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Shigeyuki Yokoyama

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Publications

TOP 3
Wakiyama Motoaki; Yokoyama Shigeyuki
MicroRNA-Mediated mRNA Deadenylation and Repression of Protein Synthesis in a Mammalian Cell-Free System.
Aoki Masaaki; Matsuda Takayoshi; Tomo Yasuko; Miyata Yukako; Inoue Makoto; Kigawa Takanori; Yokoyama Shigeyuki
Automated system for high-throughput protein production using the dialysis cell-free method.
Arai Ryoichi; Murayama Kazutaka; Uchikubo-Kamo Tomomi; Nishimoto Madoka; Toyama Mitsutoshi; Kuramitsu Seiki; Terada Takaho; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8.

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All Publications

2010: Wakiyama Motoaki; Yokoyama Shigeyuki
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: Aoki Masaaki; Matsuda Takayoshi; Tomo Yasuko; Miyata Yukako; Inoue Makoto; Kigawa Takanori; Yokoyama Shigeyuki
Automated system for high-throughput protein production using the dialysis cell-free method.
Protein expression and purification 2009;68(2):128-36.
2009: Arai Ryoichi; Murayama Kazutaka; Uchikubo-Kamo Tomomi; Nishimoto Madoka; Toyama Mitsutoshi; Kuramitsu Seiki; Terada Takaho; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8.
Journal of structural biology 2009;168(3):575-81.
2009: Goroncy Alexander K; Koshiba Seizo; Tochio Naoya; Tomizawa Tadashi; Sato Manami; Inoue Makato; Watanabe Satoru; Hayashizaki Yoshihide; Tanaka Akiko; Kigawa Takanori; Yokoyama Shigeyuki
NMR solution structures of actin depolymerizing factor homology domains.
Protein science : a publication of the Protein Society 2009;18(11):2384-92.
2009: Kumarevel Thirumananseri; Tanaka Tomoyuki; Bessho Yoshitaka; Shinkai Akeo; Yokoyama Shigeyuki
Crystal structure of hydrogenase maturating endopeptidase HycI from Escherichia coli.
Biochemical and biophysical research communications 2009;389(2):310-4.
2009: Kumarevel Thirumananseri; Tanaka Tomoyuki; Shinkai Akeo; Yokoyama Shigeyuki
Crystal structure of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8.
Proteins 2009;77(3):747-51.
2009: Jeyakanthan Jeyaraman; Thamotharan Subbiah; Velmurugan Devadasan; Rao Vaijayanthimala Surya Narayna; Nagarajan Shanthi; Shinkai Akeo; Kuramitsu Seiki; Yokoyama Shigeyuki
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: Goto-Ito Sakurako; Ito Takuhiro; Kuratani Mitsuo; Bessho Yoshitaka; Yokoyama Shigeyuki
Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation.
Nature structural & molecular biology 2009;16(10):1109-15.
2009: Shimono Kazumi; Goto Mie; Kikukawa Takashi; Miyauchi Seiji; Shirouzu Mikako; Kamo Naoki; Yokoyama Shigeyuki
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: Itoh Yuzuru; Chiba Shiho; Sekine Shun-Ichi; Yokoyama Shigeyuki
Crystal structure of human selenocysteine tRNA.
Nucleic acids research 2009;37(18):6259-68.
2009: He Fahu; Saito Kohei; Kobayashi Naohiro; Harada Takushi; Watanabe Satoru; Kigawa Takanori; Güntert Peter; Ohara Osamu; Tanaka Akiko; Unzai Satoru; Muto Yutaka; Yokoyama Shigeyuki
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: Hiyama Takuya B; Ito Takuhiro; Imataka Hiroaki; Yokoyama Shigeyuki
Crystal structure of the alpha subunit of human translation initiation factor 2B.
Journal of molecular biology 2009;392(4):937-51.
2009: Sumida Tomomi; Ishii Ryohei; Yanagisawa Tatsuo; Yokoyama Shigeyuki; Ito Makoto
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: Hosaka Toshiaki; Murayama Kazutaka; Kato-Murayama Miyuki; Urushibata Akiko; Akasaka Ryogo; Terada Takaho; Shirouzu Mikako; Kuramitsu Seiki; Yokoyama Shigeyuki
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: Tsuda Kengo; Kuwasako Kanako; Takahashi Mari; Someya Tatsuhiko; Inoue Makoto; Terada Takaho; Kobayashi Naohiro; Shirouzu Mikako; Kigawa Takanori; Tanaka Akiko; Sugano Sumio; Güntert Peter; Muto Yutaka; Yokoyama Shigeyuki
Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3.
Nucleic acids research 2009;37(15):5151-66.
2009: Kumarevel Thirumananseri; Tanaka Tomoyuki; Umehara Takashi; Yokoyama Shigeyuki
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: Takimoto Koji; Wakiyama Motoaki; Yokoyama Shigeyuki
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: Naganuma Masahiro; Sekine Shun-ichi; Fukunaga Ryuya; Yokoyama Shigeyuki
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: Sakamoto Keiko; Agari Yoshihiro; Agari Kazuko; Yokoyama Shigeyuki; Kuramitsu Seiki; Shinkai Akeo
X-ray crystal structure of a CRISPR-associated RAMP superfamily protein, Cmr5, from Thermus thermophilus HB8.
Proteins 2009;75(2):528-32.
2009: Kurimoto Kazuki; Kuwasako Kanako; Sandercock Alan M; Unzai Satoru; Robinson Carol V; Muto Yutaka; Yokoyama Shigeyuki
AU-rich RNA-binding induces changes in the quaternary structure of AUH.
Proteins 2009;75(2):360-72.
2009: Kawashima Toshiyuki; Bao Ying Chun; Minoshima Yukinori; Nomura Yasushi; Hatori Tomonori; Hori Tetsuya; Fukagawa Tatsuo; Fukada Toshiyuki; Takahashi Noriko; Nosaka Tetsuya; Inoue Makoto; Sato Tomohiro; Kukimoto-Niino Mutsuko; Shirouzu Mikako; Yokoyama Shigeyuki; Kitamura Toshio
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: Wang Hongfei; Takemoto Chie; Akasaka Ryogo; Uchikubo-Kamo Tomomi; Kishishita Seiichiro; Murayama Kazutaka; Terada Takaho; Chen Lirong; Liu Zhi-Jie; Wang Bi-Cheng; Sugano Sumio; Tanaka Akiko; Inoue Makoto; Kigawa Takanori; Shirouzu Mikako; Yokoyama Shigeyuki
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: Sakamoto Kensaku; Murayama Kazutaka; Oki Kenji; Iraha Fumie; Kato-Murayama Miyuki; Takahashi Masahiro; Ohtake Kazumasa; Kobayashi Takatsugu; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
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: Harada Masayo; Murakami Hirotaka; Okawa Akihiko; Okimoto Noriaki; Hiraoka Shuichi; Nakahara Taka; Akasaka Ryogo; Shiraishi Yo-Ichi; Futatsugi Noriyuki; Mizutani-Koseki Yoko; Kuroiwa Atsushi; Shirouzu Mikako; Yokoyama Shigeyuki; Taiji Makoto; Iseki Sachiko; Ornitz David M; Koseki Haruhiko
FGF9 monomer-dimer equilibrium regulates extracellular matrix affinity and tissue diffusion.
Nature genetics 2009;41(3):289-98.
2009: Tokmakov Alexander A; Terazawa Yumiko; Ikeda Mariko; Shirouzu Mikako; Fukami Yasuo; Yokoyama Shigeyuki
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: Kobayashi Takatsugu; Yanagisawa Tatsuo; Sakamoto Kensaku; Yokoyama Shigeyuki
Recognition of non-alpha-amino substrates by pyrrolysyl-tRNA synthetase.
Journal of molecular biology 2009;385(5):1352-60.
2009: Itoh Yuzuru; Sekine Shun-ichi; Matsumoto Eiko; Akasaka Ryogo; Takemoto Chie; Shirouzu Mikako; Yokoyama Shigeyuki
Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs.
Journal of molecular biology 2009;385(5):1456-69.
2009: He Fahu; Dang Weirong; Abe Chikage; Tsuda Kengo; Inoue Makoto; Watanabe Satoru; Kobayashi Naohiro; Kigawa Takanori; Matsuda Takayoshi; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Harada Takushi; Tomabechi Yuri; Terada Takaho; Shirouzu Mikako; Tanaka Akiko; Güntert Peter; Muto Yutaka; Yokoyama Shigeyuki
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.
2009: Haraguchi Yuki; Kuwasako Kanako; Muto Yutaka; Bessho Yoshitaka; Nishimoto Madoka; Yokoyama Shigeyuki; Kanai Akio; Kawai Gota; Sakamoto Taiichi
Characterization of RNA aptamers against SRP19 protein having sequences different from SRP RNA.
Nucleic acids symposium series (2004) 2009;(53):265-6.
2009: Kimoto Michiko; Sato Akira; Kawai Rie; Yokoyama Shigeyuki; Hirao Ichiro
Site-specific incorporation of functional components into RNA by transcription using unnatural base pair systems.
Nucleic acids symposium series (2004) 2009;(53):73-4.
2008: Murayama Kazutaka; Kato-Murayama Miyuki; Mishima Chiemi; Akasaka Ryogo; Shirouzu Mikako; Fukui Yasuhisa; Yokoyama Shigeyuki
Crystal structure of the Bruton's tyrosine kinase PH domain with phosphatidylinositol.
Biochemical and biophysical research communications 2008;377(1):23-8.
2008: Yanagisawa Tatsuo; Ishii Ryohei; Fukunaga Ryuya; Kobayashi Takatsugu; Sakamoto Kensaku; Yokoyama Shigeyuki
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: Ihsanawati; Nishimoto Madoka; Higashijima Kyoko; Shirouzu Mikako; Grosjean Henri; Bessho Yoshitaka; Yokoyama Shigeyuki
Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii.
Journal of molecular biology 2008;383(4):871-84.
2008: Kusano Seisuke; Kukimoto-Niino Mutsuko; Akasaka Ryogo; Toyama Mitsutoshi; Terada Takaho; Shirouzu Mikako; Shindo Takayuki; Yokoyama Shigeyuki
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: Sakamoto Keiko; Agari Yoshihiro; Yokoyama Shigeyuki; Kuramitsu Seiki; Shinkai Akeo
Functional identification of an anti-sigmaE factor from Thermus thermophilus HB8.
Gene 2008;423(2):153-9.
2008: Kukimoto-Niino Mutsuko; Sakamoto Ayako; Kanno Eiko; Hanawa-Suetsugu Kyoko; Terada Takaho; Shirouzu Mikako; Fukuda Mitsunori; Yokoyama Shigeyuki
Structural basis for the exclusive specificity of Slac2-a/melanophilin for the Rab27 GTPases.
Structure (London, England : 1993) 2008;16(10):1478-90.
