoko Matsumoto; Shigeyuki Yokoyama
Drosophila U6 promoter-driven short hairpin RNAs effectively induce RNA interference in Schneider 2 cells.
Biochemical and biophysical research communications 2005;331(4):1163-70.
2005: Ryoichi Arai; Madoka Nishimoto; Mitsutoshi Toyama; Takaho Terada; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Conserved protein TTHA1554 from Thermus thermophilus HB8 binds to glutamine synthetase and cystathionine beta-lyase.
Biochimica et biophysica acta 2005;1750(1):40-7.
2005: Junichiro Taka; Kyoko Ogasahara; Jeyaraman Jeyakanthan; Naoki Kunishima; Chizu Kuroishi; Mitsuaki Sugahara; Shigeyuki Yokoyama; Katsuhide Yutani
Stabilization due to dimer formation of phosphoribosyl anthranilate isomerase from Thermus thermophilus HB8: X-ray Analysis and DSC experiments.
Journal of biochemistry 2005;137(5):569-78.
2005: Sayuri Kurokawa; Yoshitaka Bessho; Kyoko Higashijima; Mikako Shirouzu; Shigeyuki Yokoyama; Kazuo I Watanabe; Tohru Ohama
Adaptation of intronic homing endonuclease for successful horizontal transmission.
The FEBS journal 2005;272(10):2487-96.
2005: Goshi Ishihara; Mie Goto; Mihoro Saeki; Kaori Ito; Tetsuya Hori; Takanori Kigawa; Mikako Shirouzu; Shigeyuki Yokoyama
Expression of G protein coupled receptors in a cell-free translational system using detergents and thioredoxin-fusion vectors.
Protein expression and purification 2005;41(1):27-37.
2005: Manjuli R Sharma; Chandana Barat; Daniel N Wilson; Timothy M Booth; Masahito Kawazoe; Chie Hori-Takemoto; Mikako Shirouzu; Shigeyuki Yokoyama; Paola Fucini; Rajendra K Agrawal
Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly.
Molecular cell 2005;18(3):319-29.
2005: Miyuki Kato-Murayama; Yoshitaka Bessho; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of the RNA 2'-phosphotransferase from Aeropyrum pernix K1.
Journal of molecular biology 2005;348(2):295-305.
2005: Kazuhiko Yamasaki; Takanori Kigawa; Makoto Inoue; Tomoko Yamasaki; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Yasuko Tomo; Takaho Terada; Mikako Shirouzu; Akiko Tanaka; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama
Solution structure of the major DNA-binding domain of Arabidopsis thaliana ethylene-insensitive3-like3.
Journal of molecular biology 2005;348(2):253-64.
2005: Mitsuo Kuratani; Ryohei Ishii; Yoshitaka Bessho; Ryuya Fukunaga; Toru Sengoku; Mikako Shirouzu; Shun-ichi Sekine; Shigeyuki Yokoyama
Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus.
The Journal of biological chemistry 2005;280(16):16002-8.
2005: Ryohei Ishii; Asako Minagawa; Hiroshi Takaku; Masamichi Takagi; Masayuki Nashimoto; Shigeyuki Yokoyama
Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima.
The Journal of biological chemistry 2005;280(14):14138-44.
2005: Wakana Ohashi; Satoshi Inouye; Toshio Yamazaki; Yukiko Doi-Katayama; Shigeyuki Yokoyama; Hiroshi Hirota
Backbone 1H, 13C and 15N resonance assignments for the Mg2+-bound form of the Ca2+-binding photoprotein aequorin.
Journal of biomolecular NMR 2005;31(4):375-6.
2005: Anna Scott; David Pantoja-Uceda; Seizo Koshiba; Makoto Inoue; Takanori Kigawa; Takaho Terada; Mikako Shirouzu; Akiko Tanaka; Sumio Sugano; Shigeyuki Yokoyama; Peter Güntert
Solution structure of the Src homology 2 domain from the human feline sarcoma oncogene Fes.
Journal of biomolecular NMR 2005;31(4):357-61.
2005: Naoei Yoshitani; Kazuhito Satou; Kazuki Saito; Sakura Suzuki; Hideki Hatanaka; Motoaki Seki; Kazuo Shinozaki; Hiroshi Hirota; Shigeyuki Yokoyama
A structure-based strategy for discovery of small ligands binding to functionally unknown proteins: combination of in silico screening and surface plasmon resonance measurements.
Proteomics 2005;5(6):1472-80.
2005: Kazuki Kurimoto; Yutaka Muto; Naomi Obayashi; Takaho Terada; Mikako Shirouzu; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Takanori Kigawa; Hiromi Okumura; Akiko Tanaka; Norito Shibata; Maki Kashikawa; Kiyokazu Agata; Shigeyuki Yokoyama
Crystal structure of the N-terminal RecA-like domain of a DEAD-box RNA helicase, the Dugesia japonica vasa-like gene B protein.
Journal of structural biology 2005;150(1):58-68.
2005: Noriko Handa; Takaho Terada; Yukiko Doi-Katayama; Hiroshi Hirota; Jeremy R H Tame; Sam-Yong Park; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8.
Protein science : a publication of the Protein Society 2005;14(4):1004-10.
2005: Shuhei Kimura; Kaori Ide; Aiko Kashihara; Makoto Kano; Mariko Hatakeyama; Ryoji Masui; Noriko Nakagawa; Shigeyuki Yokoyama; Seiki Kuramitsu; Akihiko Konagaya
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm.
Bioinformatics (Oxford, England) 2005;21(7):1154-63.
2005: Toshiyuki Hamada; Miwako Asanuma; Tatsuya Ueki; Fumiaki Hayashi; Naohiro Kobayashi; Shigeyuki Yokoyama; Hitoshi Michibata; Hiroshi Hirota
Solution structure of Vanabin2, a vanadium(IV)-binding protein from the vanadium-rich ascidian Ascidia sydneiensis samea.
Journal of the American Chemical Society 2005;127(12):4216-22.
2005: Nobumasa Hino; Yuko Okazaki; Takatsugu Kobayashi; Akiko Hayashi; Kensaku Sakamoto; Shigeyuki Yokoyama
Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid.
Nature methods 2005;2(3):201-6.
2005: Kazuhiko Yamasaki; Takanori Kigawa; Makoto Inoue; Masaru Tateno; Tomoko Yamasaki; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Yasuko Tomo; Nobuhiro Hayami; Takaho Terada; Mikako Shirouzu; Akiko Tanaka; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama
Solution structure of an Arabidopsis WRKY DNA binding domain.
The Plant cell 2005;17(3):944-56.
2005: Nobukazu Nameki; Naoya Tochio; Seizo Koshiba; Makoto Inoue; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Yukiko Fujikura; Miyuki Saito; Masaomi Ikari; Megumi Watanabe; Takaho Terada; Mikako Shirouzu; Mayumi Yoshida; Hiroshi Hirota; Akiko Tanaka; Yoshihide Hayashizaki; Peter Güntert; Takanori Kigawa; Shigeyuki Yokoyama
Solution structure of the PWWP domain of the hepatoma-derived growth factor family.
Protein science : a publication of the Protein Society 2005;14(3):756-64.
2005: Mutsuko Kukimoto-Niino; Rie Shibata; Kazutaka Murayama; Hiroaki Hamana; Madoka Nishimoto; Yoshitaka Bessho; Takaho Terada; Mikako Shirouzu; Seiki Kuramitsu; Shigeyuki Yokoyama
Crystal structure of a predicted phosphoribosyltransferase (TT1426) from Thermus thermophilus HB8 at 2.01 A resolution.
Protein science : a publication of the Protein Society 2005;14(3):823-7.
2005: Kazutaka Murayama; Mikako Shirouzu; Takaho Terada; Seiki Kuramitsu; Shigeyuki Yokoyama
Crystal structure of TT1662 from Thermus thermophilus HB8: a member of the alpha/beta hydrolase fold enzymes.
Proteins 2005;58(4):982-4.
2005: Alexander A Tokmakov; Tetsushi Iwasaki; Shuji Itakura; Ken-Ichi Sato; Mikako Shirouzu; Yasuo Fukami; Shigeyuki Yokoyama
Regulation of Src kinase activity during Xenopus oocyte maturation.
Developmental biology 2005;278(2):289-300.
2005: Takatsugu Kobayashi; Tetsuo Takimura; Ryo Sekine; Vincent P Kelly; Kelly Vincent; Kenji Kamata; Kensaku Sakamoto; Susumu Nishimura; Shigeyuki Yokoyama
Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.
Journal of molecular biology 2005;346(1):105-17.
2005: Ryuya Fukunaga; Shigeyuki Yokoyama
Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation.
Journal of molecular biology 2005;346(1):57-71.
2005: Alexei Nikulin; Elena Stolboushkina; Anna Perederina; Ioulia M Vassilieva; Udo Blaesi; Isabella Moll; Galina Kachalova; Shigeyuki Yokoyama; Dmitry G Vassylyev; Maria Garber; Alexey Nikulin
Structure of Pseudomonas aeruginosa Hfq protein.
Acta crystallographica. Section D, Biological crystallography 2005;61(Pt 2):141-6.
2005: Takatsugu Kobayashi; Kensaku Sakamoto; Tetsuo Takimura; Ryo Sekine; Vincent P Kelly; Kelly Vincent; Kenji Kamata; Susumu Nishimura; Shigeyuki Yokoyama
Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(5):1366-71.
2005: Shinichi Nishimura; Shigeki Matsunaga; Minoru Yoshida; Hiroshi Hirota; Shigeyuki Yokoyama; Nobuhiro Fusetani
13-Deoxytedanolide, a marine sponge-derived antitumor macrolide, binds to the 60S large ribosomal subunit.
Bioorganic & medicinal chemistry 2005;13(2):449-54.
2005: Atsushi Suenaga; Naoki Takada; Mariko Hatakeyama; Mio Ichikawa; Xiaomei Yu; Kentaro Tomii; Noriaki Okimoto; Noriyuki Futatsugi; Tetsu Narumi; Mikako Shirouzu; Shigeyuki Yokoyama; Akihiko Konagaya; Makoto Taiji
Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptides.
The Journal of biological chemistry 2005;280(2):1321-6.
2005: Michiko Kimoto; Rie Kawai; Tsuneo Mitsui; Yoko Harada; Akira Sato; Shigeyuki Yokoyama; Ichiro Hirao
Site-specific incorporation of fluorescent probes into RNA by specific transcription using unnatural base pairs.
Nucleic acids symposium series (2004) 2005;(49):287-8.
2005: Tsuneo Mitsui; Michiko Kimoto; Shigeyuki Yokoyama; Ichiro Hirao
Fluorescent properties of an unnatural nucleobase, 2-amino-6-(2-thienyl)purine, in DNA and RNA fragments.
Nucleic acids symposium series (2004) 2005;(49):285-6.
2005: Kazuma Takada; Chie Takemoto; Masahito Kawazoe; Takayuki Konno; Noriko Matsuta; Daisuke Kurita; Krisana Asano; Mikako Shirouzu; Shigeyuki Yokoyama; Akira Muto; Hyouta Himeno
Functional analysis of factors involved in trans-translation.
Nucleic acids symposium series (2004) 2005;(49):101-2.
2005: Ichiro Hirao; Tsuneo Mitsui; Michiko Kimoto; Rie Kawai; Akira Sato; Shigeyuki Yokoyama
Non-hydrogen-bonded base pairs for specific transcription.
Nucleic acids symposium series (2004) 2005;(49):33-4.
2005: Balasundaram Padmanabhan; Maria Scharlock; Kit I Tong; Yoshihiro Nakamura; MOON-IL KANG; Akira Kobayashi; Takehisa Matsumoto; Akiko Tanaka; Masayuki Yamamoto; Shigeyuki Yokoyama
Purification, crystallization and preliminary X-ray diffraction analysis of the Kelch-like motif region of mouse Keap1.
Acta crystallographica. Section F, Structural biology and crystallization communications 2005;61(Pt 1):153-5.
2005: Ryuya Fukunaga; Ryuichiro Ishitani; Osamu Nureki; Shigeyuki Yokoyama
Crystallization of leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii.
Acta crystallographica. Section F, Structural biology and crystallization communications 2005;61(Pt 1):30-2.
2005: Kazutaka Murayama; Miyuki Kato-Murayama; Kazushige Katsura; Tomomi Uchikubo-Kamo; Machiko Yamaguchi-Hirafuji; Masahito Kawazoe; Ryogo Akasaka; Kyoko Hanawa-Suetsugu; Chie Hori-Takemoto; Takaho Terada; Mikako Shirouzu; Shigeyuki Yokoyama
Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 A resolution.