2008: Jeyakanthan Jeyaraman; Rangarajan Sarani; Mridula P; Kanaujia Shankar Prasad; Shiro Yoshitsugu; Kuramitsu Seiki; Yokoyama Shigeyuki; Sekar Kanagaraj
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: Sarai Naoyuki; Kagawa Wataru; Fujikawa Norie; Saito Kengo; Hikiba Juri; Tanaka Kozo; Miyagawa Kiyoshi; Kurumizaka Hitoshi; Yokoyama Shigeyuki
Biochemical analysis of the N-terminal domain of human RAD54B.
Nucleic acids research 2008;36(17):5441-50.
2008: Agari Yoshihiro; Kashihara Aiko; Yokoyama Shigeyuki; Kuramitsu Seiki; Shinkai Akeo
Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator.
Molecular microbiology 2008;70(1):60-75.
2008: Ragunathan Preethi; Kumarevel Thirumananseri; Agari Yoshihiro; Shinkai Akeo; Kuramitsu Seiki; Yokoyama Shigeyuki; Ponnuraj Karthe
Crystal structure of ST2348, a CBS domain protein, from hyperthermophilic archaeon Sulfolobus tokodaii.
Biochemical and biophysical research communications 2008;375(1):124-8.
2008: Oki Kenji; Sakamoto Kensaku; Kobayashi Takatsugu; Sasaki Hiroshi M; Yokoyama Shigeyuki
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: Goto-Ito Sakurako; Ito Takuhiro; Ishii Ryohei; Muto Yutaka; Bessho Yoshitaka; Yokoyama Shigeyuki
Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.
Proteins 2008;72(4):1274-89.
2008: Kumarevel Thirumananseri; Nakano Noboru; Ponnuraj Karthe; Gopinath Subash C B; Sakamoto Keiko; Shinkai Akeo; Kumar Penmetcha K R; Yokoyama Shigeyuki
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: Nagata Takashi; Suzuki Sakura; Endo Ryuta; Shirouzu Mikako; Terada Takaho; Inoue Makoto; Kigawa Takanori; Kobayashi Naohiro; Güntert Peter; Tanaka Akiko; Hayashizaki Yoshihide; Muto Yutaka; Yokoyama Shigeyuki
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: Minagawa Asako; Ishii Ryohei; Takaku Hiroaki; Yokoyama Shigeyuki; Nashimoto Masayuki
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: Fukunaga Ryuya; Harada Yoko; Hirao Ichiro; Yokoyama Shigeyuki
Phosphoserine aminoacylation of tRNA bearing an unnatural base anticodon.
Biochemical and biophysical research communications 2008;372(3):480-5.
2008: Itoh Yuzuru; Sekine Shun-ichi; Kuroishi Chizu; Terada Takaho; Shirouzu Mikako; Kuramitsu Seiki; Yokoyama Shigeyuki
Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii.
RNA biology 2008;5(3):169-77.
2008: Handa Noriko; Mizohata Eiichi; Kishishita Seiichiro; Toyama Mitsutoshi; Morita Satoshi; Uchikubo-Kamo Tomomi; Akasaka Ryogo; Omori Kenji; Kotera Jun; Terada Takaho; Shirouzu Mikako; Yokoyama Shigeyuki
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: Yamamoto Misaki; Unzai Satoru; Saijo Shinya; Ito Kazuki; Mizutani Kenji; Suno-Ikeda Chiyo; Yabuki-Miyata Yukako; Terada Takaho; Toyama Mitsutoshi; Shirouzu Mikako; Kobayashi Takuya; Kakinuma Yoshimi; Yamato Ichiro; Yokoyama Shigeyuki; Iwata So; Murata Takeshi
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: Mori Masumi; Ogawa Naoko; Tanikawa Kunihiro; Dodo Sanae; Shibayama Sotaro; Yokoyama Shigeyuki; Tanaka Akiko
Contribution of structural biology to clinically validated target proteins.
Drug discovery today 2008;13(11-12):469-72.
2008: Iino Hitoshi; Naitow Hisashi; Nakamura Yuki; Nakagawa Noriko; Agari Yoshihiro; Kanagawa Mayumi; Ebihara Akio; Shinkai Akeo; Sugahara Mitsuaki; Miyano Masashi; Kamiya Nobuo; Yokoyama Shigeyuki; Hirotsu Ken; Kuramitsu Seiki
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: Kuwasako Kanako; Takahashi Mari; Tochio Naoya; Abe Chikage; Tsuda Kengo; Inoue Makoto; Terada Takaho; Shirouzu Mikako; Kobayashi Naohiro; Kigawa Takanori; Taguchi Seiichi; Tanaka Akiko; Hayashizaki Yoshihide; Güntert Peter; Muto Yutaka; Yokoyama Shigeyuki
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: Ebihara Akio; Manzoku Miho; Iino Hitoshi; Kanagawa Mayumi; Shinkai Akeo; Yokoyama Shigeyuki; Kuramitsu Seiki
Crystal structure of uncharacterized protein TTHA1756 from Thermus thermophilus HB8: Structural variety in UPF0150 family proteins.
Proteins 2008;71(4):2097-101.
2008: Kuwasako Kanako; Dohmae Naoshi; Inoue Mio; Shirouzu Mikako; Taguchi Seiichi; Güntert Peter; Séraphin Bertrand; Muto Yutaka; Yokoyama Shigeyuki
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: Padmanabhan Balasundaram; Tong Kit I; Kobayashi Akira; Yamamoto Masayuki; Yokoyama Shigeyuki
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: Yanagisawa Tatsuo; Ishii Ryohei; Fukunaga Ryuya; Kobayashi Takatsugu; Sakamoto Kensaku; Yokoyama Shigeyuki
Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase.
Journal of molecular biology 2008;378(3):634-52.
2008: Kumarevel Thirumananseri; Sakamoto Keiko; Gopinath Subash C B; Shinkai Akeo; Kumar Penmetcha K R; Yokoyama Shigeyuki
Crystal structure of an archaeal specific DNA-binding protein (Ape10b2) from Aeropyrum pernix K1.
Proteins 2008;71(3):1156-62.
2008: Padmanabhan Balasundaram; Nakamura Yoshihiro; Yokoyama Shigeyuki
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: Kishishita Seiichiro; Shimizu Katsumi; Murayama Kazutaka; Terada Takaho; Shirouzu Mikako; Yokoyama Shigeyuki; Kunishima Naoki
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: Yamasaki Kazuhiko; Kigawa Takanori; Inoue Makoto; Watanabe Satoru; Tateno Masaru; Seki Motoaki; Shinozaki Kazuo; Yokoyama Shigeyuki
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: Nishimura Mitsuhiro; Kaminishi Tatsuya; Takemoto Chie; Kawazoe Masahito; Yoshida Takuya; Tanaka Akiko; Sugano Sumio; Shirouzu Mikako; Ohkubo Tadayasu; Yokoyama Shigeyuki; Kobayashi Yuji
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: Ozaki Shogo; Kawakami Hironori; Nakamura Kenta; Fujikawa Norie; Kagawa Wataru; Park Sam-Yong; Yokoyama Shigeyuki; Kurumizaka Hitoshi; Katayama Tsutomu
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: Rangarajan Sarani; Jeyakanthan Jeyaraman; Mridula Palappetty; Sakamoto Keiko; Kitamura Yoshiaki; Agari Yoshihiro; Shinkai Akeo; Ebihara Akio; Kuramitsu Seiki; Yokoyama Shigeyuki; Sekar Kanagaraj
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: Mimasu Shinya; Sengoku Toru; Fukuzawa Seketsu; Umehara Takashi; Yokoyama Shigeyuki
Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A.
Biochemical and biophysical research communications 2008;366(1):15-22.
2008: Agari Yoshihiro; Sato Shinya; Wakamatsu Taisuke; Bessho Yoshitaka; Ebihara Akio; Yokoyama Shigeyuki; Kuramitsu Seiki; Shinkai Akeo
X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7.
Proteins 2008;70(3):1108-11.
2008: Sawano Masahide; Yamamoto Hitoshi; Ogasahara Kyoko; Kidokoro Shun-ichi; Katoh Shizue; Ohnuma Takayuki; Katoh Etsuko; Yokoyama Shigeyuki; Yutani Katsuhide
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: Kuratani Mitsuo; Bessho Yoshitaka; Nishimoto Madoka; Grosjean Henri; Yokoyama Shigeyuki
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: Hara-Yokoyama Miki; Kimura Tomoko; Kaku Hiroaki; Wakiyama Motoaki; Kaitsu Yoko; Inoue Mio; Kusano Seisuke; Shirouzu Mikako; Yokoyama Shigeyuki; Katada Toshiaki; Hirabayashi Yoshio; Takatsu Kiyoshi; Yanagishita Masaki
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: Kumarevel Thirumananseri; Tanaka Tomoyuki; Nishio Megumi; Gopinath Subash C B; Takio Koji; Shinkai Akeo; Kumar Penmetcha K R; Yokoyama Shigeyuki
Crystal structure of the MarR family regulatory protein, ST1710, from Sulfolobus tokodaii strain 7.
Journal of structural biology 2008;161(1):9-17.
2008: Kimoto Michiko; Kawai Rie; Mitsui Tsuneo; Yokoyama Shigeyuki; Hirao Ichiro
Efficient PCR amplification by an unnatural base pair system.
Nucleic acids symposium series (2004) 2008;(52):469-70.
2008: Kimoto Michiko; Kawai Rie; Mitsui Tsuneo; Yokoyama Shigeyuki; Hirao Ichiro
Sequences around the unnatural base pair in DNA templates for efficient replication.
Nucleic acids symposium series (2004) 2008;(52):457-8.
2007: Yabuki Takashi; Motoda Yoko; Hanada Kazuharu; Nunokawa Emi; Saito Miyuki; Seki Eiko; Inoue Makoto; Kigawa Takanori; Yokoyama Shigeyuki
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: Xie Yong; Takemoto Chie; Kishishita Seiichiro; Uchikubo-Kamo Tomomi; Murayama Kazutaka; Chen Lirong; Liu Zhi Jie; Wang Bi Cheng; Manzoku Miho; Ebihara Akio; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
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: Handa Noriko; Kishishita Seiichiro; Morita Satoshi; Akasaka Ryogo; Jin Zhongmin; Chrzas John; Chen Lirong; Liu Zhi-Jie; Wang Bi-Cheng; Sugano Sumio; Tanaka Akiko; Terada Takaho; Shirouzu Mikako; Yokoyama Shigeyuki
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: Kuratani Mitsuo; Yoshikawa Yuka; Bessho Yoshitaka; Higashijima Kyoko; Ishii Takeshi; Shibata Rie; Takahashi Seizo; Yutani Katsuhide; Yokoyama Shigeyuki
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: Hirao Ichiro; Mitsui Tsuneo; Kimoto Michiko; Yokoyama Shigeyuki
An efficient unnatural base pair for PCR amplification.
Journal of the American Chemical Society 2007;129(50):15549-55.
2007: Olsen Shaun K; Ota Naruhisa; Kishishita Seiichiro; Kukimoto-Niino Mutsuko; Murayama Kazutaka; Uchiyama Hidemi; Toyama Mitsutoshi; Terada Takaho; Shirouzu Mikako; Kanagawa Osami; Yokoyama Shigeyuki
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: Shinkai Akeo; Ohbayashi Naomi; Terada Takaho; Shirouzu Mikako; Kuramitsu Seiki; Yokoyama Shigeyuki
Identification of promoters recognized by RNA polymerase-sigmaE holoenzyme from Thermus thermophilus HB8.
Journal of bacteriology 2007;189(23):8758-64.
2007: Kawasaki Y; Sagara M; Shibata Y; Shirouzu M; Yokoyama S; Akiyama T
Identification and characterization of Asef2, a guanine-nucleotide exchange factor specific for Rac1 and Cdc42.
Oncogene 2007;26(55):7620-267.
2007: Nakano Noboru; Kumarevel Thirumananseri; Matsunaga Emiko; Shinkai Akeo; Kuramitsu Seiki; Yokoyama Shigeyuki
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: Nishimura Mitsuhiro; Kaminishi Tatsuya; Kawazoe Masahito; Shirouzu Mikako; Takemoto Chie; Yokoyama Shigeyuki; Tanaka Akiko; Sugano Sumio; Yoshida Takuya; Ohkubo Tadayasu; Kobayashi Yuji
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: Datta Partha P; Wilson Daniel N; Kawazoe Masahito; Swami Neil K; Kaminishi Tatsuya; Sharma Manjuli R; Booth Timothy M; Takemoto Chie; Fucini Paola; Yokoyama Shigeyuki; Agrawal Rajendra K
Structural aspects of RbfA action during small ribosomal subunit assembly.
Molecular cell 2007;28(3):434-45.
2007: Goto-Ito Sakurako; Ishii Ryohei; Ito Takuhiro; Shibata Rie; Fusatomi Emiko; Sekine Shun Ichi; Bessho Yoshitaka; Yokoyama Shigeyuki
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: Kimoto Michiko; Moriyama Kei; Yokoyama Shigeyuki; Hirao Ichiro
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: Shinkai Akeo; Sekine Shun-Ichi; Urushibata Akiko; Terada Takaho; Shirouzu Mikako; Yokoyama Shigeyuki
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: Kobayashi Naohiro; Iwahara Junji; Koshiba Seizo; Tomizawa Tadashi; Tochio Naoya; Güntert Peter; Kigawa Takanori; Yokoyama Shigeyuki
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: Suzuki Sakura; Tatsuguchi Ayako; Matsumoto Eiko; Kawazoe Masahito; Kaminishi Tatsuya; Shirouzu Mikako; Muto Yutaka; Takemoto Chie; Yokoyama Shigeyuki
Structural characterization of the ribosome maturation protein, RimM.
Journal of bacteriology 2007;189(17):6397-406.
2007: Keyamura Kenji; Fujikawa Norie; Ishida Takuma; Ozaki Shogo; Su'etsugu Masayuki; Fujimitsu Kazuyuki; Kagawa Wataru; Yokoyama Shigeyuki; Kurumizaka Hitoshi; Katayama Tsutomu
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: Ishii Ryohei; Minagawa Asako; Takaku Hiroaki; Takagi Masamichi; Nashimoto Masayuki; Yokoyama Shigeyuki
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: He Fahu; Umehara Takashi; Tsuda Kengo; Inoue Makoto; Kigawa Takanori; Matsuda Takayoshi; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Terada Takaho; Shirouzu Mikako; Tanaka Akiko; Sugano Sumio; Muto Yutaka; Yokoyama Shigeyuki
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: Doi-Katayama Yukiko; Hayashi Fumiaki; Inoue Makoto; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Kigawa Takanori; Yoshida Mayumi; Shirouzu Mikako; Terada Takaho; Hayashizaki Yoshihide; Yokoyama Shigeyuki; Hirota Hiroshi
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: Nakamura Yoshihiro; Umehara Takashi; Tanaka Akiko; Horikoshi Masami; Padmanabhan Balasundaram; Yokoyama Shigeyuki
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: Umehara Takashi; Wakamori Masatoshi; Tanaka Akiko; Padmanabhan Balasundaram; Yokoyama Shigeyuki
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: Masutani Mamiko; Sonenberg Nahum; Yokoyama Shigeyuki; Imataka Hiroaki
Reconstitution reveals the functional core of mammalian eIF3.
The EMBO journal 2007;26(14):3373-83.
2007: Inagaki Eiji; Ohshima Noriyasu; Sakamoto Keiko; Babayeva Nigar D; Kato Hiroaki; Yokoyama Shigeyuki; Tahirov Tahir H
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: Fukunaga Ryuya; Yokoyama Shigeyuki
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: Nakamura Yoshihiro; Umehara Takashi; Hamana Hiroaki; Hayashizaki Yoshihide; Inoue Makoto; Kigawa Takanori; Shirouzu Mikako; Terada Takaho; Tanaka Akiko; Padmanabhan Balasundaram; Yokoyama Shigeyuki
Crystal structure analysis of the PHD domain of the transcription co-activator Pygopus.
Journal of molecular biology 2007;370(1):80-92.
2007: Kobayashi Tominari; Mikami Satoshi; Yokoyama Shigeyuki; Imataka Hiroaki
An improved cell-free system for picornavirus synthesis.
Journal of virological methods 2007;142(1-2):182-8.
2007: Kanaujia Shankar Prasad; Ranjani Chellamuthu Vasuki; Jeyakanthan Jeyaraman; Nishida Masami; Kitamura Yoshiaki; Baba Seiki; Ebihara Akio; Shimizu Nobutaka; Nakagawa Noriko; Shinkai Akeo; Yamamoto Masaki; Kuramitsu Seiki; Shiro Yoshitsugu; Sekar Kanagaraj; Yokoyama Shigeyuki
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: Shimada Atsushi; Niwa Hideaki; Tsujita Kazuya; Suetsugu Shiro; Nitta Koji; Hanawa-Suetsugu Kyoko; Akasaka Ryogo; Nishino Yuri; Toyama Mitsutoshi; Chen Lirong; Liu Zhi-Jie; Wang Bi-Cheng; Yamamoto Masaki; Terada Takaho; Miyazawa Atsuo; Tanaka Akiko; Sugano Sumio; Shirouzu Mikako; Nagayama Kuniaki; Takenawa Tadaomi; Yokoyama Shigeyuki
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: Bessho Yoshitaka; Shibata Rie; Sekine Shun-ichi; Murayama Kazutaka; Higashijima Kyoko; Hori-Takemoto Chie; Shirouzu Mikako; Kuramitsu Seiki; Yokoyama Shigeyuki
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: Yoneyama Misao; Tochio Naoya; Umehara Takashi; Koshiba Seizo; Inoue Makoto; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Watanabe Satoru; Tomo Yasuko; Nishimura Yuji; Harada Takushi; Terada Takaho; Shirouzu Mikako; Hayashizaki Yoshihide; Ohara Osamu; Tanaka Akiko; Kigawa Takanori; Yokoyama Shigeyuki
Structural and functional differences of SWIRM domain subtypes.
Journal of molecular biology 2007;369(1):222-38.
2007: Fukunaga Ryuya; Yokoyama Shigeyuki
The C-terminal domain of the archaeal leucyl-tRNA synthetase prevents misediting of isoleucyl-tRNA(Ile).
Biochemistry 2007;46(17):4985-96.
2007: Shinkai Akeo; Kira Satoshi; Nakagawa Noriko; Kashihara Aiko; Kuramitsu Seiki; Yokoyama Shigeyuki
Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8.
Journal of bacteriology 2007;189(10):3891-901.
2007: Arai Ryoichi; Ito Kaori; Ohnishi Tetsuo; Ohba Hisako; Akasaka Ryogo; Bessho Yoshitaka; Hanawa-Suetsugu Kyoko; Yoshikawa Takeo; Shirouzu Mikako; Yokoyama Shigeyuki
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: Kanaujia Shankar Prasad; Ranjani Chellamuthu Vasuki; Jeyakanthan Jeyaraman; Ohmori Miwa; Agari Kazuko; Kitamura Yoshiaki; Baba Seiki; Ebihara Akio; Shinkai Akeo; Kuramitsu Seiki; Shiro Yoshitsugu; Sekar Kanagaraj; Yokoyama Shigeyuki
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: Fukunaga Ryuya; Yokoyama Shigeyuki
Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.
Nature structural & molecular biology 2007;14(4):272-9.
2007: Takada Kazuma; Takemoto Chie; Kawazoe Masahito; Konno Takayuki; Hanawa-Suetsugu Kyoko; Lee Sungga; Shirouzu Mikako; Yokoyama Shigeyuki; Muto Akira; Himeno Hyouta
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: Himeno Hyouta; Kurita Daisuke; Takada Kazuma; Konno Takayuki; Hanawa-Suetsugu Kyoko; Takemoto Chie; Kawazoe Masahito; Yokoyama Shigeyuki; Nameki Nobukazu; Kawai Gota; Muto Akira
[Molecular mechanism of trans-translation]
Seikagaku. The Journal of Japanese Biochemical Society 2007;79(3):213-21.
2007: Kaminishi Tatsuya; Wilson Daniel N; Takemoto Chie; Harms Joerg M; Kawazoe Masahito; Schluenzen Frank; Hanawa-Suetsugu Kyoko; Shirouzu Mikako; Fucini Paola; Yokoyama Shigeyuki
A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction.
Structure (London, England : 1993) 2007;15(3):289-97.
2007: Connell Sean R; Takemoto Chie; Wilson Daniel N; Wang Hongfei; Murayama Kazutaka; Terada Takaho; Shirouzu Mikako; Rost Maximilian; Schüler Martin; Giesebrecht Jan; Dabrowski Marylena; Mielke Thorsten; Fucini Paola; Yokoyama Shigeyuki; Spahn Christian M T
Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
Molecular cell 2007;25(5):751-64.
2007: Fukunaga Ryuya; Yokoyama Shigeyuki
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: Nakamura Yoshihiro; Umehara Takashi; Tanaka Akiko; Horikoshi Masami; Padmanabhan Balasundaram; Yokoyama Shigeyuki
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: Okazaki Nobuo; Kumei Maki; Manzoku Miho; Kuramitsu Seiki; Shirouzu Mikako; Shinkai Akeo; Yokoyama Shigeyuki
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: Fukunaga Ryuya; Yokoyama Shigeyuki
Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii.
Acta crystallographica. Section D, Biological crystallography 2007;63(Pt 3):390-400.
2007: Yoshikawa Seiko; Arai Ryoichi; Kinoshita Yukiko; Uchikubo-Kamo Tomomi; Wakamatsu Taisuke; Akasaka Ryogo; Masui Ryoji; Terada Takaho; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
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: Shibata Rie; Bessho Yoshitaka; Shinkai Akeo; Nishimoto Madoka; Fusatomi Emiko; Terada Takaho; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structure and RNA-binding analysis of the archaeal transcription factor NusA.