Acta crystallographica. Section F, Structural biology and crystallization communications 2005;61(Pt 1):26-9.
2005: Kei Moriyama; Michiko Kimoto; Tsuneo Mitsui; Shigeyuki Yokoyama; Ichiro Hirao
Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs.
Nucleic acids research 2005;33(15):e129.
2005: Yoshinori Tanaka; Hitoshi Kurumizaka; Shigeyuki Yokoyama
CpG methylation of the CENP-B box reduces human CENP-B binding.
The FEBS journal 2005;272(1):282-9.
2005: Hiroaki Sakai; Hongfei Wang; Chie Takemoto-Hori; Tatsuya Kaminishi; Hiroto Yamaguchi; Yuki Kamewari; Takaho Terada; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8.
Journal of structural biology 2005;149(1):99-110.
2005: David Pantoja-Uceda; Blanca López-Méndez; Seizo Koshiba; Makoto Inoue; Takanori Kigawa; Takaho Terada; Mikako Shirouzu; Akiko Tanaka; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama; Peter Güntert
Solution structure of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana.
Protein science : a publication of the Protein Society 2005;14(1):224-30.
2005: Azusa Seto; Kazutaka Murayama; Mitsutoshi Toyama; Akio Ebihara; Noriko Nakagawa; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
ATP-induced structural change of dephosphocoenzyme A kinase from Thermus thermophilus HB8.
Proteins 2005;58(1):235-42.
2004: Hideo Ogiso; Noriko Kagi; Eiko Matsumoto; Madoka Nishimoto; Ryoichi Arai; Mikako Shirouzu; Junsei Mimura; Yoshiaki Fujii-Kuriyama; Shigeyuki Yokoyama
Phosphorylation analysis of 90 kDa heat shock protein within the cytosolic arylhydrocarbon receptor complex.
Biochemistry 2004;43(49):15510-9.
2004: Mitsuhiro Nishimura; Takuya Yoshida; Mikako Shirouzu; Takaho Terada; Seiki Kuramitsu; Shigeyuki Yokoyama; Tadayasu Ohkubo; Yuji Kobayashi
Solution structure of ribosomal protein L16 from Thermus thermophilus HB8.
Journal of molecular biology 2004;344(5):1369-83.
2004: Anna Scott; David Pantoja-Uceda; Seizo Koshiba; Makoto Inoue; Takanori Kigawa; Takaho Terada; Mikako Shirouzu; Akiko Tanaka; Sumio Sugano; Shigeyuki Yokoyama; Peter Güntert
NMR assignment of the SH2 domain from the human feline sarcoma oncogene FES.
Journal of biomolecular NMR 2004;30(4):463-4.
2004: Kazuhiko Yamasaki; Takanori Kigawa; Makoto Inoue; Masaru Tateno; Tomoko Yamasaki; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Yasuko Tomo; Nobuhiro Hayami; Takaho Terada; Mikako Shirouzu; Takashi Osanai; Akiko Tanaka; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama
Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1.
The Plant cell 2004;16(12):3448-59.
2004: Seiichiro Kishishita; Ayako Tatsuguchi; Ryoko Ushikoshi-Nakayama; Takaho Terada; Seiki Kuramitsu; Sam-Yong Park; Jeremy R H Tame; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of a conserved hypothetical protein TT1751 from Thermus thermophilus HB8.
Proteins 2004;57(4):883-7.
2004: Mutsuko Kukimoto-Niino; Kazutaka Murayama; Miyuki Kato-Murayama; Miki Idaka; Yoshitaka Bessho; Ayako Tatsuguchi; Ryoko Ushikoshi-Nakayama; Takaho Terada; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8.
Protein science : a publication of the Protein Society 2004;13(11):3038-42.
2004: Eisuke Chikayama; Atsushi Kurotani; Yutaka Kuroda; Shigeyuki Yokoyama
ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences.
Bioinformatics (Oxford, England) 2004;20(16):2836-8.
2004: Ichiro Hirao; Yoko Harada; Michiko Kimoto; Tsuneo Mitsui; Tsuyoshi Fujiwara; Shigeyuki Yokoyama
A two-unnatural-base-pair system toward the expansion of the genetic code.
Journal of the American Chemical Society 2004;126(41):13298-305.
2004: Ichiro Hirao; Tsuyoshi Fujiwara; Michiko Kimoto; Shigeyuki Yokoyama
Unnatural base pairs between 2- and 6-substituted purines and 2-oxo(1H)pyridine for expansion of the genetic alphabet.
Bioorganic & medicinal chemistry letters 2004;14(19):4887-90.
2004: Ryuya Fukunaga; Shigeyuki Yokoyama
Crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii.
Acta crystallographica. Section D, Biological crystallography 2004;60(Pt 10):1916-8.
2004: Ryuya Fukunaga; Shigeyuki Yokoyama
Crystallization and preliminary X-ray crystallographic study of the editing domain of Thermus thermophilus isoleucyl-tRNA synthetase complexed with pre- and post-transfer editing-substrate analogues.
Acta crystallographica. Section D, Biological crystallography 2004;60(Pt 10):1900-2.
2004: Neratur K Lokanath; Ikuya Shiromizu; Noriyasu Ohshima; Yuichi Nodake; Mitsuaki Sugahara; Shigeyuki Yokoyama; Seiki Kuramitsu; Masashi Miyano; Naoki Kunishima
Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability.
Acta crystallographica. Section D, Biological crystallography 2004;60(Pt 10):1816-23.
2004: Hongfei Wang; Chie Takemoto; Kazutaka Murayama; Hiroaki Sakai; Ayako Tatsuguchi; Takaho Terada; Mikako Shirouzu; Seiki Kuramitsu; Shigeyuki Yokoyama
Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8.
Protein science : a publication of the Protein Society 2004;13(10):2806-10.
2004: Kohei Saito; Takanori Kigawa; Seizo Koshiba; Kazuo Sato; Yo Matsuo; Ayako Sakamoto; Tetsuo Takagi; Mikako Shirouzu; Takashi Yabuki; Emi Nunokawa; Eiko Seki; Takayoshi Matsuda; Masaaki Aoki; Yukako Miyata; Noriko Hirakawa; Makoto Inoue; Takaho Terada; Takahiro Nagase; Reiko Kikuno; Manabu Nakayama; Osamu Ohara; Akiko Tanaka; Shigeyuki Yokoyama
The CAP-Gly domain of CYLD associates with the proline-rich sequence in NEMO/IKKgamma.
Structure (London, England : 1993) 2004;12(9):1719-28.
2004: Marina N Vassylyeva; Anna Perederina; Vladimir Svetlov; Shigeyuki Yokoyama; Irina Artsimovitch; Dmitry G Vassylyev
Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription factor DksA from Escherichia coli.
Acta crystallographica. Section D, Biological crystallography 2004;60(Pt 9):1611-3.
2004: Yoshimasa Takizawa; Takashi Kinebuchi; Wataru Kagawa; Shigeyuki Yokoyama; Takehiko Shibata; Hitoshi Kurumizaka
Mutational analyses of the human Rad51-Tyr315 residue, a site for phosphorylation in leukaemia cells.
Genes to cells : devoted to molecular & cellular mechanisms 2004;9(9):781-90.
2004: Kensaku Sakamoto; Satoshi Ishimaru; Takatsugu Kobayashi; James R Walker; Shigeyuki Yokoyama
The Escherichia coli argU10(Ts) phenotype is caused by a reduction in the cellular level of the argU tRNA for the rare codons AGA and AGG.
Journal of bacteriology 2004;186(17):5899-905.
2004: Sachiko Yoshiba; Takushi Ooga; Noriko Nakagawa; Takehiko Shibata; Yorinao Inoue; Shigeyuki Yokoyama; Seiki Kuramitsu; Ryoji Masui
Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal.
The Journal of biological chemistry 2004;279(35):37163-74.
2004: Rima Enomoto; Takashi Kinebuchi; Makoto Sato; Hideshi Yagi; Takehiko Shibata; Hitoshi Kurumizaka; Shigeyuki Yokoyama
Positive role of the mammalian TBPIP/HOP2 protein in DMC1-mediated homologous pairing.
The Journal of biological chemistry 2004;279(34):35263-72.
2004: Anna Perederina; Vladimir Svetlov; Marina N Vassylyeva; Tahir Tahirov; Shigeyuki Yokoyama; Irina Artsimovitch; Dmitry G Vassylyev
Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription.
Cell 2004;118(3):297-309.
2004: Nobukazu Nameki; Misao Yoneyama; Seizo Koshiba; Naoya Tochio; Makoto Inoue; Eiko Seki; Takayoshi Matsuda; Yasuko Tomo; Takushi Harada; Kohei Saito; Naohiro Kobayashi; Takashi Yabuki; Masaaki Aoki; Emi Nunokawa; Natsuko Matsuda; Noriko Sakagami; Takaho Terada; Mikako Shirouzu; Mayumi Yoshida; Hiroshi Hirota; Takashi Osanai; Akiko Tanaka; Takahiro Arakawa; piero carninci; Jun Kawai; Yoshihide Hayashizaki; Kengo Kinoshita; Peter Güntert; Takanori Kigawa; Shigeyuki Yokoyama
Solution structure of the RWD domain of the mouse GCN2 protein.
Protein science : a publication of the Protein Society 2004;13(8):2089-100.
2004: Paul Reay; Kazuhiko Yamasaki; Takaho Terada; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Structural and sequence comparisons arising from the solution structure of the transcription elongation factor NusG from Thermus thermophilus.
Proteins 2004;56(1):40-51.
2004: Kyoko Hanawa-Suetsugu; Shun-ichi Sekine; Hiroaki Sakai; Chie Hori-Takemoto; Takaho Terada; Satoru Unzai; Jeremy R H Tame; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of elongation factor P from Thermus thermophilus HB8.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(26):9595-600.
2004: Mariko Hatakeyama; N Yumoto; X Yu; Mikako Shirouzu; Shigeyuki Yokoyama; Akihiko Konagaya
Transformation potency of ErbB heterodimer signaling is determined by B-Raf kinase.
Oncogene 2004;23(29):5023-31.
2004: Michiko Kimoto; Shigeyuki Yokoyama; Ichiro Hirao
A quantitative, non-radioactive single-nucleotide insertion assay for analysis of DNA replication fidelity by using an automated DNA sequencer.
Biotechnology letters 2004;26(12):999-1005.
2004: David Pantoja-Uceda; Blanca López-Méndez; Seizo Koshiba; Takanori Kigawa; Mikako Shirouzu; Takaho Terada; Makoto Inoue; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Hiroshi Hirota; Mayumi Yoshida; Akiko Tanaka; Takashi Osanai; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama; Peter Güntert
NMR assignment of the hypothetical rhodanese domain At4g01050 from Arabidopsis thaliana.
Journal of biomolecular NMR 2004;29(2):207-8.
2004: Blanca López-Méndez; David Pantoja-Uceda; Tadashi Tomizawa; Seizo Koshiba; Takanori Kigawa; Mikako Shirouzu; Takaho Terada; Makoto Inoue; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Hiroshi Hirota; Mayumi Yoshida; Akiko Tanaka; Takashi Osanai; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama; Peter Güntert
NMR assignment of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thaliana.
Journal of biomolecular NMR 2004;29(2):205-6.
2004: Masayuki Endo; Tsuneo Mitsui; Taeko Okuni; Michiko Kimoto; Ichiro Hirao; Shigeyuki Yokoyama
Unnatural base pairs mediate the site-specific incorporation of an unnatural hydrophobic component into RNA transcripts.
Bioorganic & medicinal chemistry letters 2004;14(10):2593-6.
2004: Takashi Wada; Mikako Shirouzu; Takaho Terada; Yuki Kamewari; Sam-Yong Park; Jeremy R H Tame; Seiki Kuramitsu; Shigeyuki Yokoyama
Crystal structure of the conserved hypothetical protein TT1380 from Thermus thermophilus HB8.
Proteins 2004;55(3):778-80.
2004: Yasuhiro Katsura; Mikako Shirouzu; Hiroto Yamaguchi; Ryuichiro Ishitani; Osamu Nureki; Seiki Kuramitsu; Hideyuki Hayashi; Shigeyuki Yokoyama
Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV.
Proteins 2004;55(3):487-92.
2004: Takashi Kinebuchi; Wataru Kagawa; Rima Enomoto; Kozo Tanaka; Kiyoshi Miyagawa; Takehiko Shibata; Hitoshi Kurumizaka; Shigeyuki Yokoyama
Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmc1.
Molecular cell 2004;14(3):363-74.
2004: Yoshinori Tanaka; Maki Tawaramoto-Sasanuma; Shinichi Kawaguchi; Tsutomu Ohta; Kinya Yoda; Hitoshi Kurumizaka; Shigeyuki Yokoyama
Expression and purification of recombinant human histones.
Methods (San Diego, Calif.) 2004;33(1):3-11.
2004: Tahir Tahirov; Eiji Inagaki; Noriyasu Ohshima; Tomoe Kitao; Chizu Kuroishi; Yoko Ukita; Koji Takio; Masanori Kobayashi; Seiki Kuramitsu; Shigeyuki Yokoyama; Masashi Miyano
Crystal structure of purine nucleoside phosphorylase from Thermus thermophilus.
Journal of molecular biology 2004;337(5):1149-60.
2004: Takeshi Hosaka; Norimasa Tamehiro; Namthip Chumpolkulwong; Chie Hori-Takemoto; Mikako Shirouzu; Shigeyuki Yokoyama; Kozo Ochi
The novel mutation K87E in ribosomal protein S12 enhances protein synthesis activity during the late growth phase in Escherichia coli.
Molecular genetics and genomics : MGG 2004;271(3):317-24.
2004: Mutsuko Kukimoto-Niino; Kazutaka Murayama; Mio Inoue; Takaho Terada; Jeremy R H Tame; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8.
Journal of molecular biology 2004;337(3):761-70.
2004: Takeshi Maeda; Makoto Inoue; Seizo Koshiba; Takashi Yabuki; Masaaki Aoki; Emi Nunokawa; Eiko Seki; Takayoshi Matsuda; Yoko Motoda; Atsuo Kobayashi; Fumiko Hiroyasu; Mikako Shirouzu; Takaho Terada; Nobuhiro Hayami; Yoshiko Ishizuka; Naoko Shinya; Ayako Tatsuguchi; Mayumi Yoshida; Hiroshi Hirota; Yo Matsuo; Kazutoshi Tani; Takahiro Arakawa; piero carninci; Jun Kawai; Yoshihide Hayashizaki; Takanori Kigawa; Shigeyuki Yokoyama
Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16).
The Journal of biological chemistry 2004;279(13):13174-82.
2004: Kazuhiko Yamasaki; Takanori Kigawa; Makoto Inoue; Masaru Tateno; Tomoko Yamasaki; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Emi Nunokawa; Yoshiko Ishizuka; Takaho Terada; Mikako Shirouzu; Takashi Osanai; Akiko Tanaka; Motoaki Seki; Kazuo Shinozaki; Shigeyuki Yokoyama
A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors.
Journal of molecular biology 2004;337(1):49-63.
2004: Namthip Chumpolkulwong; Chie Hori-Takemoto; Takeshi Hosaka; Takashi Inaoka; Takanori Kigawa; Mikako Shirouzu; Kozo Ochi; Shigeyuki Yokoyama
Effects of Escherichia coli ribosomal protein S12 mutations on cell-free protein synthesis.
European journal of biochemistry / FEBS 2004;271(6):1127-34.
2004: Ryuya Fukunaga; Shuya Fukai; Ryuichiro Ishitani; Osamu Nureki; Shigeyuki Yokoyama
Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine.
The Journal of biological chemistry 2004;279(9):8396-402.
2004: Toru Sengoku; Osamu Nureki; Naoshi Dohmae; Akira Nakamura; Shigeyuki Yokoyama
Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue.
Acta crystallographica. Section D, Biological crystallography 2004;60(Pt 2):320-2.
2004: Yoshiaki Kise; Sang Won Lee; Sang Gyu Park; Shuya Fukai; Toru Sengoku; Ryohei Ishii; Shigeyuki Yokoyama; Sunghoon Kim; Osamu Nureki
A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase.
Nature structural & molecular biology 2004;11(2):149-56.
2004: Takuma Kasai; Makoto Inoue; Seizo Koshiba; Takashi Yabuki; Masaaki Aoki; Emi Nunokawa; Eiko Seki; Takayoshi Matsuda; Natsuko Matsuda; Yasuko Tomo; Mikako Shirouzu; Takaho Terada; Naomi Obayashi; Hiroaki Hamana; Naoko Shinya; Ayako Tatsuguchi; Satoko Yasuda; Mayumi Yoshida; Hiroshi Hirota; Yo Matsuo; Kazutoshi Tani; Harukazu Suzuki; Takahiro Arakawa; piero carninci; Jun Kawai; Yoshihide Hayashizaki; Takanori Kigawa; Shigeyuki Yokoyama
Solution structure of a BolA-like protein from Mus musculus.
Protein science : a publication of the Protein Society 2004;13(2):545-8.
2004: Rie Kawai; Michiko Kimoto; Tsuneo Mitsui; Shigeyuki Yokoyama; Ichiro Hirao
Site-specific fluorescent labeling of RNA by a base-pair expanded transcription system.
Nucleic acids symposium series (2004) 2004;(48):35-6.
2004: Takanori Kigawa; Takashi Yabuki; Natsuko Matsuda; Takayoshi Matsuda; Rie Nakajima; Akiko Tanaka; Shigeyuki Yokoyama
Preparation of Escherichia coli cell extract for highly productive cell-free protein expression.
Journal of structural and functional genomics 2004;5(1-2):63-8.
2004: Hiroshi Yokoyama; Naoyuki Sarai; Wataru Kagawa; Rima Enomoto; Takehiko Shibata; Hitoshi Kurumizaka; Shigeyuki Yokoyama
Preferential binding to branched DNA strands and strand-annealing activity of the human Rad51B, Rad51C, Rad51D and Xrcc2 protein complex.
Nucleic acids research 2004;32(8):2556-65.
2004: Michiko Kimoto; Masayuki Endo; Tsuneo Mitsui; Taeko Okuni; Ichiro Hirao; Shigeyuki Yokoyama
Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs.
Chemistry & biology 2004;11(1):47-55.
2004: Norie Fujikawa; Hitoshi Kurumizaka; Osamu Nureki; Yoshinori Tanaka; Mitsuyoshi Yamazoe; Sota Hiraga; Shigeyuki Yokoyama
Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein.
Nucleic acids research 2004;32(1):82-92.
2004: Hitomi Takahashi; Eiji Inagaki; Yayoi Fujimoto; Chizu Kuroishi; Yuichi Nodake; Yuki Nakamura; Fumio Arisaka; Katsuhide Yutani; Seiki Kuramitsu; Shigeyuki Yokoyama; Masaki Yamamoto; Masashi Miyano; Tahir Tahirov
Structure and implications for the thermal stability of phosphopantetheine adenylyltransferase from Thermus thermophilus.
Acta crystallographica. Section D, Biological crystallography 2004;60(Pt 1):97-104.
2003: Maki S Tawaramoto; Sam-Yong Park; Yoshinori Tanaka; Osamu Nureki; Hitoshi Kurumizaka; Shigeyuki Yokoyama
Crystal structure of the human centromere protein B (CENP-B) dimerization domain at 1.65-A resolution.
The Journal of biological chemistry 2003;278(51):51454-61.
2003: Tsuneo Mitsui; Michiko Kimoto; Akira Sato; Shigeyuki Yokoyama; Ichiro Hirao
An unnatural hydrophobic base, 4-propynylpyrrole-2-carbaldehyde, as an efficient pairing partner of 9-methylimidazo[(4,5)-b]pyridine.
Bioorganic & medicinal chemistry letters 2003;13(24):4515-8.
2003: Neratur K Lokanath; Ikuya Shiromizu; Yuichi Nodake; Mitsuaki Sugahara; Shigeyuki Yokoyama; Seiki Kuramitsu; Masashi Miyano; Naoki Kunishima
Crystallization and preliminary X-ray crystallographic studies of NADP-dependent 3-hydroxyisobutyrate dehydrogenase from Thermus thermophilus HB8.
Acta crystallographica. Section D, Biological crystallography 2003;59(Pt 12):2294-6.
2003: Azusa Seto; Mikako Shirouzu; Takaho Terada; Kazutaka Murayama; Seiki Kuramitsu; Shigeyuki Yokoyama
Crystal structure of a hypothetical protein, TT1725, from Thermus thermophilus HB8 at 1.7 A resolution.
Proteins 2003;53(3):768-71.
2003: Mayuko Okabe; Kozo Tomita; Ryuichiro Ishitani; Ryohei Ishii; Nono Takeuchi; Fumio Arisaka; Osamu Nureki; Shigeyuki Yokoyama
Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure.
The EMBO journal 2003;22(21):5918-27.
2003: Jun Hoseki; Akihiro Okamoto; Ryoji Masui; Takehiko Shibata; Yorinao Inoue; Shigeyuki Yokoyama; Seiki Kuramitsu
Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8.
Journal of molecular biology 2003;333(3):515-26.
2003: Akiko Kobayashi; Tetsuro Kokubo; Yoshimi Ota; Shigeyuki Yokoyama
Promoter-specific function of the TATA element in undifferentiated P19 cells.
Biochemical and biophysical research communications 2003;310(2):458-63.
2003: Sachiko Yoshiba; Noriko Nakagawa; Ryoji Masui; Takehiko Shibata; Yorinao Inoue; Shigeyuki Yokoyama; Seiki Kuramitsu
Overproduction, crystallization and preliminary diffraction data of ADP-ribose pyrophosphatase from Thermus thermophilus HB8.
Acta crystallographica. Section D, Biological crystallography 2003;59(Pt 10):1840-2.
2003: Hiroaki Sakai; Marina N Vassylyeva; Takanori Matsuura; Shun-ichi Sekine; Kazumi Gotoh; Makoto Nishiyama; Takaho Terada; Mikako Shirouzu; Seiki Kuramitsu; Dmitry G Vassylyev; Shigeyuki Yokoyama
Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8.
Journal of molecular biology 2003;332(3):729-40.
2003: Marina N Vassylyeva; Hiroaki Sakai; Takanori Matsuura; Shun-ichi Sekine; Makoto Nishiyama; Takaho Terada; Mikako Shirouzu; Seiki Kuramitsu; Dmitry G Vassylyev; Shigeyuki Yokoyama
Cloning, expression, purification, crystallization and initial crystallographic analysis of the lysine-biosynthesis LysX protein from Thermus thermophilus HB8.
Acta crystallographica. Section D, Biological crystallography 2003;59(Pt 9):1651-2.
2003: Ryohei Ishii; Osamu Nureki; Shigeyuki Yokoyama
Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus.
The Journal of biological chemistry 2003;278(34):32397-404.
2003: Takashi Wada; Tomohisa Kuzuyama; Shinya Satoh; Seiki Kuramitsu; Shigeyuki Yokoyama; Satoru Unzai; Jeremy R H Tame; Sam-Yong Park
Crystal structure of 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis.
The Journal of biological chemistry 2003;278(32):30022-7.
2003: Noriko Handa; Takaho Terada; Yuki Kamewari; Hiroaki Hamana; Jeremy R H Tame; Sam-Yong Park; Kengo Kinoshita; Motonori Ota; Haruki Nakamura; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8.
Protein science : a publication of the Protein Society 2003;12(8):1621-32.
2003: Hitoshi Kurumizaka; Rima Enomoto; Maki Nakada; Keiko Eda; Shigeyuki Yokoyama; Takehiko Shibata
Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein.
Nucleic acids research 2003;31(14):4041-50.
2003: Mariko Hatakeyama; Shuhei Kimura; Takashi Naka; Takuji Kawasaki; Noriko Yumoto; Mio Ichikawa; Jae-Hoon Kim; Kazuki Saito; Mihoro Saeki; Mikako Shirouzu; Shigeyuki Yokoyama; Akihiko Konagaya
A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling.
The Biochemical journal 2003;373(Pt 2):451-63.
2003: Takashi Wada; Mikako Shirouzu; Takaho Terada; Yoshiko Ishizuka; Takayoshi Matsuda; Takanori Kigawa; Seiki Kuramitsu; Sam-Yong Park; Jeremy R H Tame; Shigeyuki Yokoyama
Structure of a conserved CoA-binding protein synthesized by a cell-free system.
Acta crystallographica. Section D, Biological crystallography 2003;59(Pt 7):1213-8.