Biochemical and biophysical research communications 2007;355(1):122-8.
2007: Dong Xuesong; Kato-Murayama Miyuki; Muramatsu Tomonari; Mori Hirotada; Shirouzu Mikako; Bessho Yoshitaka; Yokoyama Shigeyuki
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: Matsuda Takayoshi; Koshiba Seizo; Tochio Naoya; Seki Eiko; Iwasaki Noriyuki; Yabuki Takashi; Inoue Makoto; Yokoyama Shigeyuki; Kigawa Takanori
Improving cell-free protein synthesis for stable-isotope labeling.
Journal of biomolecular NMR 2007;37(3):225-9.
2007: Perez G I; Acton B M; Jurisicova A; Perkins G A; White A; Brown J; Trbovich A M; Kim M-R; Fissore R; Xu J; Ahmady A; D'Estaing S G; Li H; Kagawa W; Kurumizaka H; Yokoyama S; Okada H; Mak T W; Ellisman M H; Casper R F; Tilly J L
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: Yoshitani Naoei; Saito Kazuki; Saikawa Wakana; Asanuma Miwako; Yokoyama Shigeyuki; Hirota Hiroshi
NTA-mediated protein capturing strategy in screening experiments for small organic molecules by surface plasmon resonance.
Proteomics 2007;7(4):494-9.
2007: Nakamura Yoshihiro; Nakano Kazumi; Umehara Takashi; Kimura Mayumi; Hayashizaki Yoshihide; Tanaka Akiko; Horikoshi Masami; Padmanabhan Balasundaram; Yokoyama Shigeyuki
Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome.
Structure (London, England : 1993) 2007;15(2):179-89.
2007: Kanaujia Shankar Prasad; Ranjani Chellamuthu Vasuki; Jeyakanthan Jeyaraman; Baba Seiki; Kuroishi Chizu; Ebihara Akio; Shinkai Akeo; Kuramitsu Seiki; Shiro Yoshitsugu; Sekar Kanagaraj; Yokoyama Shigeyuki
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: Tanaka Hiroaki; Umehara Takashi; Inaka Koji; Takahashi Sachiko; Shibata Rie; Bessho Yoshitaka; Sato Masaru; Sugiyama Shigeru; Fusatomi Emiko; Terada Takaho; Shirouzu Mikako; Sano Satoshi; Motohara Moritoshi; Kobayashi Tomoyuki; Tanaka Tetsuo; Tanaka Akiko; Yokoyama Shigeyuki
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: Kondo Naoyuki; Nakagawa Noriko; Ebihara Akio; Chen Lirong; Liu Zhi-Jie; Wang Bi-Cheng; Yokoyama Shigeyuki; Kuramitsu Seiki; Masui Ryoji
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: Ohnishi Satoshi; Güntert Peter; Koshiba Seizo; Tomizawa Tadashi; Akasaka Ryogo; Tochio Naoya; Sato Manami; Inoue Makoto; Harada Takushi; Watanabe Satoru; Tanaka Akiko; Shirouzu Mikako; Kigawa Takanori; Yokoyama Shigeyuki
Solution structure of an atypical WW domain in a novel beta-clam-like dimeric form.
FEBS letters 2007;581(3):462-8.
2007: Murayama Kazutaka; Shirouzu Mikako; Kawasaki Yoshihiro; Kato-Murayama Miyuki; Hanawa-Suetsugu Kyoko; Sakamoto Ayako; Katsura Yasuhiro; Suenaga Atsushi; Toyama Mitsutoshi; Terada Takaho; Taiji Makoto; Akiyama Tetsu; Yokoyama Shigeyuki
Crystal structure of the rac activator, Asef, reveals its autoinhibitory mechanism.
The Journal of biological chemistry 2007;282(7):4238-42.
2007: Nakamura Yoshihiro; Umehara Takashi; Nakano Kazumi; Jang Moon Kyoo; Shirouzu Mikako; Morita Satoshi; Uda-Tochio Hiroko; Hamana Hiroaki; Terada Takaho; Adachi Naruhiko; Matsumoto Takehisa; Tanaka Akiko; Horikoshi Masami; Ozato Keiko; Padmanabhan Balasundaram; Yokoyama Shigeyuki
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: Kodama Koichiro; Fukuzawa Seketsu; Nakayama Hiroshi; Sakamoto Kensaku; Kigawa Takanori; Yabuki Takashi; Matsuda Natsuko; Shirouzu Mikako; Takio Koji; Yokoyama Shigeyuki; Tachibana Kazuo
Site-specific functionalization of proteins by organopalladium reactions.
Chembiochem : a European journal of chemical biology 2007;8(2):232-8.
2007: Kanaujia Shankar Prasad; Ranjani Chellamuthu Vasuki; Jeyakanthan Jeyaraman; Baba Seiki; Chen Lirong; Liu Zhi-Jie; Wang Bi-Cheng; Nishida Masami; Ebihara Akio; Shinkai Akeo; Kuramitsu Seiki; Shiro Yoshitsugu; Sekar Kanagaraj; Yokoyama Shigeyuki
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.
2007: Takada Kazuma; Takemoto Chie; Kawazoe Masahito; Shirouzu Mikako; Yokoyama Shigeyuki; Muto Akira; Himeno Hyouta
Thermus thermophilus tmRNA and trans-translation.
Nucleic acids symposium series (2004) 2007;(51):369-70.
2007: Hirao Ichiro; Mitsui Tsuneo; Kimoto Michiko; Yokoyama Shigeyuki
Development of an unnatural base pair for efficient PCR amplification.
Nucleic acids symposium series (2004) 2007;(51):9-10.
2007: Kimoto Michiko; Mitsui Tsuneo; Harada Yoko; Sato Akira; Yokoyama Shigeyuki; Hirao Ichiro
Fluorescent probing for RNA molecules by an unnatural base-pair system.
Nucleic acids research 2007;35(16):5360-9.
2006: Hiyama Takuya B; Zhao Min; Kitago Yu; Yao Min; Sekine Shun-Ichi; Terada Takaho; Kuroishi Chizu; Liu Zhi-Jie; Rose John P; Kuramitsu Seiki; Shirouzu Mikako; Watanabe Nobuhisa; Yokoyama Shigeyuki; Tanaka Isao; Wang Bi-Cheng
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: Sekine Shun-ichi; Shichiri Mika; Bernier Stéphane; Chênevert Robert; Lapointe Jacques; Yokoyama Shigeyuki
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: Handa Noriko; Kukimoto-Niino Mutsuko; Akasaka Ryogo; Murayama Kazutaka; Terada Takaho; Inoue Makoto; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Nunokawa Emi; Tanaka Akiko; Hayashizaki Yoshihide; Kigawa Takanori; Shirouzu Mikako; Yokoyama Shigeyuki
Structure of the UNC5H2 death domain.
Acta crystallographica. Section D, Biological crystallography 2006;62(Pt 12):1502-9.
2006: Mikami Satoshi; Kobayashi Tominari; Yokoyama Shigeyuki; Imataka Hiroaki
A hybridoma-based in vitro translation system that efficiently synthesizes glycoproteins.
Journal of biotechnology 2006;127(1):65-78.
2006: Tochio Naoya; Koshiba Seizo; Kobayashi Naohiro; Inoue Makoto; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Tomo Yasuko; Motoda Yoko; Kobayashi Atsuo; Tanaka Akiko; Hayashizaki Yoshihide; Terada Takaho; Shirouzu Mikako; Kigawa Takanori; Yokoyama Shigeyuki
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: Suetsugu Shiro; Murayama Kazutaka; Sakamoto Ayako; Hanawa-Suetsugu Kyoko; Seto Azusa; Oikawa Tsukasa; Mishima Chiemi; Shirouzu Mikako; Takenawa Tadaomi; Yokoyama Shigeyuki
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: Morikubo Noriko; Fukuda Yoriyuki; Ohtake Kazumasa; Shinya Naoko; Kiga Daisuke; Sakamoto Kensaku; Asanuma Miwako; Hirota Hiroshi; Yokoyama Shigeyuki; Hoshino Tsutomu
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: Sasaki Hiroshi M; Sekine Shun-ichi; Sengoku Toru; Fukunaga Ryuya; Hattori Motoyuki; Utsunomiya Yukiko; Kuroishi Chizu; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
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: Schluenzen Frank; Takemoto Chie; Wilson Daniel N; Kaminishi Tatsuya; Harms Joerg M; Hanawa-Suetsugu Kyoko; Szaflarski Witold; Kawazoe Masahito; Shirouzu Mikako; Nierhaus Knud H; Yokoyama Shigeyuki; Fucini Paola
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: Kodama Koichiro; Fukuzawa Seketsu; Sakamoto Kensaku; Nakayama Hiroshi; Kigawa Takanori; Yabuki Takashi; Matsuda Natsuko; Shirouzu Mikako; Takio Koji; Tachibana Kazuo; Yokoyama Shigeyuki
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: Handa Noriko; Kukimoto-Niino Mutsuko; Akasaka Ryogo; Kishishita Seiichiro; Murayama Kazutaka; Terada Takaho; Inoue Makoto; Kigawa Takanori; Kose Shingo; Imamoto Naoko; Tanaka Akiko; Hayashizaki Yoshihide; Shirouzu Mikako; Yokoyama Shigeyuki
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: Kukimoto-Niino Mutsuko; Takagi Tetsuo; Akasaka Ryogo; Murayama Kazutaka; Uchikubo-Kamo Tomomi; Terada Takaho; Inoue Makoto; Watanabe Satoru; Tanaka Akiko; Hayashizaki Yoshihide; Kigawa Takanori; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structure of the RUN domain of the RAP2-interacting protein x.
The Journal of biological chemistry 2006;281(42):31843-53.
2006: Tokmakov Alexander A; Terazawa Yumiko; Ikeda Mariko; Shirouzu Mikako; Yokoyama Shigeyuki
Coupled transcription-and-translation in Xenopus oocyte and egg extracts.
Journal of biotechnology 2006;125(4):557-64.
2006: Nakano Noboru; Okazaki Nobuo; Satoh Shinya; Takio Koji; Kuramitsu Seiki; Shinkai Akeo; Yokoyama Shigeyuki
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: Inagaki Eiji; Ohshima Noriyasu; Takahashi Hitomi; Kuroishi Chizu; Yokoyama Shigeyuki; Tahirov Tahir H
Crystal structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase.
Journal of molecular biology 2006;362(3):490-501.
2006: Hirao Ichiro; Kimoto Michiko; Mitsui Tsuneo; Fujiwara Tsuyoshi; Kawai Rie; Sato Akira; Harada Yoko; Yokoyama Shigeyuki
An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA.
Nature methods 2006;3(9):729-35.