2003: Miyuki Kato; Mikako Shirouzu; Takaho Terada; Hiroto Yamaguchi; Kazutaka Murayama; Hiroaki Sakai; Seiki Kuramitsu; Shigeyuki Yokoyama
Crystal structure of the 2'-5' RNA ligase from Thermus thermophilus HB8.
Journal of molecular biology 2003;329(5):903-11.
2003: Takatsugu Kobayashi; Osamu Nureki; Ryuichiro Ishitani; Anna Yaremchuk; Michael Tukalo; Stephen Cusack; Kensaku Sakamoto; Shigeyuki Yokoyama
Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion.
Nature structural biology 2003;10(6):425-32.
2003: Atsushi Suenaga; Mariko Hatakeyama; Mio Ichikawa; Xiaomei Yu; Noriyuki Futatsugi; Tetsu Narumi; Kazuhiko Fukui; Takaho Terada; Makoto Taiji; Mikako Shirouzu; Shigeyuki Yokoyama; Akihiko Konagaya
Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides.
Biochemistry 2003;42(18):5195-200.
2003: Tsuneo Mitsui; Aya Kitamura; Michiko Kimoto; Taiko To; Akira Sato; Ichiro Hirao; Shigeyuki Yokoyama
An unnatural hydrophobic base pair with shape complementarity between pyrrole-2-carbaldehyde and 9-methylimidazo[(4,5)-b]pyridine.
Journal of the American Chemical Society 2003;125(18):5298-307.
2003: Ryuichiro Ishitani; Osamu Nureki; Nobukazu Nameki; Norihiro Okada; Susumu Nishimura; Shigeyuki Yokoyama
Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme.
Cell 2003;113(3):383-94.
2003: Tatsuya Kaminishi; Hiroaki Sakai; Chie Takemoto-Hori; Takaho Terada; Noriko Nakagawa; Nobuko Maoka; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama
Crystallization and preliminary X-ray diffraction analysis of ribosomal protein L11 methyltransferase from Thermus thermophilus HB8.
Acta crystallographica. Section D, Biological crystallography 2003;59(Pt 5):930-2.
2003: Norie Fujikawa; Hitoshi Kurumizaka; Osamu Nureki; Takaho Terada; Mikako Shirouzu; Tsutomu Katayama; Shigeyuki Yokoyama
Structural basis of replication origin recognition by the DnaA protein.
Nucleic acids research 2003;31(8):2077-86.
2003: Masatoshi Yoshimasu; Hideki Aihara; Yutaka Ito; Sundaresan Rajesh; Satoko Ishibe; Tsutomu Mikawa; Shigeyuki Yokoyama; Takehiko Shibata
An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes.
Nucleic acids research 2003;31(6):1735-43.
2003: Shun-ichi Sekine; Osamu Nureki; Daniel Y Dubois; Stéphane Bernier; Robert Chênevert; Jacques Lapointe; Dmitry G Vassylyev; Shigeyuki Yokoyama
ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding.
The EMBO journal 2003;22(3):676-88.
2003: Shigeyuki Yokoyama
Protein expression systems for structural genomics and proteomics.
Current opinion in chemical biology 2003;7(1):39-43.
2003: Tatsuhiko Someya; Nobukazu Nameki; Haruko Hosoi; Sakura Suzuki; Hideki Hatanaka; Michiko Fujii; Takaho Terada; Mikako Shirouzu; Yorinao Inoue; Takehiko Shibata; Seiki Kuramitsu; Shigeyuki Yokoyama; Gota Kawai
Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus.
FEBS letters 2003;535(1-3):94-100.
2003: Hiroshi Yokoyama; Hitoshi Kurumizaka; Shukuko Ikawa; Shigeyuki Yokoyama; Takehiko Shibata
Holliday junction binding activity of the human Rad51B protein.
The Journal of biological chemistry 2003;278(4):2767-72.
2003: Norie Fujikawa; Hitoshi Kurumizaka; Mitsuyoshi Yamazoe; Sota Hiraga; Shigeyuki Yokoyama
Identification of functional domains of the Escherichia coli SeqA protein.
Biochemical and biophysical research communications 2003;300(3):699-705.
2003: Makoto Endo; Mikako Shirouzu; Shigeyuki Yokoyama
The Cdc42 binding and scaffolding activities of the fission yeast adaptor protein Scd2.
The Journal of biological chemistry 2003;278(2):843-52.
2003: Takanori Tanaka; Yutaka Kuroda; Shigeyuki Yokoyama
Characteristics and prediction of domain linker sequences in multi-domain proteins.
Journal of structural and functional genomics 2003;4(2-3):79-85.
2003: Kazuma Takada; Chie Hori-Takemoto; Masahito Kawazoe; SungGa Lee; Mikako Shirouzu; Shigeyuki Yokoyama; Akira Muto; Hyouta Himeno
In vitro analysis of the initial steps of trans-translation.
Nucleic acids research. Supplement (2001) 2003;(3):287-8.
2003: Kei Moriyama; Michiko Kimoto; Tsuneo Mitsui; Shigeyuki Yokoyama; Ichiro Hirao
Simple preparation of biotinylated RNA by transcription via an unnatural base pair.
Nucleic acids research. Supplement (2001) 2003;(3):277-8.
2003: Ichiro Hirao; Tsuneo Mitsui; Michiko Kimoto; Yoko Harada; Shigeyuki Yokoyama
An unnatural base pair for efficient incorporation of nucleotide analogs into RNAs.
Nucleic acids research. Supplement (2001) 2003;(3):215-6.
2003: Shuya Fukai; Osamu Nureki; Shun-ichi Sekine; Atsushi Shimada; Dmitry G Vassylyev; Shigeyuki Yokoyama
Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase.
RNA (New York, N.Y.) 2003;9(1):100-11.
2003: Hiroyuki Kishida; Takashi Wada; Satoru Unzai; Tomohisa Kuzuyama; Motoki Takagi; Takaho Terada; Mikako Shirouzu; Shigeyuki Yokoyama; Jeremy R H Tame; Sam-Yong Park
Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis.
Acta crystallographica. Section D, Biological crystallography 2003;59(Pt 1):23-31.
2002: Kensaku Sakamoto; Akiko Hayashi; Ayako Sakamoto; Daisuke Kiga; Hiroshi Nakayama; Akiko Soma; Takatsugu Kobayashi; Makoto Kitabatake; Koji Takio; Kazuki Saito; Mikako Shirouzu; Ichiro Hirao; Shigeyuki Yokoyama
Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells.
Nucleic acids research 2002;30(21):4692-9.
2002: Satoshi Akanuma; Takanori Kigawa; Shigeyuki Yokoyama
Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(21):13549-53.
2002: Hiroyasu Furukawa; Toshiyuki Hamada; Mariko K Hayashi; Tatsuya Haga; Yutaka Muto; Hiroshi Hirota; Shigeyuki Yokoyama; Kazuo Nagasawa; Masaji Ishiguro
Conformation of ligands bound to the muscarinic acetylcholine receptor.
Molecular pharmacology 2002;62(4):778-87.
2002: Hideo Ogiso; Ryuichiro Ishitani; Osamu Nureki; Shuya Fukai; Mari Yamanaka; Jae-Hoon Kim; Kazuki Saito; Ayako Sakamoto; Mio Inoue; Mikako Shirouzu; Shigeyuki Yokoyama
Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains.
Cell 2002;110(6):775-87.
2002: Kay Fukushima; Jun Kikuchi; Seizo Koshiba; Takanori Kigawa; Yutaka Kuroda; Shigeyuki Yokoyama
Solution structure of the DFF-C domain of DFF45/ICAD. A structural basis for the regulation of apoptotic DNA fragmentation.
Journal of molecular biology 2002;321(2):317-27.
2002: Wataru Kagawa; Hitoshi Kurumizaka; Ryuichiro Ishitani; Shuya Fukai; Osamu Nureki; Takehiko Shibata; Shigeyuki Yokoyama
Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form.
Molecular cell 2002;10(2):359-71.
2002: Daisuke Kiga; Kensaku Sakamoto; Koichiro Kodama; Takanori Kigawa; Takayoshi Matsuda; Takashi Yabuki; Mikako Shirouzu; Yoko Harada; Hiroshi Nakayama; Koji Takio; Yoshinori Hasegawa; Yaeta Endo; Ichiro Hirao; Shigeyuki Yokoyama
An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(15):9715-20.
2002: Osamu Nureki; Mikako Shirouzu; Kyoko Hashimoto; Ryuichiro Ishitani; Takaho Terada; Masatada Tamakoshi; Tairo Oshima; Masao Chijimatsu; Koji Takio; Dmitry G Vassylyev; Takehiko Shibata; Yorinao Inoue; Seiki Kuramitsu; Shigeyuki Yokoyama
An enzyme with a deep trefoil knot for the active-site architecture.
Acta crystallographica. Section D, Biological crystallography 2002;58(Pt 7):1129-37.
2002: Makoto Kitabatake; Kamilah Ali; Arnold Demain; Kensaku Sakamoto; Shigeyuki Yokoyama; Dieter Söll
Indolmycin resistance of Streptomyces coelicolor A3(2) by induced expression of one of its two tryptophanyl-tRNA synthetases.
The Journal of biological chemistry 2002;277(26):23882-7.
2002: Naoto Ohtani; Noriko Nakagawa; Jun Hoseki; Akio Ebihara; Shinya Satoh; Yoshihiro Agari; Shin-ichiro Kobayashi; Kazuko Agari; Nobuko Maoka; Ryoji Masui; Kunio Miki; Shigeyuki Yokoyama; Seiki Kuramitsu
[An exhaustive overproduction of bacterial proteins].
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 2002;47(8 Suppl):1009-13.
2002: Ryuichiro Ishitani; Osamu Nureki; Shuya Fukai; Teiya Kijimoto; Nobukazu Nameki; Masakatsu Watanabe; Hisao Kondo; Mitsuo Sekine; Norihiro Okada; Susumu Nishimura; Shigeyuki Yokoyama
Crystal structure of archaeosine tRNA-guanine transglycosylase.
Journal of molecular biology 2002;318(3):665-77.
2002: Hitoshi Kurumizaka; Shukuko Ikawa; Maki Nakada; Rima Enomoto; Wataru Kagawa; Takashi Kinebuchi; Mitsuyoshi Yamazoe; Shigeyuki Yokoyama; Takehiko Shibata
Homologous pairing and ring and filament structure formation activities of the human Xrcc2*Rad51D complex.
The Journal of biological chemistry 2002;277(16):14315-20.
2002: Jun Kikuchi; Junji Iwahara; Takanori Kigawa; Yota Murakami; Tsuneko Okazaki; Shigeyuki Yokoyama
Solution structure determination of the two DNA-binding domains in the Schizosaccharomyces pombe Abp1 protein by a combination of dipolar coupling and diffusion anisotropy restraints.
Journal of biomolecular NMR 2002;22(4):333-47.
2002: Aya Kitamura; Yutaka Muto; Satoru Watanabe; Insil Kim; Takuhiro Ito; Yoichi Nishiya; Kensaku Sakamoto; Takashi Ohtsuki; Gota Kawai; Kimitsuna Watanabe; Kazumi Hosono; Hiroshi Takaku; Etsuko Katoh; Toshimasa Yamazaki; Tan Inoue; Shigeyuki Yokoyama
Solution structure of an RNA fragment with the P7/P9.0 region and the 3'-terminal guanosine of the tetrahymena group I intron.
RNA (New York, N.Y.) 2002;8(4):440-51.
2002: Takaho Terada; Osamu Nureki; Ryuichiro Ishitani; alexandre ambrogelly; Michael Ibba; Dieter Söll; Shigeyuki Yokoyama
Functional convergence of two lysyl-tRNA synthetases with unrelated topologies.
Nature structural biology 2002;9(4):257-62.
2002: Ichiro Hirao; Takashi Ohtsuki; Tsuyoshi Fujiwara; Tsuneo Mitsui; Tomoko Yokogawa; Taeko Okuni; Hiroshi Nakayama; Koji Takio; Takashi Yabuki; Takanori Kigawa; Koichiro Kodama; Takashi Yokogawa; Kazuya Nishikawa; Shigeyuki Yokoyama
An unnatural base pair for incorporating amino acid analogs into proteins.
Nature biotechnology 2002;20(2):177-82.
2002: Tsuneo Mitsui; Michiko Kimoto; Yoko Harada; Akira Sato; Aya Kitamura; Taiko To; Ichiro Hirao; Shigeyuki Yokoyama
Enzymatic incorporation of an unnatural base pair between 4-propynyl-pyrrole-2-carbaldehyde and 9-methyl-imidazo [(4,5)-b]pyridine into nucleic acids.
Nucleic acids research. Supplement (2001) 2002;(2):219-20.
2002: Ichiro Hirao; Michiko Kimoto; Tsuneo Mitsui; Yoko Harada; Tsuyoshi Fujiwara; Akira Sato; Shigeyuki Yokoyama
An unnatural base pair between imidazolin-2-one and 2-amino-6-(2-thienyl)purine in replication and transcription.
Nucleic acids research. Supplement (2001) 2002;(2):37-8.
2002: Satoshi Miyazaki; Yutaka Kuroda; Shigeyuki Yokoyama
Characterization and prediction of linker sequences of multi-domain proteins by a neural network.
Journal of structural and functional genomics 2002;2(1):37-51.
2002: Takanori Kigawa; Emi Yamaguchi-Nunokawa; Koichiro Kodama; Takayoshi Matsuda; Takashi Yabuki; Natsuko Matsuda; Ryuichiro Ishitani; Osamu Nureki; Shigeyuki Yokoyama
Selenomethionine incorporation into a protein by cell-free synthesis.
Journal of structural and functional genomics 2002;2(1):29-35.
2002: Seizo Koshiba; Takanori Kigawa; Akira Kikuchi; Shigeyuki Yokoyama
Solution structure of the epsin N-terminal homology (ENTH) domain of human epsin.
Journal of structural and functional genomics 2002;2(1):1-8.
2002: Michiko Kimoto; Mikako Shirouzu; Shin Mizutani; Hiroshi Koide; Yoshito Kaziro; Ichiro Hirao; Shigeyuki Yokoyama
Anti-(Raf-1) RNA aptamers that inhibit Ras-induced Raf-1 activation.
European journal of biochemistry / FEBS 2002;269(2):697-704.
2001: Takashi Nakama; Osamu Nureki; Shigeyuki Yokoyama
Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase.
The Journal of biological chemistry 2001;276(50):47387-93.
2001: Yoshinori Tanaka; Osamu Nureki; Hitoshi Kurumizaka; Shuya Fukai; S Kawaguchi; M Ikuta; J Iwahara; T Okazaki; Shigeyuki Yokoyama
Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA.
The EMBO journal 2001;20(23):6612-8.
2001: K Kurimoto; Shuya Fukai; Osamu Nureki; Y Muto; Shigeyuki Yokoyama
Crystal structure of human AUH protein, a single-stranded RNA binding homolog of enoyl-CoA hydratase.
Structure (London, England : 1993) 2001;9(12):1253-63.
2001: Daisuke Kiga; Kensaku Sakamoto; S Sato; Ichiro Hirao; Shigeyuki Yokoyama
Shifted positioning of the anticodon nucleotide residues of amber suppressor tRNA species by Escherichia coli arginyl-tRNA synthetase.
European journal of biochemistry / FEBS 2001;268(23):6207-13.
2001: Atsuko Shimada; Osamu Nureki; Mieko Goto; Shuji Takahashi; Shigeyuki Yokoyama
Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(24):13537-42.
2001: Ryuichiro Ishitani; Osamu Nureki; Teiya Kijimoto; Masakatsu Watanabe; Hisao Kondo; Nobukazu Nameki; Norihiro Okada; Susumu Nishimura; Shigeyuki Yokoyama
Crystallization and preliminary X-ray analysis of the archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii.
Acta crystallographica. Section D, Biological crystallography 2001;57(Pt 11):1659-62.
2001: Wataru Kagawa; Hitoshi Kurumizaka; Shukuko Ikawa; Shigeyuki Yokoyama; Takehiko Shibata
Homologous pairing promoted by the human Rad52 protein.
The Journal of biological chemistry 2001;276(37):35201-8.
2001: T Fujiwara; M Kimoto; Hiroshi Sugiyama; Ichiro Hirao; Shigeyuki Yokoyama
Synthesis of 6-(2-thienyl)purine nucleoside derivatives that form unnatural base pairs with pyridin-2-one nucleosides.
Bioorganic & medicinal chemistry letters 2001;11(16):2221-3.
2001: Takehiko Shibata; T Nishinaka; Tsutomu Mikawa; Hideki Aihara; Hitoshi Kurumizaka; Shigeyuki Yokoyama; Yutaka Ito
Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: a possible advantage of DNA over RNA as genomic material.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(15):8425-32.
2001: Shigeyuki Yokoyama; K Tachibana; Hiroyuki Nakanishi; Yasunori Yamamoto; Kenji Irie; Kenji Mandai; A Nagafuchi; Morito Monden; Yoshimi Takai
alpha-catenin-independent recruitment of ZO-1 to nectin-based cell-cell adhesion sites through afadin.
Molecular biology of the cell 2001;12(6):1595-609.
2001: Hitoshi Kurumizaka; Shukuko Ikawa; Maki Nakada; K Eda; Wataru Kagawa; M Takata; S Takeda; Shigeyuki Yokoyama; Takehiko Shibata
Homologous-pairing activity of the human DNA-repair proteins Xrcc3.Rad51C.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(10):5538-43.
2001: Toshiaki Sakisaka; T Taniguchi; Hiroyuki Nakanishi; Kiyohisa Takahashi; M Miyahara; Wataru Ikeda; Shigeyuki Yokoyama; Ying-Feng Peng; Koichi Yamanishi; Yoshimi Takai
Requirement of interaction of nectin-1alpha/HveC with afadin for efficient cell-cell spread of herpes simplex virus type 1.
Journal of virology 2001;75(10):4734-43.
2001: Takashi Itoh; Seizo Koshiba; Takanori Kigawa; Akira Kikuchi; Shigeyuki Yokoyama; Tadaomi Takenawa
Role of the ENTH domain in phosphatidylinositol-4,5-bisphosphate binding and endocytosis.
Science (New York, N.Y.) 2001;291(5506):1047-51.
2001: Atsuko Shimada; Osamu Nureki; Naoshi Dohmae; Koji Takio; Shigeyuki Yokoyama
Gene cloning, expression, crystallization and preliminary X-ray analysis of Thermus thermophilus arginyl-tRNA synthetase.
Acta crystallographica. Section D, Biological crystallography 2001;57(Pt 2):272-5.
2001: S Kawaguchi; J Müller; D Linde; Seiki Kuramitsu; T Shibata; Yorinao Inoue; D G Vassylyev; Shigeyuki Yokoyama
The crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus.
The EMBO journal 2001;20(3):562-9.
2001: Takaho Terada; Mikako Shirouzu; Y Fukumori; F Fujimori; Y Ito; Takanori Kigawa; Shigeyuki Yokoyama; T Uchida
Solution structure of the human parvulin-like peptidyl prolyl cis/trans isomerase, hPar14.
Journal of molecular biology 2001;305(4):917-26.
2001: Hiroyuki Asanuma; Daisuke Tamaru; T Yoshida; Akira Yamazawa; Tsuneo Mitsui; Taeko Okuni; Michiko Kimoto; Ichiro Hirao; Shigeyuki Yokoyama; Makoto Komiyama
Photo-regulation of RNA polymerase reaction by use of modified DNA carrying an azobenzene.
Nucleic acids research. Supplement (2001) 2001;(1):55-6.
2001: Ichiro Hirao; Tsuneo Mitsui; T Fujiwara; Michiko Kimoto; T To; Taeko Okuni; A Sato; Y Harada; Shigeyuki Yokoyama
Efforts toward creating unnatural base pairs for an expanded genetic code.
Nucleic acids research. Supplement (2001) 2001;(1):17-8.
2001: Osamu Nureki; Shuya Fukai; Shun-ichi Sekine; Atsuko Shimada; Takaho Terada; Takashi Nakama; Mikako Shirouzu; Dmitry G Vassylyev; Shigeyuki Yokoyama
Structural basis for amino acid and tRNA recognition by class I aminoacyl-tRNA synthetases.
Cold Spring Harbor symposia on quantitative biology 2001;66():167-73.
2000: Y Kuroda; K Tani; Y Matsuo; Shigeyuki Yokoyama
Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics.
Protein science : a publication of the Protein Society 2000;9(12):2313-21.
2000: Ying-Feng Peng; Kenji Mandai; Toshiaki Sakisaka; Noriko Okabe; Y Yamamoto; Shigeyuki Yokoyama; Akira Mizoguchi; Hitoshi Shiozaki; Morito Monden; Yoshimi Takai
Ankycorbin: a novel actin cytoskeleton-associated protein.
Genes to cells : devoted to molecular & cellular mechanisms 2000;5(12):1001-8.
2000: Shuya Fukai; Osamu Nureki; Shun-ichi Sekine; Atsuko Shimada; J Tao; Dmitry G Vassylyev; Shigeyuki Yokoyama
Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase.
Cell 2000;103(5):793-803.
2000: Shigeyuki Yokoyama; H Hirota; Takanori Kigawa; Takashi Yabuki; M Shirouzu; Takaho Terada; Y Ito; Y Matsuo; Y Kuroda; Y Nishimura; Y Kyogoku; K Miki; R Masui; S Kuramitsu
Structural genomics projects in Japan.
Nature structural biology 2000;7 Suppl():943-5.
2000: T Yasuda; T Ohtsuka; E Inoue; Shigeyuki Yokoyama; Toshiaki Sakisaka; A Kodama; K Takaishi; Yoshimi Takai
Importance of spatial activation of Cdc42 and rac small G proteins by frabin for microspike formation in MDCK cells.
Genes to cells : devoted to molecular & cellular mechanisms 2000;5(7):583-91.
2000: Insil Kim; Yutaka Muto; Satoru Watanabe; Aya Kitamura; Yasuhiro Futamura; Shigeyuki Yokoyama; Kazumi Hosono; Gota Kawai; Hiroshi Takaku; N Dohmae; K Takio; H Saskamoto; Yoshiro Shimura
Interactions of a didomain fragment of the Drosophila sex-lethal protein with single-stranded uridine-rich oligoribonucleotides derived from the transformer and Sex-lethal messenger RNA precursors: NMR with residue-selective [5-2H]uridine substitutions.
Journal of biomolecular NMR 2000;17(2):153-65.
2000: Kensaku Sakamoto; H Gouzu; Ken Komiya; Daisuke Kiga; Shigeyuki Yokoyama; T Yokomori; Masami Hagiya
Molecular computation by DNA hairpin formation.
Science (New York, N.Y.) 2000;288(5469):1223-6.
2000: A Satoh; K Takai; R Ouchi; Shigeyuki Yokoyama; Hiroshi Takaku
Effects of anticodon 2'-O-methylations on tRNA codon recognition in an Escherichia coli cell-free translation.
RNA (New York, N.Y.) 2000;6(5):680-6.
2000: M Inoue; Yutaka Muto; H Sakamoto; Shigeyuki Yokoyama
NMR studies on functional structures of the AU-rich element-binding domains of Hu antigen C.
Nucleic acids research 2000;28(8):1743-50.
2000: T Kanda; K Takai; Shigeyuki Yokoyama; Hiroshi Takaku
Specific inactivation of Escherichia coli tRNA(Phe) by antisense DNA-treatment under Mg2+-deficient conditions.
Bioorganic & medicinal chemistry 2000;8(3):675-9.
2000: I Hirao; K Madin; Y Endo; Shigeyuki Yokoyama; A D Ellington
RNA aptamers that bind to and inhibit the ribosome-inactivating protein, pepocin.
The Journal of biological chemistry 2000;275(7):4943-8.
2000: Ichiro Hirao; T Fujiwara; Michiko Kimoto; Tsuneo Mitsui; Taeko Okuni; T Ohtsuki; Shigeyuki Yokoyama
Unnatural base pairs between 2-amino-6-(2-thienyl)purine and the complementary bases.
Nucleic acids symposium series 2000;(44):261-2.
2000: T Fujiwara; H Sugiyama; Ichiro Hirao; Shigeyuki Yokoyama
Synthesis of 6-(2-thienyl)purine nucleoside derivatives toward the expansion of the genetic code.
Nucleic acids symposium series 2000;(44):43-4.
2000: T Kanda; K Takai; Shigeyuki Yokoyama; Hiroshi Takaku
An easy cell-free protein synthesis system dependent on the addition of crude Escherichia coli tRNA.