2006: Okumura Hiromi; Nakazawa Junko; Tsuganezawa Keiko; Usui Takeo; Osada Hiroyuki; Matsumoto Takehisa; Tanaka Akiko; Yokoyama Shigeyuki
Phenothiazine and carbazole-related compounds inhibit mitotic kinesin Eg5 and trigger apoptosis in transformed culture cells.
Toxicology letters 2006;166(1):44-52.
2006: Dong Xuesong; Bessho Yoshitaka; Shibata Rie; Nishimoto Madoka; Shirouzu Mikako; Kuramitsu Seiki; Yokoyama Shigeyuki
Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8.
RNA biology 2006;3(3):115-22.
2006: Tanaka Tomoyuki; Sawano Masahide; Ogasahara Kyoko; Sakaguchi Yasushi; Bagautdinov Bagautdin; Katoh Etsuko; Kuroishi Chizu; Shinkai Akeo; Yokoyama Shigeyuki; Yutani Katsuhide
Hyper-thermostability of CutA1 protein, with a denaturation temperature of nearly 150 degrees C.
FEBS letters 2006;580(17):4224-30.
2006: Iwasaki Wataru; Sekine Shun-ichi; Kuroishi Chizu; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase.
Journal of molecular biology 2006;360(2):329-42.
2006: Hattori Motoyuki; Mizohata Eiichi; Tatsuguchi Ayako; Shibata Rie; Kishishita Seiichiro; Murayama Kazutaka; Terada Takaho; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structure of the single-domain rhodanese homologue TTHA0613 from Thermus thermophilus HB8.
Proteins 2006;64(1):284-7.
2006: Matsuda Takayoshi; Kigawa Takanori; Koshiba Seizo; Inoue Makoto; Aoki Masaaki; Yamasaki Kazuhiko; Seki Motoaki; Shinozaki Kazuo; Yokoyama Shigeyuki
Cell-free synthesis of zinc-binding proteins.
Journal of structural and functional genomics 2006;7(2):93-100.
2006: Fukunaga Ryuya; Yokoyama Shigeyuki
Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase.
Journal of molecular biology 2006;359(4):901-12.
2006: Minagawa Asako; Takaku Hiroaki; Shibata Hirotaka S; Ishii Ryohei; Takagi Masamichi; Yokoyama Shigeyuki; Nashimoto Masayuki
Substrate recognition ability differs among various prokaryotic tRNase Zs.
Biochemical and biophysical research communications 2006;345(1):385-93.
2006: Ito Kaori; Arai Ryoichi; Fusatomi Emiko; Kamo-Uchikubo Tomomi; Kawaguchi Shin-Ichi; Akasaka Ryogo; Terada Takaho; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
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: Hamada Toshiyuki; Ito Yoko; Abe Takamasa; Hayashi Fumiaki; Güntert Peter; Inoue Makoto; Kigawa Takanori; Terada Takaho; Shirouzu Mikako; Yoshida Mayumi; Tanaka Akiko; Sugano Sumio; Yokoyama Shigeyuki; Hirota Hiroshi
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: Wakiyama Motoaki; Kaitsu Yoko; Yokoyama Shigeyuki
Cell-free translation system from Drosophila S2 cells that recapitulates RNAi.
Biochemical and biophysical research communications 2006;343(4):1067-71.
2006: Sengoku Toru; Nureki Osamu; Nakamura Akira; Kobayashi Satoru; Yokoyama Shigeyuki
Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.
Cell 2006;125(2):287-300.
2006: Arai Ryoichi; Yoshikawa Seiko; Murayama Kazutaka; Imai Yuzuru; Takahashi Ryosuke; Shirouzu Mikako; Yokoyama Shigeyuki
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: Yamasaki Kazuhiko; Kigawa Takanori; Inoue Makoto; Yamasaki Tomoko; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Tomo Yasuko; Terada Takaho; Shirouzu Mikako; Tanaka Akiko; Seki Motoaki; Shinozaki Kazuo; Yokoyama Shigeyuki
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: Hondoh Takayuki; Kato Atsushi; Yokoyama Shigeyuki; Kuroda Yutaka
Computer-aided NMR assay for detecting natively folded structural domains.
Protein science : a publication of the Protein Society 2006;15(4):871-83.
2006: Mikami Satoshi; Masutani Mamiko; Sonenberg Nahum; Yokoyama Shigeyuki; Imataka Hiroaki
An efficient mammalian cell-free translation system supplemented with translation factors.
Protein expression and purification 2006;46(2):348-57.
2006: Chumpolkulwong Namthip; Sakamoto Kensaku; Hayashi Akiko; Iraha Fumie; Shinya Naoko; Matsuda Natsuko; Kiga Daisuke; Urushibata Akiko; Shirouzu Mikako; Oki Kenji; Kigawa Takanori; Yokoyama Shigeyuki
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: Tochio Naoya; Umehara Takashi; Koshiba Seizo; Inoue Makoto; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Watanabe Satoru; Tomo Yasuko; Hanada Masaru; Ikari Masaomi; Sato Miyuki; Terada Takaho; Nagase Takahiro; Ohara Osamu; Shirouzu Mikako; Tanaka Akiko; Kigawa Takanori; Yokoyama Shigeyuki
Solution structure of the SWIRM domain of human histone demethylase LSD1.
Structure (London, England : 1993) 2006;14(3):457-68.
2006: Padmanabhan Balasundaram; Tong Kit I; Ohta Tsutomu; Nakamura Yoshihiro; Scharlock Maria; Ohtsuji Makiko; Kang Moon-Il; Kobayashi Akira; Yokoyama Shigeyuki; Yamamoto Masayuki
Structural basis for defects of Keap1 activity provoked by its point mutations in lung cancer.
Molecular cell 2006;21(5):689-700.
2006: Enomoto Rima; Kinebuchi Takashi; Sato Makoto; Yagi Hideshi; Kurumizaka Hitoshi; Yokoyama Shigeyuki
Stimulation of DNA strand exchange by the human TBPIP/Hop2-Mnd1 complex.
The Journal of biological chemistry 2006;281(9):5575-81.
2006: Tokmakov Alexander A; Matsumoto Eiko; Shirouzu Mikako; Yokoyama Shigeyuki
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: Inagaki Eiji; Sakamoto Keiko; Obayashi Naomi; Terada Takaho; Shirouzu Mikako; Bessho Yoshitaka; Kuroishi Chizu; Kuramitsu Seiki; Shinkai Akeo; Yokoyama Shigeyuki
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: Arai Ryoichi; Kukimoto-Niino Mutsuko; Kuroishi Chizu; Bessho Yoshitaka; Shirouzu Mikako; Yokoyama Shigeyuki
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: Komiya Ken; Sakamoto Kensaku; Kameda Atsushi; Yamamoto Masahito; Ohuchi Azuma; Kiga Daisuke; Yokoyama Shigeyuki; Hagiya Masami
DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing.
Bio Systems 2006;83(1):18-25.
2006: Kuratani Mitsuo; Sakai Hiroaki; Takahashi Masahiro; Yanagisawa Tatsuo; Kobayashi Takatsugu; Murayama Kazutaka; Chen Lirong; Liu Zhi-Jie; Wang Bi-Cheng; Kuroishi Chizu; Kuramitsu Seiki; Terada Takaho; Bessho Yoshitaka; Shirouzu Mikako; Sekine Shun-ichi; Yokoyama Shigeyuki
Crystal structures of tyrosyl-tRNA synthetases from Archaea.
Journal of molecular biology 2006;355(3):395-408.
2006: Kodama Koichiro; Fukuzawa Seketsu; Nakayama Hiroshi; Kigawa Takanori; Sakamoto Kensaku; Yabuki Takashi; Matsuda Natsuko; Shirouzu Mikako; Takio Koji; Tachibana Kazuo; Yokoyama Shigeyuki
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: Hino Nobumasa; Hayashi Akiko; Sakamoto Kensaku; Yokoyama Shigeyuki
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: Hirao Ichiro; Kimoto Michiko; Mitsui Tsuneo; Fujiwara Tsuyoshi; Kawai Rie; Sato Akira; Harada Yoko; Yokoyama Shigeyuki
An unnatural base pair system for in vitro replication and transcription.
Nucleic acids symposium series (2004) 2006;(50):33-4.
2006: Sarai Naoyuki; Kagawa Wataru; Kinebuchi Takashi; Kagawa Ako; Tanaka Kozo; Miyagawa Kiyoshi; Ikawa Shukuko; Shibata Takehiko; Kurumizaka Hitoshi; Yokoyama Shigeyuki
Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein.
Nucleic acids research 2006;34(16):4429-37.
2006: Minagawa Asako; Takaku Hiroaki; Ishii Ryohei; Takagi Masamichi; Yokoyama Shigeyuki; Nashimoto Masayuki
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: Miyazaki Satoshi; Kuroda Yutaka; Yokoyama Shigeyuki
Identification of putative domain linkers by a neural network - application to a large sequence database.
BMC bioinformatics 2006;7():323.
2006: Tanaka Takanori; Yokoyama Shigeyuki; Kuroda Yutaka
Improvement of domain linker prediction by incorporating loop-length-dependent characteristics.
Biopolymers 2006;84(2):161-8.
2005: Padmanabhan Balasundaram; Kataoka Kazuhiro; Umehara Takashi; Adachi Naruhiko; Yokoyama Shigeyuki; Horikoshi Masami
Structural similarity between histone chaperone Cia1p/Asf1p and DNA-binding protein NF-kappaB.
Journal of biochemistry 2005;138(6):821-9.
2005: Nameki Nobukazu; Someya Tatsuhiko; Okano Satoshi; Suemasa Reiko; Kimoto Michiko; Hanawa-Suetsugu Kyoko; Terada Takaho; Shirouzu Mikako; Hirao Ichiro; Takaku Hiroshi; Himeno Hyouta; Muto Akira; Kuramitsu Seiki; Yokoyama Shigeyuki; Kawai Gota
Interaction analysis between tmRNA and SmpB from Thermus thermophilus.
Journal of biochemistry 2005;138(6):729-39.
2005: Kawai Rie; Kimoto Michiko; Ikeda Shuji; Mitsui Tsuneo; Endo Masayuki; Yokoyama Shigeyuki; Hirao Ichiro
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: Hattori Motoyuki; Mizohata Eiichi; Manzoku Miho; Bessho Yoshitaka; Murayama Kazutaka; Terada Takaho; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8.
Proteins 2005;61(4):1117-20.
2005: Tanaka Yoshinori; Tachiwana Hiroaki; Yoda Kinya; Masumoto Hiroshi; Okazaki Tsuneko; Kurumizaka Hitoshi; Yokoyama Shigeyuki
Human centromere protein B induces translational positioning of nucleosomes on alpha-satellite sequences.
The Journal of biological chemistry 2005;280(50):41609-18.
2005: Umehara Takashi; Otta Yumi; Tsuganezawa Keiko; Matsumoto Takehisa; Tanaka Akiko; Horikoshi Masami; Padmanabhan Balasundaram; Yokoyama Shigeyuki
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: Mizohata Eiichi; Sakai Hiroaki; Fusatomi Emiko; Terada Takaho; Murayama Kazutaka; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon Aeropyrum pernix K1.
Journal of molecular biology 2005;354(2):317-29.
2005: Pioszak Augen A; Murayama Kazutaka; Nakagawa Noriko; Ebihara Akio; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
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: Fukunaga Ryuya; Yokoyama Shigeyuki
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: Tukalo Michael; Yaremchuk Anna; Fukunaga Ryuya; Yokoyama Shigeyuki; Cusack Stephen
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: Tanaka Yoko; Nakagawa Noriko; Kuramitsu Seiki; Yokoyama Shigeyuki; Masui Ryoji
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: Lokanath Neratur K; Ohshima Noriyasu; Takio Koji; Shiromizu Ikuya; Kuroishi Chizu; Okazaki Nobuo; Kuramitsu Seiki; Yokoyama Shigeyuki; Miyano Masashi; Kunishima Naoki
Crystal structure of novel NADP-dependent 3-hydroxyisobutyrate dehydrogenase from Thermus thermophilus HB8.
Journal of molecular biology 2005;352(4):905-17.
2005: Kunishima Naoki; Asada Yukuhiko; Sugahara Mayumi; Ishijima Jun; Nodake Yuichi; Sugahara Mitsuaki; Miyano Masashi; Kuramitsu Seiki; Yokoyama Shigeyuki; Sugahara Michihiro
A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAI.
Journal of molecular biology 2005;352(1):212-28.
2005: Li Hua; Inoue Makoto; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Nunokawa Emi; Motoda Yoko; Kobayashi Atsuo; Terada Takaho; Shirouzu Mikako; Koshiba Seizo; Lin Yi-Jan; Güntert Peter; Suzuki Harukazu; Hayashizaki Yoshihide; Kigawa Takanori; Yokoyama Shigeyuki
Solution structure of the mouse enhancer of rudimentary protein reveals a novel fold.
Journal of biomolecular NMR 2005;32(4):329-34.
2005: Fukunaga Ryuya; Yokoyama Shigeyuki
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: Kinebuchi Takashi; Kagawa Wataru; Kurumizaka Hitoshi; Yokoyama Shigeyuki
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: Arai Ryoichi; Kukimoto-Niino Mutsuko; Uda-Tochio Hiroko; Morita Satoshi; Uchikubo-Kamo Tomomi; Akasaka Ryogo; Etou Yuuka; Hayashizaki Yoshihide; Kigawa Takanori; Terada Takaho; Shirouzu Mikako; Yokoyama Shigeyuki
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: Mitsui Tsuneo; Kimoto Michiko; Harada Yoko; Yokoyama Shigeyuki; Hirao Ichiro
An efficient unnatural base pair for a base-pair-expanded transcription system.
Journal of the American Chemical Society 2005;127(24):8652-8.
2005: Arai Ryoichi; Nishimoto Madoka; Toyama Mitsutoshi; Terada Takaho; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
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: Wakiyama Motoaki; Matsumoto Tomoko; Yokoyama Shigeyuki
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: Taka Junichiro; Ogasahara Kyoko; Jeyakanthan Jeyaraman; Kunishima Naoki; Kuroishi Chizu; Sugahara Mitsuaki; Yokoyama Shigeyuki; Yutani Katsuhide
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: Kurokawa Sayuri; Bessho Yoshitaka; Higashijima Kyoko; Shirouzu Mikako; Yokoyama Shigeyuki; Watanabe Kazuo I; Ohama Takeshi
Adaptation of intronic homing endonuclease for successful horizontal transmission.
The FEBS journal 2005;272(10):2487-96.
2005: Ishihara Goshi; Goto Mie; Saeki Mihoro; Ito Kaori; Hori Tetsuya; Kigawa Takanori; Shirouzu Mikako; Yokoyama Shigeyuki
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: Ohashi Wakana; Inouye Satoshi; Yamazaki Toshio; Doi-Katayama Yukiko; Yokoyama Shigeyuki; Hirota Hiroshi
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: Scott Anna; Pantoja-Uceda David; Koshiba Seizo; Inoue Makoto; Kigawa Takanori; Terada Takaho; Shirouzu Mikako; Tanaka Akiko; Sugano Sumio; Yokoyama Shigeyuki; Güntert Peter
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: Sharma Manjuli R; Barat Chandana; Wilson Daniel N; Booth Timothy M; Kawazoe Masahito; Hori-Takemoto Chie; Shirouzu Mikako; Yokoyama Shigeyuki; Fucini Paola; Agrawal Rajendra K
Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly.
Molecular cell 2005;18(3):319-29.
2005: Kato-Murayama Miyuki; Bessho Yoshitaka; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structure of the RNA 2'-phosphotransferase from Aeropyrum pernix K1.
Journal of molecular biology 2005;348(2):295-305.
2005: Yamasaki Kazuhiko; Kigawa Takanori; Inoue Makoto; Yamasaki Tomoko; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Tomo Yasuko; Terada Takaho; Shirouzu Mikako; Tanaka Akiko; Seki Motoaki; Shinozaki Kazuo; Yokoyama Shigeyuki
Solution structure of the major DNA-binding domain of Arabidopsis thaliana ethylene-insensitive3-like3.
Journal of molecular biology 2005;348(2):253-64.
2005: Yoshitani Naoei; Satou Kazuhito; Saito Kazuki; Suzuki Sakura; Hatanaka Hideki; Seki Motoaki; Shinozaki Kazuo; Hirota Hiroshi; Yokoyama Shigeyuki
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: Kurimoto Kazuki; Muto Yutaka; Obayashi Naomi; Terada Takaho; Shirouzu Mikako; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Kigawa Takanori; Okumura Hiromi; Tanaka Akiko; Shibata Norito; Kashikawa Maki; Agata Kiyokazu; Yokoyama Shigeyuki
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: Handa Noriko; Terada Takaho; Doi-Katayama Yukiko; Hirota Hiroshi; Tame Jeremy R H; Park Sam-Yong; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
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: Ishii Ryohei; Minagawa Asako; Takaku Hiroaki; Takagi Masamichi; Nashimoto Masayuki; Yokoyama Shigeyuki
Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima.
The Journal of biological chemistry 2005;280(14):14138-44.
2005: Kuratani Mitsuo; Ishii Ryohei; Bessho Yoshitaka; Fukunaga Ryuya; Sengoku Toru; Shirouzu Mikako; Sekine Shun-Ichi; Yokoyama Shigeyuki
Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus.
The Journal of biological chemistry 2005;280(16):16002-8.
2005: Kimura Shuhei; Ide Kaori; Kashihara Aiko; Kano Makoto; Hatakeyama Mariko; Masui Ryoji; Nakagawa Noriko; Yokoyama Shigeyuki; Kuramitsu Seiki; Konagaya Akihiko
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm.
Bioinformatics (Oxford, England) 2005;21(7):1154-63.
2005: Hamada Toshiyuki; Asanuma Miwako; Ueki Tatsuya; Hayashi Fumiaki; Kobayashi Naohiro; Yokoyama Shigeyuki; Michibata Hitoshi; Hirota Hiroshi
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: Hino Nobumasa; Okazaki Yuko; Kobayashi Takatsugu; Hayashi Akiko; Sakamoto Kensaku; Yokoyama Shigeyuki
Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid.
Nature methods 2005;2(3):201-6.
2005: Yamasaki Kazuhiko; Kigawa Takanori; Inoue Makoto; Tateno Masaru; Yamasaki Tomoko; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Tomo Yasuko; Hayami Nobuhiro; Terada Takaho; Shirouzu Mikako; Tanaka Akiko; Seki Motoaki; Shinozaki Kazuo; Yokoyama Shigeyuki
Solution structure of an Arabidopsis WRKY DNA binding domain.
The Plant cell 2005;17(3):944-56.
2005: Nameki Nobukazu; Tochio Naoya; Koshiba Seizo; Inoue Makoto; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Fujikura Yukiko; Saito Miyuki; Ikari Masaomi; Watanabe Megumi; Terada Takaho; Shirouzu Mikako; Yoshida Mayumi; Hirota Hiroshi; Tanaka Akiko; Hayashizaki Yoshihide; Güntert Peter; Kigawa Takanori; Yokoyama Shigeyuki
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: Kukimoto-Niino Mutsuko; Shibata Rie; Murayama Kazutaka; Hamana Hiroaki; Nishimoto Madoka; Bessho Yoshitaka; Terada Takaho; Shirouzu Mikako; Kuramitsu Seiki; Yokoyama Shigeyuki
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: Murayama Kazutaka; Shirouzu Mikako; Terada Takaho; Kuramitsu Seiki; Yokoyama Shigeyuki
Crystal structure of TT1662 from Thermus thermophilus HB8: a member of the alpha/beta hydrolase fold enzymes.
Proteins 2005;58(4):982-4.
2005: Nikulin Alexey; Stolboushkina Elena; Perederina Anna; Vassilieva Ioulia; Blaesi Udo; Moll Isabella; Kachalova Galina; Yokoyama Shigeyuki; Vassylyev Dmitry; Garber Maria; Nikonov Stanislav
Structure of Pseudomonas aeruginosa Hfq protein.
Acta crystallographica. Section D, Biological crystallography 2005;61(Pt 2):141-6.
2005: Tokmakov Alexander; Iwasaki Tetsushi; Itakura Shuji; Sato Ken-Ichi; Shirouzu Mikako; Fukami Yasuo; Yokoyama Shigeyuki
Regulation of Src kinase activity during Xenopus oocyte maturation.
Developmental biology 2005;278(2):289-300.
2005: Kobayashi Takatsugu; Sakamoto Kensaku; Takimura Tetsuo; Sekine Ryo; Kelly Vincent P; Kamata Kenji; Nishimura Susumu; Yokoyama Shigeyuki
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: Kobayashi Takatsugu; Takimura Tetsuo; Sekine Ryo; Kelly Vincent P; Kamata Kenji; Sakamoto Kensaku; Nishimura Susumu; Yokoyama Shigeyuki
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: Fukunaga Ryuya; Yokoyama Shigeyuki
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: Padmanabhan Balasundaram; Scharlock Maria; Tong Kit I; Nakamura Yoshihiro; Kang Moon-Il; Kobayashi Akira; Matsumoto Takehisa; Tanaka Akiko; Yamamoto Masayuki; Yokoyama Shigeyuki
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: Fukunaga Ryuya; Ishitani Ryuichiro; Nureki Osamu; Yokoyama Shigeyuki
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: Murayama Kazutaka; Kato-Murayama Miyuki; Katsura Kazushige; Uchikubo-Kamo Tomomi; Yamaguchi-Hirafuji Machiko; Kawazoe Masahito; Akasaka Ryogo; Hanawa-Suetsugu Kyoko; Hori-Takemoto Chie; Terada Takaho; Shirouzu Mikako; Yokoyama Shigeyuki
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: Tanaka Yoshinori; Kurumizaka Hitoshi; Yokoyama Shigeyuki
CpG methylation of the CENP-B box reduces human CENP-B binding.