Journal of biochemistry 2000;127(1):37-41.
1999: T Kamei; Takashi Matozaki; Toshiaki Sakisaka; A Kodama; Shigeyuki Yokoyama; Ying-Feng Peng; K Nakano; K Takaishi; Yoshimi Takai
Coendocytosis of cadherin and c-Met coupled to disruption of cell-cell adhesion in MDCK cells--regulation by Rho, Rac and Rab small G proteins.
Oncogene 1999;18(48):6776-84.
1999: Kensaku Sakamoto; Daisuke Kiga; Ken Komiya; H Gouzu; Shigeyuki Yokoyama; S Ikeda; H Sugiyama; Masami Hagiya
State transitions by molecules.
Bio Systems 1999;52(1-3):81-91.
1999: Hitoshi Kurumizaka; Hideki Aihara; Wataru Kagawa; Takehiko Shibata; Shigeyuki Yokoyama
Human Rad51 amino acid residues required for Rad52 binding.
Journal of molecular biology 1999;291(3):537-48.
1999: Takaaki Ito; Y Muto; M R Green; Shigeyuki Yokoyama
Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)).
The EMBO journal 1999;18(16):4523-34.
1999: Hideki Aihara; Yutaka Ito; Hitoshi Kurumizaka; Shigeyuki Yokoyama; Takehiko Shibata
The N-terminal domain of the human Rad51 protein binds DNA: structure and a DNA binding surface as revealed by NMR.
Journal of molecular biology 1999;290(2):495-504.
1999: K Takai; Hiroshi Takaku; Shigeyuki Yokoyama
In vitro codon-reading specificities of unmodified tRNA molecules with different anticodons on the sequence background of Escherichia coli tRNASer.
Biochemical and biophysical research communications 1999;257(3):662-7.
1999: N Handa; Osamu Nureki; K Kurimoto; Insil Kim; H Sakamoto; Yoshiro Shimura; Yutaka Muto; Shigeyuki Yokoyama
Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein.
Nature 1999;398(6728):579-85.
1999: Shun-ichi Sekine; Osamu Nureki; M Tateno; Shigeyuki Yokoyama
The identity determinants required for the discrimination between tRNAGlu and tRNAAsp by glutamyl-tRNA synthetase from Escherichia coli.
European journal of biochemistry / FEBS 1999;261(2):354-60.
1999: K Takai; S Okumura; Kazumi Hosono; Shigeyuki Yokoyama; Hiroshi Takaku
A single uridine modification at the wobble position of an artificial tRNA enhances wobbling in an Escherichia coli cell-free translation system.
FEBS letters 1999;447(1):1-4.
1999: Shigeyuki Yokoyama; H Shirataki; Toshiaki Sakisaka; Yoshimi Takai
Three splicing variants of tomosyn and identification of their syntaxin-binding region.
Biochemical and biophysical research communications 1999;256(1):218-22.
1999: S Koshiba; Shigeyuki Yokoyama
[Structural biology for PH and other domains involved in signal transduction].
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 1999;44(4 Suppl):368-79.
1999: T Terada; Y Ito; Mikako Shirouzu; M Tateno; K Hashimoto; Takanori Kigawa; T Ebisuzaki; K Takio; T Shibata; Shigeyuki Yokoyama; BO Smith; Ernest D Laue; J A Cooper
Nuclear magnetic resonance and molecular dynamics studies on the interactions of the Ras-binding domain of Raf-1 with wild-type and mutant Ras proteins.
Journal of molecular biology 1999;286(1):219-32.
1999: Seizo Koshiba; Takanori Kigawa; Junji Iwahara; A Kikuchi; Shigeyuki Yokoyama
Solution structure of the Eps15 homology domain of a human POB1 (partner of RalBP1).
FEBS letters 1999;442(2-3):138-42.
1999: Takanori Kigawa; Takashi Yabuki; Y Yoshida; M Tsutsui; Y Ito; T Shibata; Shigeyuki Yokoyama
Cell-free production and stable-isotope labeling of milligram quantities of proteins.
FEBS letters 1999;442(1):15-9.
1999: N Horie; Z Yamaizumi; Yoshiyuki Kuchino; K Takai; E Goldman; T Miyazawa; Susumu Nishimura; Shigeyuki Yokoyama
Modified nucleosides in the first positions of the anticodons of tRNA(Leu)4 and tRNA(Leu)5 from Escherichia coli.
Biochemistry 1999;38(1):207-17.
1999: Insil Kim; Yutaka Muto; Kazumi Hosono; Aya Kitamura; Satoru Watanabe; Takashi Ohtsuki; Gota Kawai; Hiroshi Takaku; Kunitomo Watanabe; H Sakamoto; Yoshiro Shimura; Shigeyuki Yokoyama
NMR signal assignment of the polyuridine tract of the single-stranded RNA complexed with Sxl RBD1-RBD2 by using residue selective [5-(2)H]uridine substitutions.
Nucleic acids symposium series 1999;(42):203-4.
1999: Aya Kitamura; Yutaka Muto; Satoru Watanabe; Insil Kim; Takuhiro Ito; Y Nishiya; Takashi Ohtsuki; Gota Kawai; Kunitomo Watanabe; Kazumi Hosono; Hiroshi Takaku; Etsuko Katoh; T Yamazaki; T Inoue; Shigeyuki Yokoyama
The guanosine binding mechanism of the Tetrahymena group I intron.
Nucleic acids symposium series 1999;(42):191-2.
1998: Takanori Kigawa; Makoto Endo; Y Ito; Mikako Shirouzu; A Kikuchi; Shigeyuki Yokoyama
Solution structure of the Ras-binding domain of RGL.
FEBS letters 1998;441(3):413-8.
1998: Michiko Kimoto; K Sakamoto; Mikako Shirouzu; Ichiro Hirao; Shigeyuki Yokoyama
RNA aptamers that specifically bind to the Ras-binding domain of Raf-1.
FEBS letters 1998;441(2):322-6.
1998: T Kanda; K Takai; Shigeyuki Yokoyama; Hiroshi Takaku
Knocking out a specific tRNA species within unfractionated Escherichia coli tRNA by using antisense (complementary) oligodeoxyribonucleotides.
FEBS letters 1998;440(3):273-6.
1998: Katsura Asano; T Niimi; Shigeyuki Yokoyama; K Mizobuchi
Structural basis for binding of the plasmid ColIb-P9 antisense Inc RNA to its target RNA with the 5'-rUUGGCG-3' motif in the loop sequence.
The Journal of biological chemistry 1998;273(19):11826-38.
1998: J H Kim; Mikako Shirouzu; T Kataoka; D Bowtell; Shigeyuki Yokoyama
Activation of Ras and its downstream extracellular signal-regulated protein kinases by the CDC25 homology domain of mouse Son-of-sevenless 1 (mSos1).
Oncogene 1998;16(20):2597-607.
1998: Y Fujita; H Shirataki; Toshiaki Sakisaka; T Asakura; Tomoko Ohya; H Kotani; Shigeyuki Yokoyama; H Nishioka; Y Matsuura; Akira Mizoguchi; R H Scheller; Yoshimi Takai
Tomosyn: a syntaxin-1-binding protein that forms a novel complex in the neurotransmitter release process.
Neuron 1998;20(5):905-15.
1998: Osamu Nureki; Dmitry G Vassylyev; M Tateno; Atsuko Shimada; Takashi Nakama; Shuya Fukai; M Konno; Tamara Lynn Hendrickson; Paul Schimmel; Shigeyuki Yokoyama
Enzyme structure with two catalytic sites for double-sieve selection of substrate.
Science (New York, N.Y.) 1998;280(5363):578-82.
1998: Daisuke Kiga; Yasuhiro Futamura; Kensaku Sakamoto; Shigeyuki Yokoyama
An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition.
Nucleic acids research 1998;26(7):1755-60.
1998: Junji Iwahara; Takanori Kigawa; Katsumi Kitagawa; H Masumoto; T Okazaki; Shigeyuki Yokoyama
A helix-turn-helix structure unit in human centromere protein B (CENP-B).
The EMBO journal 1998;17(3):827-37.
1997: Hideki Aihara; Yutaka Ito; Hitoshi Kurumizaka; T Terada; Shigeyuki Yokoyama; Takehiko Shibata
An interaction between a specified surface of the C-terminal domain of RecA protein and double-stranded DNA for homologous pairing.
Journal of molecular biology 1997;274(2):213-21.
1997: Kazumi Hosono; H Gozu; H Hosaka; Kensaku Sakamoto; Shigeyuki Yokoyama; K Takai; Hiroshi Takaku
Cleavage effect of oligoribonucleotides substituted at the cleavage sites with modified pyrimidine- and purine-nucleosides.
Biochimica et biophysica acta 1997;1354(3):211-8.
1997: M Inoue; Yutaka Muto; H Sakamoto; Takanori Kigawa; K Takio; Yoshiro Shimura; Shigeyuki Yokoyama
A characteristic arrangement of aromatic amino acid residues in the solution structure of the amino-terminal RNA-binding domain of Drosophila sex-lethal.
Journal of molecular biology 1997;272(1):82-94.
1997: Taroh Kinoshita; Mikako Shirouzu; Akira Kamiya; K Hashimoto; Shigeyuki Yokoyama; Atsushi Miyajima
Raf/MAPK and rapamycin-sensitive pathways mediate the anti-apoptotic function of p21Ras in IL-3-dependent hematopoietic cells.
Oncogene 1997;15(6):619-27.
1997: Yoshiaki Ito; Kazuhiko Yamasaki; Junji Iwahara; Takaho Terada; Akira Kamiya; Mikako Shirouzu; Yutaka Muto; Gota Kawai; Shigeyuki Yokoyama; E D Laue; M Wälchli; Tatsuhiro Shibata; Susumu Nishimura; T Miyazawa
Regional polysterism in the GTP-bound form of the human c-Ha-Ras protein.
Biochemistry 1997;36(30):9109-19.
1997: Seizo Koshiba; Takanori Kigawa; J H Kim; Mikako Shirouzu; D Bowtell; Shigeyuki Yokoyama
The solution structure of the pleckstrin homology domain of mouse Son-of-sevenless 1 (mSos1).
Journal of molecular biology 1997;269(4):579-91.
1997: Insil Kim; Yutaka Muto; M Inoue; Satoru Watanabe; Aya Kitamura; Shigeyuki Yokoyama; Kazumi Hosono; Hiroshi Takaku; A Ono; M Kainosho; H Sakamoto; Yoshiro Shimura
NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the Drosophila sex-lethal protein with target RNA fragments with site-specific [3-15N]uridine substitutions.
Nucleic acids research 1997;25(8):1565-9.
1997: T Kanda; K Takai; Shigeyuki Yokoyama; Hiroshi Takaku
Removing tRNA from a cell-free protein synthesis system for use in protein production.
Nucleic acids symposium series 1997;(37):319-20.
1997: H Shirakura; Kazumi Hosono; Gota Kawai; K Takai; Takashi Ohtsuki; Kunitomo Watanabe; Kensaku Sakamoto; Shigeyuki Yokoyama; Hiroshi Takaku
Study on site specific cleavage of RNA.
Nucleic acids symposium series 1997;(37):217-8.
1997: A Satoh; K Takai; Shigeyuki Yokoyama; Hiroshi Takaku
Codon recognition by artificial tRNA molecules with modified nucleosides in the anticodon.
Nucleic acids symposium series 1997;(37):117-8.
1997: R Ouchi; K Takai; Shigeyuki Yokoyama; Hiroshi Takaku
Codon reading properties of tRNA variants substituted within the anticodon loop.
Nucleic acids symposium series 1997;(37):115-6.
1996: BO Smith; Y Ito; Andrew R C Raine; S Teichmann; L Ben-Tovim; Daniel Nietlispach; R W Broadhurst; T Terada; M Kelly; H Oschkinat; T Shibata; Shigeyuki Yokoyama; Ernest D Laue
An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types.
Journal of biomolecular NMR 1996;8(3):360-8.
1996: H Miyaguchi; H Narita; K Sakamoto; Shigeyuki Yokoyama
An antibiotic-binding motif of an RNA fragment derived from the A-site-related region of Escherichia coli 16S rRNA.
Nucleic acids research 1996;24(19):3700-6.
1996: K Takai; Hiroshi Takaku; Shigeyuki Yokoyama
Codon-reading specificity of an unmodified form of Escherichia coli tRNA1Ser in cell-free protein synthesis.
Nucleic acids research 1996;24(15):2894-9.