The FEBS journal 2005;272(1):282-9.
2005: Sakai Hiroaki; Wang Hongfei; Takemoto-Hori Chie; Kaminishi Tatsuya; Yamaguchi Hiroto; Kamewari Yuki; Terada Takaho; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8.
Journal of structural biology 2005;149(1):99-110.
2005: Nishimura Shinichi; Matsunaga Shigeki; Yoshida Minoru; Hirota Hiroshi; Yokoyama Shigeyuki; Fusetani Nobuhiro
13-Deoxytedanolide, a marine sponge-derived antitumor macrolide, binds to the 60S large ribosomal subunit.
Bioorganic & medicinal chemistry 2005;13(2):449-54.
2005: Pantoja-Uceda David; López-Méndez Blanca; Koshiba Seizo; Inoue Makoto; Kigawa Takanori; Terada Takaho; Shirouzu Mikako; Tanaka Akiko; Seki Motoaki; Shinozaki Kazuo; Yokoyama Shigeyuki; Güntert Peter
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: Seto Azusa; Murayama Kazutaka; Toyama Mitsutoshi; Ebihara Akio; Nakagawa Noriko; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
ATP-induced structural change of dephosphocoenzyme A kinase from Thermus thermophilus HB8.
Proteins 2005;58(1):235-42.
2005: Suenaga Atsushi; Takada Naoki; Hatakeyama Mariko; Ichikawa Mio; Yu Xiaomei; Tomii Kentaro; Okimoto Noriaki; Futatsugi Noriyuki; Narumi Tetsu; Shirouzu Mikako; Yokoyama Shigeyuki; Konagaya Akihiko; Taiji Makoto
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: Kimoto Michiko; Kawai Rie; Mitsui Tsuneo; Harada Yoko; Sato Akira; Yokoyama Shigeyuki; Hirao Ichiro
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: Mitsui Tsuneo; Kimoto Michiko; Yokoyama Shigeyuki; Hirao Ichiro
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: Takada Kazuma; Takemoto Chie; Kawazoe Masahito; Konno Takayuki; Matsuta Noriko; Kurita Daisuke; Asano Krisana; Shirouzu Mikako; Yokoyama Shigeyuki; Muto Akira; Himeno Hyouta
Functional analysis of factors involved in trans-translation.
Nucleic acids symposium series (2004) 2005;(49):101-2.
2005: Hirao Ichiro; Mitsui Tsuneo; Kimoto Michiko; Kawai Rie; Sato Akira; Yokoyama Shigeyuki
Non-hydrogen-bonded base pairs for specific transcription.
Nucleic acids symposium series (2004) 2005;(49):33-4.
2005: Moriyama Kei; Kimoto Michiko; Mitsui Tsuneo; Yokoyama Shigeyuki; Hirao Ichiro
Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs.
Nucleic acids research 2005;33(15):e129.
2004: Scott Anna; Pantoja-Uceda David; Koshiba Seizo; Inoue Makoto; Kigawa Takanori; Terada Takaho; Shirouzu Mikako; Tanaka Akiko; Sugano Sumio; Yokoyama Shigeyuki; Güntert Peter
NMR assignment of the SH2 domain from the human feline sarcoma oncogene FES.
Journal of biomolecular NMR 2004;30(4):463-4.
2004: Ogiso Hideo; Kagi Noriko; Matsumoto Eiko; Nishimoto Madoka; Arai Ryoichi; Shirouzu Mikako; Mimura Junsei; Fujii-Kuriyama Yoshiaki; Yokoyama Shigeyuki
Phosphorylation analysis of 90 kDa heat shock protein within the cytosolic arylhydrocarbon receptor complex.
Biochemistry 2004;43(49):15510-9.
2004: Nishimura Mitsuhiro; Yoshida Takuya; Shirouzu Mikako; Terada Takaho; Kuramitsu Seiki; Yokoyama Shigeyuki; Ohkubo Tadayasu; Kobayashi Yuji
Solution structure of ribosomal protein L16 from Thermus thermophilus HB8.
Journal of molecular biology 2004;344(5):1369-83.
2004: Yamasaki Kazuhiko; Kigawa Takanori; Inoue Makoto; Tateno Masaru; Yamasaki Tomoko; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Tomo Yasuko; Hayami Nobuhiro; Terada Takaho; Shirouzu Mikako; Osanai Takashi; Tanaka Akiko; Seki Motoaki; Shinozaki Kazuo; Yokoyama Shigeyuki
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: Kishishita Seiichiro; Tatsuguchi Ayako; Ushikoshi-Nakayama Ryoko; Terada Takaho; Kuramitsu Seiki; Park Sam-Yong; Tame Jeremy R H; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structure of a conserved hypothetical protein TT1751 from Thermus thermophilus HB8.
Proteins 2004;57(4):883-7.
2004: Kukimoto-Niino Mutsuko; Murayama Kazutaka; Kato-Murayama Miyuki; Idaka Miki; Bessho Yoshitaka; Tatsuguchi Ayako; Ushikoshi-Nakayama Ryoko; Terada Takaho; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8.
Protein science : a publication of the Protein Society 2004;13(11):3038-42.
2004: Chikayama Eisuke; Kurotani Atsushi; Kuroda Yutaka; Yokoyama Shigeyuki
ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences.
Bioinformatics (Oxford, England) 2004;20(16):2836-8.
2004: Hirao Ichiro; Harada Yoko; Kimoto Michiko; Mitsui Tsuneo; Fujiwara Tsuyoshi; Yokoyama Shigeyuki
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: Fukunaga Ryuya; Yokoyama Shigeyuki
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: Fukunaga Ryuya; Yokoyama Shigeyuki
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: Lokanath Neratur K; Shiromizu Ikuya; Ohshima Noriyasu; Nodake Yuichi; Sugahara Mitsuaki; Yokoyama Shigeyuki; Kuramitsu Seiki; Miyano Masashi; Kunishima Naoki
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: Hirao Ichiro; Fujiwara Tsuyoshi; Kimoto Michiko; Yokoyama Shigeyuki
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: Wang Hongfei; Takemoto Chie Hori; Murayama Kazutaka; Sakai Hiroaki; Tatsuguchi Ayako; Terada Takaho; Shirouzu Mikako; Kuramitsu Seiki; Yokoyama Shigeyuki
Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8.
Protein science : a publication of the Protein Society 2004;13(10):2806-10.
2004: Saito Kohei; Kigawa Takanori; Koshiba Seizo; Sato Kazuo; Matsuo Yo; Sakamoto Ayako; Takagi Tetsuo; Shirouzu Mikako; Yabuki Takashi; Nunokawa Emi; Seki Eiko; Matsuda Takayoshi; Aoki Masaaki; Miyata Yukako; Hirakawa Noriko; Inoue Makoto; Terada Takaho; Nagase Takahiro; Kikuno Reiko; Nakayama Manabu; Ohara Osamu; Tanaka Akiko; Yokoyama Shigeyuki
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: Vassylyeva Marina N; Perederina Anna A; Svetlov Vladimir; Yokoyama Shigeyuki; Artsimovitch Irina; Vassylyev Dmitry G
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: Takizawa Yoshimasa; Kinebuchi Takashi; Kagawa Wataru; Yokoyama Shigeyuki; Shibata Takehiko; Kurumizaka Hitoshi
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: Sakamoto Kensaku; Ishimaru Satoshi; Kobayashi Takatsugu; Walker James R; Yokoyama Shigeyuki
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: Perederina Anna; Svetlov Vladimir; Vassylyeva Marina N; Tahirov Tahir H; Yokoyama Shigeyuki; Artsimovitch Irina; Vassylyev Dmitry G
Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription.
Cell 2004;118(3):297-309.
2004: Nameki Nobukazu; Yoneyama Misao; Koshiba Seizo; Tochio Naoya; Inoue Makoto; Seki Eiko; Matsuda Takayoshi; Tomo Yasuko; Harada Takushi; Saito Kohei; Kobayashi Naohiro; Yabuki Takashi; Aoki Masaaki; Nunokawa Emi; Matsuda Natsuko; Sakagami Noriko; Terada Takaho; Shirouzu Mikako; Yoshida Mayumi; Hirota Hiroshi; Osanai Takashi; Tanaka Akiko; Arakawa Takahiro; Carninci Piero; Kawai Jun; Hayashizaki Yoshihide; Kinoshita Kengo; Güntert Peter; Kigawa Takanori; Yokoyama Shigeyuki
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: Yoshiba Sachiko; Ooga Takushi; Nakagawa Noriko; Shibata Takehiko; Inoue Yorinao; Yokoyama Shigeyuki; Kuramitsu Seiki; Masui Ryoji
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: Enomoto Rima; Kinebuchi Takashi; Sato Makoto; Yagi Hideshi; Shibata Takehiko; Kurumizaka Hitoshi; Yokoyama Shigeyuki
Positive role of the mammalian TBPIP/HOP2 protein in DMC1-mediated homologous pairing.
The Journal of biological chemistry 2004;279(34):35263-72.
2004: Reay Paul; Yamasaki Kazuhiko; Terada Takaho; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
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: Kimoto Michiko; Yokoyama Shigeyuki; Hirao Ichiro
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: Hanawa-Suetsugu Kyoko; Sekine Shun-ichi; Sakai Hiroaki; Hori-Takemoto Chie; Terada Takaho; Unzai Satoru; Tame Jeremy R H; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
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: Hatakeyama M; Yumoto N; Yu X; Shirouzu M; Yokoyama S; Konagaya A
Transformation potency of ErbB heterodimer signaling is determined by B-Raf kinase.
Oncogene 2004;23(29):5023-31.
2004: Pantoja-Uceda David; López-Méndez Blanca; Koshiba Seizo; Kigawa Takanori; Shirouzu Mikako; Terada Takaho; Inoue Makoto; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Hirota Hiroshi; Yoshida Mayumi; Tanaka Akiko; Osanai Takashi; Seki Motoaki; Shinozaki Kazuo; Yokoyama Shigeyuki; Güntert Peter
NMR assignment of the hypothetical rhodanese domain At4g01050 from Arabidopsis thaliana.
Journal of biomolecular NMR 2004;29(2):207-8.
2004: López-Méndez Blanca; Pantoja-Uceda David; Tomizawa Tadashi; Koshiba Seizo; Kigawa Takanori; Shirouzu Mikako; Terada Takaho; Inoue Makoto; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Hirota Hiroshi; Yoshida Mayumi; Tanaka Akiko; Osanai Takashi; Seki Motoaki; Shinozaki Kazuo; Yokoyama Shigeyuki; Güntert Peter
NMR assignment of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thaliana.
Journal of biomolecular NMR 2004;29(2):205-6.