1996: M Shinkai; T Masuda; Ken-Ichi Kariya; Masako Tamada; M Shirouzu; Shigeyuki Yokoyama; Tohru Kataoka
Difference in the mechanism of interaction of Raf-1 and B-Raf with H-Ras.
Biochemical and biophysical research communications 1996;223(3):729-34.
1996: K Sakamoto; Gota Kawai; Satoru Watanabe; T Niimi; N Hayashi; Yutaka Muto; K Watanabe; T Satoh; M Sekine; Shigeyuki Yokoyama
NMR studies of the effects of the 5'-phosphate group on conformational properties of 5-methylaminomethyluridine found in the first position of the anticodon of Escherichia coli tRNA(Arg)4.
Biochemistry 1996;35(21):6533-8.
1996: Satoru Watanabe; Gota Kawai; Yutaka Muto; K Watanabe; T Inoue; Shigeyuki Yokoyama
An RNA fragment consisting of the P7 and P9.0 stems and the 3'-terminal guanosine of the Tetrahymena group I intron.
Nucleic acids research 1996;24(7):1337-44.
1996: S Sekine; Osamu Nureki; K Sakamoto; T Niimi; M Tateno; M Go; T Kohno; A Brisson; J Lapointe; Shigeyuki Yokoyama
Major identity determinants in the "augmented D helix" of tRNA(Glu) from Escherichia coli.
Journal of molecular biology 1996;256(4):685-700.
1996: K Akasaka; Masako Tamada; F Wang; Ken-Ichi Kariya; Fumi Shima; Akira Kikuchi; M Yamamoto; M Shirouzu; Shigeyuki Yokoyama; Tohru Kataoka
Differential structural requirements for interaction of Ras protein with its distinct downstream effectors.
The Journal of biological chemistry 1996;271(10):5353-60.
1995: CD Hu; Ken-Ichi Kariya; Masako Tamada; K Akasaka; M Shirouzu; Shigeyuki Yokoyama; Tohru Kataoka
Cysteine-rich region of Raf-1 interacts with activator domain of post-translationally modified Ha-Ras.
The Journal of biological chemistry 1995;270(51):30274-7.
1995: M Tateno; Osamu Nureki; S Sekine; K Kaneda; M Go; Shigeyuki Yokoyama
A three-dimensional structure model of the complex of glutamyl-tRNA synthetase and its cognate tRNA.
FEBS letters 1995;377(1):77-81.
1995: T Taguchi; K Kitajima; T Niimi; Yutaka Muto; Shigeyuki Yokoyama; S Inoue; Y Inoue
Complete assignments of 13C NMR resonances to all the carbon atoms of the trimannosido-di-N-acetylchitobiosyl structure in a pentaantennary decasaccharide glycopeptide.
Carbohydrate research 1995;275(1):185-91.
1995: Takanori Kigawa; Yutaka Muto; Shigeyuki Yokoyama
Cell-free synthesis and amino acid-selective stable isotope labeling of proteins for NMR analysis.
Journal of biomolecular NMR 1995;6(2):129-34.
1995: S Nureki; Shigeyuki Yokoyama
[Mechanism of tRNA-recognition by aminoacyl-tRNA synthetases].
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 1995;40(10):1609-19.
1995: T Hatta; K Takai; Shigeyuki Yokoyama; H Nakashima; Naoki Yamamoto; Hiroshi Takaku
Phosphorothioate oligonucleotides block reverse transcription by the Rnase H activity associated with the HIV-1 polymerase.
Biochemical and biophysical research communications 1995;211(3):1041-6.
1995: J Liu; Y Gagnon; J Gauthier; L Furenlid; P J L'Heureux; M Auger; Osamu Nureki; Shigeyuki Yokoyama; J Lapointe
The zinc-binding site of Escherichia coli glutamyl-tRNA synthetase is located in the acceptor-binding domain. Studies by extended x-ray absorption fine structure, molecular modeling, and site-directed mutagenesis.
The Journal of biological chemistry 1995;270(25):15162-9.
1995: Osamu Nureki; D G Vassylyev; K Katayanagi; T Shimizu; S Sekine; Takanori Kigawa; Takayuki Miyazawa; Shigeyuki Yokoyama; K Morikawa
Architectures of class-defining and specific domains of glutamyl-tRNA synthetase.
Science (New York, N.Y.) 1995;267(5206):1958-65.
1995: T Taguchi; K Kitajima; Yutaka Muto; Shigeyuki Yokoyama; S Inoue; Y Inoue
Proton NMR study of the trimannosyl unit in a pentaantennary N-linked decasaccharide structure. Complete assignment of the proton resonances and conformational characterization.
European journal of biochemistry / FEBS 1995;228(3):822-9.
1995: Junko Fujita-Yoshigaki; Mikako Shirouzu; Yoshiaki Ito; S Hattori; Shunsuke Furuyama; Susumu Nishimura; Shigeyuki Yokoyama
A constitutive effector region on the C-terminal side of switch I of the Ras protein.
The Journal of biological chemistry 1995;270(9):4661-7.
1995: Ritsuko Yamamoto-Honda; Kazuyuki Tobe; Yasushi Kaburagi; Keisuke Ueki; S Asai; M Yachi; Mikako Shirouzu; J Yodoi; Yasuo Akanuma; Shigeyuki Yokoyama
Upstream mechanisms of glycogen synthase activation by insulin and insulin-like growth factor-I. Glycogen synthase activation is antagonized by wortmannin or LY294002 but not by rapamycin or by inhibiting p21ras.
The Journal of biological chemistry 1995;270(6):2729-34.
1995: S Okumura; K Takai; Shigeyuki Yokoyama; Hiroshi Takaku
Codon recognition by tRNA molecules with a modified or unmodified uridine at the first position of the anticodon.
Nucleic acids symposium series 1995;(34):203-4.
1995: Insil Kim; Satoru Watanabe; Yutaka Muto; Kazumi Hosono; K Takai; Hiroshi Takaku; Gota Kawai; K Watanabe; Shigeyuki Yokoyama
Selective deuteration of RNA for NMR signal assignment.
Nucleic acids symposium series 1995;(34):123-4.
1994: H Hosaka; I Sakabe; Kensaku Sakamoto; Shigeyuki Yokoyama; Hiroshi Takaku
Sequence-specific cleavage of oligoribonucleotide capable of forming a stem and loop structure.
The Journal of biological chemistry 1994;269(31):20090-4.
1994: H Hosaka; I Sakabe; Kensaku Sakamoto; T Niimi; Shigeyuki Yokoyama; Hiroshi Takaku
Characterization of the secondary structure of an oligonucleotide corresponding to the autocleavage site of a precursor RNA from bacteriophage T4.
Biochimica et biophysica acta 1994;1218(3):351-6.
1994: Mikako Shirouzu; H Koide; Junko Fujita-Yoshigaki; H Oshio; Y Toyama; K Yamasaki; S A Fuhrman; E Villafranca; Y Kaziro; Shigeyuki Yokoyama
Mutations that abolish the ability of Ha-Ras to associate with Raf-1.
Oncogene 1994;9(8):2153-7.
1994: H Koide; Shigeyuki Yokoyama; Y Katayama; Yutaka Muto; Takanori Kigawa; T Kohno; H Takusari; M Oishi; S Takahashi; K Tsukumo
Receptor-binding affinities of human epidermal growth factor variants having unnatural amino acid residues in position 23.
Biochemistry 1994;33(23):7470-6.
1994: K Takai; N Horie; Z Yamaizumi; Susumu Nishimura; Takayuki Miyazawa; Shigeyuki Yokoyama
Recognition of UUN codons by two leucine tRNA species from Escherichia coli.
FEBS letters 1994;344(1):31-4.
1994: Osamu Nureki; Shigeyuki Yokoyama
[Aminoacyl-tRNA synthetase].
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 1994;39(7):1215-25.
1994: Osamu Nureki; T Niimi; Takashi Muramatsu; H Kanno; T Kohno; C Florentz; Richard Giegé; Shigeyuki Yokoyama
Molecular recognition of the identity-determinant set of isoleucine transfer RNA from Escherichia coli.
Journal of molecular biology 1994;236(3):710-24.
1994: K Yamasaki; Mikako Shirouzu; Yutaka Muto; Junko Fujita-Yoshigaki; H Koide; Yoshiaki Ito; Gota Kawai; S Hattori; Shigeyuki Yokoyama; Susumu Nishimura
Site-directed mutagenesis, fluorescence, and two-dimensional NMR studies on microenvironments of effector region aromatic residues of human c-Ha-Ras protein.
Biochemistry 1994;33(1):65-73.
1993: S Yajima; Yutaka Muto; S Morikawa; H Nakamura; Shigeyuki Yokoyama; Haruhiko Masaki; T Uozumi
The three-dimensional structure of the colicin E3 immunity protein by distance geometry calculation.
FEBS letters 1993;333(3):257-60.
1993: T Hatta; S G Kim; H Nakashima; Naoki Yamamoto; Kensaku Sakamoto; Shigeyuki Yokoyama; Hiroshi Takaku
Mechanisms of the inhibition of reverse transcription by unmodified and modified antisense oligonucleotides.
FEBS letters 1993;330(2):161-4.
1993: K Sakamoto; Gota Kawai; T Niimi; T Satoh; M Sekine; Z Yamaizumi; Susumu Nishimura; Takayuki Miyazawa; Shigeyuki Yokoyama
A modified uridine in the first position of the anticodon of a minor species of arginine tRNA, the argU gene product, from Escherichia coli.
European journal of biochemistry / FEBS 1993;216(2):369-75.
1993: Osamu Nureki; T Kohno; K Sakamoto; Takayuki Miyazawa; Shigeyuki Yokoyama
Chemical modification and mutagenesis studies on zinc binding of aminoacyl-tRNA synthetases.
The Journal of biological chemistry 1993;268(21):15368-73.
1993: Takaki Hiwasa; Junko Fujita-Yoshigaki; Mikako Shirouzu; H Koide; T Sawada; Shigeru Sakiyama; Shigeyuki Yokoyama
c-Ha-Ras mutants with point mutations in Gln-Val-Val region have reduced inhibitory activity toward cathepsin B.
Cancer letters 1993;69(3):161-5.
1993: Yutaka Muto; K Yamasaki; Yoshiaki Ito; S Yajima; Haruhiko Masaki; T Uozumi; M Wälchli; Susumu Nishimura; Takayuki Miyazawa; Shigeyuki Yokoyama
Sequence-specific 1H and 15N resonance assignments and secondary structure of GDP-bound human c-Ha-Ras protein in solution.
Journal of biomolecular NMR 1993;3(2):165-84.
1993: H Tanaka; H Hosaka; R Takahashi; Y Imamura; K Takai; Shigeyuki Yokoyama; Hiroshi Takaku
Importance of specific purine-pyrimidine amino and hydroxyl groups for efficient cleavage by a hammerhead ribozyme.
Nucleic acids symposium series 1993;(29):175-6.
1993: T Niimi; Gota Kawai; M Takayanagi; T Noguchi; N Hayashi; T Kohno; Y Muto; K Watanabe; Takayuki Miyazawa; Shigeyuki Yokoyama
A 15N-1H nuclear magnetic resonance study on the interaction between isoleucine tRNA and isoleucyl-tRNA synthetase from Escherichia coli.
Biochimie 1993;75(12):1109-15.
1993: T Hatta; S Kim; Shigeyuki Yokoyama; Hiroshi Takaku
Mechanisms of the inhibition of reverse transcription by unmodified and modified antisense oligonucleotides.
Nucleic acids symposium series 1993;(29):67-8.
1992: S G Kim; S Tsukahara; Shigeyuki Yokoyama; Hiroshi Takaku
The influence of oligodeoxyribonucleotide phosphorothioate pyrimidine strands on triplex formation.
FEBS letters 1992;314(1):29-32.
1992: Junko Fujita-Yoshigaki; Yoshiaki Ito; K Yamasaki; Yutaka Muto; Takayuki Miyazawa; Susumu Nishimura; Shigeyuki Yokoyama
Guanine-nucleotide binding activity, interaction with GTPase-activating protein and solution conformation of the human c-Ha-Ras protein catalytic domain are retained upon deletion of C-terminal 18 amino acid residues.
Journal of protein chemistry 1992;11(6):731-9.
1992: Junko Fujita-Yoshigaki; Shigeyuki Yokoyama; N Shindo-Okada; Susumu Nishimura
Azatyrosine inhibits neurite outgrowth of PC12 cells induced by oncogenic Ras.
Oncogene 1992;7(10):2019-24.
1992: S Yajima; Yutaka Muto; Shigeyuki Yokoyama; Haruhiko Masaki; T Uozumi
The secondary structure of the colicin E3 immunity protein as studied by 1H-1H and 1H-15N two-dimensional NMR spectroscopy.
Biochemistry 1992;31(24):5578-86.
1992: S Koide; Shigeyuki Yokoyama; Hiroshi Matsuzawa; Takayuki Miyazawa; T Ohta
Conformational equilibrium of an enzyme catalytic site in the allosteric transition.
Biochemistry 1992;31(23):5362-8.
1992: Mikako Shirouzu; Junko Fujita-Yoshigaki; Yoshiaki Ito; H Koide; Susumu Nishimura; Shigeyuki Yokoyama
A glutamic acid residue at position 31 of Ras protein is essential to the signal transduction for neurite outgrowth of PC12 cells and the stimulation of GTPase activity by GAPRas.
Oncogene 1992;7(3):475-80.
1992: Osamu Nureki; K Suzuki; M Hara-Yokoyama; T Kohno; Hiroshi Matsuzawa; T Ohta; T Shimizu; K Morikawa; Takayuki Miyazawa; Shigeyuki Yokoyama
Glutamyl-tRNA synthetase from Thermus thermophilus HB8. Molecular cloning of the gltX gene and crystallization of the overproduced protein.
European journal of biochemistry / FEBS 1992;204(2):465-72.
1992: Gota Kawai; Y Yamamoto; T Kamimura; T Masegi; M Sekine; T Hata; T Iimori; T Watanabe; Takayuki Miyazawa; Shigeyuki Yokoyama
Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2'-hydroxyl group.
Biochemistry 1992;31(4):1040-6.
1992: T Kohno; H Koide; Shigeyuki Yokoyama; T Miyazawa
[Alloprotein].
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 1992;37(3 Suppl):646-53.
1992: K Yamasaki; Yutaka Muto; Yoshiaki Ito; M Wälchli; Takayuki Miyazawa; Susumu Nishimura; Shigeyuki Yokoyama
A 1H-15N NMR study of human c-Ha-ras protein: biosynthetic incorporation of 15N-labeled amino acids.
Journal of biomolecular NMR 1992;2(1):71-82.
1991: Junko Fujita-Yoshigaki; Mikako Shirouzu; H Koide; Susumu Nishimura; Shigeyuki Yokoyama
Identification of amino acid residues of Ras protein that are essential for signal-transducing activity but not for enhancement of GTPase activity by GAP.
FEBS letters 1991;294(3):187-90.
1991: H Hosaka; T Ogawa; Kensaku Sakamoto; Shigeyuki Yokoyama; Hiroshi Takaku
Cleavage reaction of a synthetic oligoribonucleotide corresponding to the autocleavage site of a precursor RNA from bacteriophage T4.
FEBS letters 1991;293(1-2):204-6.
1991: Takanori Kigawa; Shigeyuki Yokoyama
A continuous cell-free protein synthesis system for coupled transcription-translation.
Journal of biochemistry 1991;110(2):166-8.
1991: M Kanou; H Ohomori; K Nagai; Shigeyuki Yokoyama; R J Suhadolnik; Robert W Sobol; Hiroshi Takaku
Purine 8-substitution modulates the ribonuclease L binding and activation abilities of 2',5'-oligoadenylates.
Biochemical and biophysical research communications 1991;176(2):769-74.
1991: Osamu Nureki; Takashi Muramatsu; K Suzuki; D Kohda; Hiroshi Matsuzawa; T Ohta; Takayuki Miyazawa; Shigeyuki Yokoyama
Methionyl-tRNA synthetase gene from an extreme thermophile, Thermus thermophilus HB8. Molecular cloning, primary-structure analysis, expression in Escherichia coli, and site-directed mutagenesis.
The Journal of biological chemistry 1991;266(5):3268-77.
1991: Osamu Nureki; M Tateno; T Niimi; T Kohno; Takashi Muramatsu; H Kanno; Yutaka Muto; R Giege; Shigeyuki Yokoyama
Mechanisms of molecular recognition of tRNAs by aminoacyl-tRNA synthetases.
Nucleic acids symposium series 1991;(25):165-6.
1990: A Kanamori; S Inoue; M Iwasaki; K Kitajima; G Kawai; Shigeyuki Yokoyama; Y Inoue
Deaminated neuraminic acid-rich glycoprotein of rainbow trout egg vitelline envelope. Occurrence of a novel alpha-2,8-linked oligo(deaminated neuraminic acid) structure in O-linked glycan chains.
The Journal of biological chemistry 1990;265(35):21811-9.
1990: M Kanou; H Ohomori; Hiroshi Takaku; Shigeyuki Yokoyama; Gota Kawai; R J Suhadolnik; R Sobol
Chemical synthesis and biological activities of analogues of 2',5'-oligoadenylates containing 8-substituted adenosine derivatives.
Nucleic acids research 1990;18(15):4439-46.
1990: T Kohno; D Kohda; M Haruki; Shigeyuki Yokoyama; Takayuki Miyazawa
Nonprotein amino acid furanomycin, unlike isoleucine in chemical structure, is charged to isoleucine tRNA by isoleucyl-tRNA synthetase and incorporated into protein.
The Journal of biological chemistry 1990;265(12):6931-5.
1990: M Haruki; R Matsumoto; M Hara-Yokoyama; Takayuki Miyazawa; Shigeyuki Yokoyama
Conformational changes of aminoacyl-tRNA and uncharged tRNA upon complex formation with polypeptide chain elongation factor Tu.
FEBS letters 1990;263(2):361-4.
1990: Takashi Muramatsu; Shigeyuki Yokoyama
[Identity of tRNA].
Nihon rinsho. Japanese journal of clinical medicine 1990;48(3):639-46.
1990: H Koide; Shigeyuki Yokoyama; T Miyazawa
[Biosynthesis of alloprotein].
Nihon rinsho. Japanese journal of clinical medicine 1990;48(1):208-13.
1990: H Komatsu; T Ichikawa; Hiroshi Takaku; Shigeyuki Yokoyama; Gota Kawai
Recognition by restriction endodeoxyribonuclease EcoRI of octadeoxyribonucleotides containing modified sugar and base moieties.
Nucleic acids symposium series 1990;(22):95-6.
1990: K Nagai; Shigeyuki Yokoyama; Gota Kawai; R J Shuhadlnik; Hiroshi Takaku
Synthesis and biological activities of 8-substituted 2-5A analogues.
Nucleic acids symposium series 1990;(22):13-4.
1990: Takashi Muramatsu; Osamu Nureki; H Kanno; T Niimi; M Tateno; T Kohno; Gota Kawai; Takayuki Miyazawa; Yutaka Muto; Shigeyuki Yokoyama
Recognition of tRNA identity determinants by aminoacyl-tRNA synthetases.
Nucleic acids symposium series 1990;(22):119-20.
1989: A Hata-Tanaka; Gota Kawai; K Yamasaki; Yoshiaki Ito; H Kajiura; J M Ha; Takayuki Miyazawa; Shigeyuki Yokoyama; Susumu Nishimura
Spin-labeling proton NMR study on aromatic amino acid residues in the guanine nucleotide binding site of human c-Ha-ras(1-171) protein.
Biochemistry 1989;28(24):9550-6.
1989: J M Ha; Yoshiaki Ito; Gota Kawai; Takayuki Miyazawa; K i Miura; Eiko Ohtsuka; S Noguchi; Susumu Nishimura; Shigeyuki Yokoyama
Conformation of guanosine 5'-diphosphate as bound to a human c-Ha-ras mutant protein: a nuclear Overhauser effect study.
Biochemistry 1989;28(21):8411-6.
1989: Takaki Hiwasa; Shigeyuki Yokoyama; J Fujita; E Kominami; N Katunuma; Shigeru Sakiyama
Potentiation of cysteine proteinase-inhibitor activity of full-length Ha-ras oncogene products by denaturation-renaturation.
Biochemistry international 1989;19(3):593-601.
1989: K Yamasaki; Gota Kawai; Yoshiaki Ito; Yutaka Muto; J Fujita; Takayuki Miyazawa; Susumu Nishimura; Shigeyuki Yokoyama
Conformation change of effector-region residues in antiparallel beta-sheet of human c-Ha-ras protein on GDP----GTP gamma S exchange: a two-dimensional NMR study.
Biochemical and biophysical research communications 1989;162(3):1054-62.
1989: S Koide; Shigeyuki Yokoyama; Hiroshi Matsuzawa; Takayuki Miyazawa; T Ohta
Conformation of NAD+ bound to allosteric L-lactate dehydrogenase activated by chemical modification.
The Journal of biological chemistry 1989;264(15):8676-9.
1988: Takashi Muramatsu; Kiyotaka Nishikawa; F Nemoto; Yoshiyuki Kuchino; Susumu Nishimura; Takayuki Miyazawa; Shigeyuki Yokoyama
Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification.
Nature 1988;336(6195):179-81.
1988: S Kotani; A Ikai; Gota Kawai; S Maekawa; Shigeyuki Yokoyama; H Sakai
Microtubule-assembly inhibitor protein. Its distribution, localization and physicochemical properties.
European journal of biochemistry / FEBS 1988;176(3):573-80.
1988: H Koide; Shigeyuki Yokoyama; Gota Kawai; J M Ha; T Oka; S Kawai; T Miyake; T Fuwa; Takayuki Miyazawa
Biosynthesis of a protein containing a nonprotein amino acid by Escherichia coli: L-2-aminohexanoic acid at position 21 in human epidermal growth factor.
Proceedings of the National Academy of Sciences of the United States of America 1988;85(17):6237-41.
1988: Takashi Muramatsu; Shigeyuki Yokoyama; N Horie; A Matsuda; Takuya Ueda; Z Yamaizumi; Yoshiyuki Kuchino; Susumu Nishimura; Takayuki Miyazawa
A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli.
The Journal of biological chemistry 1988;263(19):9261-7.
1988: Takaki Hiwasa; Shigeru Sakiyama; Shigeyuki Yokoyama; J M Ha; S Noguchi; Y Bando; E Kominami; N Katunuma
Degradation of epidermal growth factor receptors by cathepsin L-like protease: inhibition of the degradation by c-Ha-ras gene products.
FEBS letters 1988;233(2):367-70.
1988: Takaki Hiwasa; Shigeru Sakiyama; Shigeyuki Yokoyama; J M Ha; J Fujita; S Noguchi; Y Bando; E Kominami; N Katunuma
Inhibition of cathepsin L-induced degradation of epidermal growth factor receptors by c-Ha-ras gene products.
Biochemical and biophysical research communications 1988;151(1):78-85.
1988: Gota Kawai; Shigeyuki Yokoyama; T Hasegawa; K Murao; H Ishikura; Susumu Nishimura; Takayuki Miyazawa
Two-dimensional NMR analyses of dynamic structures of tRNA and the regulation of codon recognition by post-transcriptional modifications.
Nucleic acids symposium series 1988;(19):105-6.
1987: D Kohda; Gota Kawai; Shigeyuki Yokoyama; M Kawakami; S Mizushima; Takayuki Miyazawa
NMR analyses of the conformations of L-isoleucine and L-valine bound to Escherichia coli isoleucyl-tRNA synthetase.
Biochemistry 1987;26(20):6531-8.
1987: Takaki Hiwasa; Shigeru Sakiyama; S Noguchi; J M Ha; T Miyazawa; Shigeyuki Yokoyama
Degradation of a cAMP-binding protein is inhibited by human c-Ha-ras gene products.
Biochemical and biophysical research communications 1987;146(2):731-8.
1987: Takaki Hiwasa; Shigeyuki Yokoyama; J M Ha; S Noguchi; Shigeru Sakiyama
c-Ha-ras gene products are potent inhibitors of cathepsins B and L.
FEBS letters 1987;211(1):23-6.
1987: Shigeyuki Yokoyama; K Watanabe; Takayuki Miyazawa
Dynamic structures and functions of transfer ribonucleic acids from extreme thermophiles.
Advances in biophysics 1987;23():115-47.
1986: Shigeyuki Yokoyama; M Haruki; M Hara-Yokoyama; Takayuki Miyazawa
Circular dichroism analyses of tRNA X protein interactions.
Nucleic acids symposium series 1986;(17):199-201.