2004: Kinebuchi Takashi; Kagawa Wataru; Enomoto Rima; Tanaka Kozo; Miyagawa Kiyoshi; Shibata Takehiko; Kurumizaka Hitoshi; Yokoyama Shigeyuki
Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmc1.
Molecular cell 2004;14(3):363-74.
2004: Endo Masayuki; Mitsui Tsuneo; Okuni Taeko; Kimoto Michiko; Hirao Ichiro; Yokoyama Shigeyuki
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: Wada Takashi; Shirouzu Mikako; Terada Takaho; Kamewari Yuki; Park Sam-Yong; Tame Jeremy R H; Kuramitsu Seiki; Yokoyama Shigeyuki
Crystal structure of the conserved hypothetical protein TT1380 from Thermus thermophilus HB8.
Proteins 2004;55(3):778-80.
2004: Katsura Yasuhiro; Shirouzu Mikako; Yamaguchi Hiroto; Ishitani Ryuichiro; Nureki Osamu; Kuramitsu Seiki; Hayashi Hideyuki; Yokoyama Shigeyuki
Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV.
Proteins 2004;55(3):487-92.
2004: Tanaka Yoshinori; Tawaramoto-Sasanuma Maki; Kawaguchi Shinichi; Ohta Tsutomu; Yoda Kinya; Kurumizaka Hitoshi; Yokoyama Shigeyuki
Expression and purification of recombinant human histones.
Methods (San Diego, Calif.) 2004;33(1):3-11.
2004: Tahirov Tahir H; Inagaki Eiji; Ohshima Noriyasu; Kitao Tomoe; Kuroishi Chizu; Ukita Yoko; Takio Koji; Kobayashi Masanori; Kuramitsu Seiki; Yokoyama Shigeyuki; Miyano Masashi
Crystal structure of purine nucleoside phosphorylase from Thermus thermophilus.
Journal of molecular biology 2004;337(5):1149-60.
2004: Hosaka T; Tamehiro N; Chumpolkulwong N; Hori-Takemoto C; Shirouzu M; Yokoyama S; Ochi K
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: Kukimoto-Niino Mutsuko; Murayama Kazutaka; Inoue Mio; Terada Takaho; Tame Jeremy R H; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8.
Journal of molecular biology 2004;337(3):761-70.
2004: Chumpolkulwong Namthip; Hori-Takemoto Chie; Hosaka Takeshi; Inaoka Takashi; Kigawa Takanori; Shirouzu Mikako; Ochi Kozo; Yokoyama Shigeyuki
Effects of Escherichia coli ribosomal protein S12 mutations on cell-free protein synthesis.
European journal of biochemistry / FEBS 2004;271(6):1127-34.
2004: Yamasaki Kazuhiko; Kigawa Takanori; Inoue Makoto; Tateno Masaru; Yamasaki Tomoko; Yabuki Takashi; Aoki Masaaki; Seki Eiko; Matsuda Takayoshi; Nunokawa Emi; Ishizuka Yoshiko; Terada Takaho; Shirouzu Mikako; Osanai Takashi; Tanaka Akiko; Seki Motoaki; Shinozaki Kazuo; Yokoyama Shigeyuki
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: Maeda Takeshi; Inoue Makoto; Koshiba Seizo; Yabuki Takashi; Aoki Masaaki; Nunokawa Emi; Seki Eiko; Matsuda Takayoshi; Motoda Yoko; Kobayashi Atsuo; Hiroyasu Fumiko; Shirouzu Mikako; Terada Takaho; Hayami Nobuhiro; Ishizuka Yoshiko; Shinya Naoko; Tatsuguchi Ayako; Yoshida Mayumi; Hirota Hiroshi; Matsuo Yo; Tani Kazutoshi; Arakawa Takahiro; Carninci Piero; Kawai Jun; Hayashizaki Yoshihide; Kigawa Takanori; Yokoyama Shigeyuki
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: Sengoku Toru; Nureki Osamu; Dohmae Naoshi; Nakamura Akira; Yokoyama Shigeyuki
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: Kise Yoshiaki; Lee Sang Won; Park Sang Gyu; Fukai Shuya; Sengoku Toru; Ishii Ryohei; Yokoyama Shigeyuki; Kim Sunghoon; Nureki Osamu
A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase.
Nature structural & molecular biology 2004;11(2):149-56.
2004: Kasai Takuma; Inoue Makoto; Koshiba Seizo; Yabuki Takashi; Aoki Masaaki; Nunokawa Emi; Seki Eiko; Matsuda Takayoshi; Matsuda Natsuko; Tomo Yasuko; Shirouzu Mikako; Terada Takaho; Obayashi Naomi; Hamana Hiroaki; Shinya Naoko; Tatsuguchi Ayako; Yasuda Satoko; Yoshida Mayumi; Hirota Hiroshi; Matsuo Yo; Tani Kazutoshi; Suzuki Harukazu; Arakawa Takahiro; Carninci Piero; Kawai Jun; Hayashizaki Yoshihide; Kigawa Takanori; Yokoyama Shigeyuki
Solution structure of a BolA-like protein from Mus musculus.
Protein science : a publication of the Protein Society 2004;13(2):545-8.
2004: Fukunaga Ryuya; Fukai Shuya; Ishitani Ryuichiro; Nureki Osamu; Yokoyama Shigeyuki
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: Kimoto Michiko; Endo Masayuki; Mitsui Tsuneo; Okuni Taeko; Hirao Ichiro; Yokoyama Shigeyuki
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: Takahashi Hitomi; Inagaki Eiji; Fujimoto Yayoi; Kuroishi Chizu; Nodake Yuichi; Nakamura Yuki; Arisaka Fumio; Yutani Katsuhide; Kuramitsu Seiki; Yokoyama Shigeyuki; Yamamoto Masaki; Miyano Masashi; Tahirov Tahir H
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.
2004: Kawai Rie; Kimoto Michiko; Mitsui Tsuneo; Yokoyama Shigeyuki; Hirao Ichiro
Site-specific fluorescent labeling of RNA by a base-pair expanded transcription system.
Nucleic acids symposium series (2004) 2004;(48):35-6.
2004: Kigawa Takanori; Yabuki Takashi; Matsuda Natsuko; Matsuda Takayoshi; Nakajima Rie; Tanaka Akiko; Yokoyama Shigeyuki
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: Yokoyama Hiroshi; Sarai Naoyuki; Kagawa Wataru; Enomoto Rima; Shibata Takehiko; Kurumizaka Hitoshi; Yokoyama Shigeyuki
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: Fujikawa Norie; Kurumizaka Hitoshi; Nureki Osamu; Tanaka Yoshinori; Yamazoe Mitsuyoshi; Hiraga Sota; Yokoyama Shigeyuki
Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein.
Nucleic acids research 2004;32(1):82-92.
2003: Lokanath Neratur K; Shiromizu Ikuya; Nodake Yuichi; Sugahara Mitsuaki; Yokoyama Shigeyuki; Kuramitsu Seiki; Miyano Masashi; Kunishima Naoki
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: Mitsui Tsuneo; Kimoto Michiko; Sato Akira; Yokoyama Shigeyuki; Hirao Ichiro
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: Tawaramoto Maki S; Park Sam-Yong; Tanaka Yoshinori; Nureki Osamu; Kurumizaka Hitoshi; Yokoyama Shigeyuki
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: Okabe Mayuko; Tomita Kozo; Ishitani Ryuichiro; Ishii Ryohei; Takeuchi Nono; Arisaka Fumio; Nureki Osamu; Yokoyama Shigeyuki
Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure.
The EMBO journal 2003;22(21):5918-27.
2003: Seto Azusa; Shirouzu Mikako; Terada Takaho; Murayama Kazutaka; Kuramitsu Seiki; Yokoyama Shigeyuki
Crystal structure of a hypothetical protein, TT1725, from Thermus thermophilus HB8 at 1.7 A resolution.
Proteins 2003;53(3):768-71.
2003: Hoseki Jun; Okamoto Akihiro; Masui Ryoji; Shibata Takehiko; Inoue Yorinao; Yokoyama Shigeyuki; Kuramitsu Seiki
Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8.
Journal of molecular biology 2003;333(3):515-26.
2003: Kobayashi Akiko; Kokubo Tetsuro; Ota Yoshimi; Yokoyama Shigeyuki
Promoter-specific function of the TATA element in undifferentiated P19 cells.
Biochemical and biophysical research communications 2003;310(2):458-63.
2003: Yoshiba Sachiko; Nakagawa Noriko; Masui Ryoji; Shibata Takehiko; Inoue Yorinao; Yokoyama Shigeyuki; Kuramitsu Seiki
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: Sakai Hiroaki; Vassylyeva Marina N; Matsuura Takanori; Sekine Shun ichi; Gotoh Kazumi; Nishiyama Makoto; Terada Takaho; Shirouzu Mikako; Kuramitsu Seiki; Vassylyev Dmitry G; Yokoyama Shigeyuki
Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8.
Journal of molecular biology 2003;332(3):729-40.
2003: Vassylyeva Marina N; Sakai Hiroaki; Matsuura Takanori; Sekine Shun-ichi; Nishiyama Makoto; Terada Takaho; Shirouzu Mikako; Kuramitsu Seiki; Vassylyev Dmitry G; Yokoyama Shigeyuki
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: Handa Noriko; Terada Takaho; Kamewari Yuki; Hamana Hiroaki; Tame Jeremy R H; Park Sam-Yong; Kinoshita Kengo; Ota Motonori; Nakamura Haruki; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
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: Wada Takashi; Kuzuyama Tomohisa; Satoh Shinya; Kuramitsu Seiki; Yokoyama Shigeyuki; Unzai Satoru; Tame Jeremy R H; Park Sam-Yong
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: Ishii Ryohei; Nureki Osamu; Yokoyama Shigeyuki
Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus.
The Journal of biological chemistry 2003;278(34):32397-404.
2003: Kurumizaka Hitoshi; Enomoto Rima; Nakada Maki; Eda Keiko; Yokoyama Shigeyuki; Shibata Takehiko
Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein.
Nucleic acids research 2003;31(14):4041-50.
2003: Wada Takashi; Shirouzu Mikako; Terada Takaho; Ishizuka Yoshiko; Matsuda Takayoshi; Kigawa Takanori; Kuramitsu Seiki; Park Sam Yong; Tame Jeremy R H; Yokoyama Shigeyuki
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: Hatakeyama Mariko; Kimura Shuhei; Naka Takashi; Kawasaki Takuji; Yumoto Noriko; Ichikawa Mio; Kim Jae-Hoon; Saito Kazuki; Saeki Mihoro; Shirouzu Mikako; Yokoyama Shigeyuki; Konagaya Akihiko
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: Kato Miyuki; Shirouzu Mikako; Terada Takaho; Yamaguchi Hiroto; Murayama Kazutaka; Sakai Hiroaki; Kuramitsu Seiki; Yokoyama Shigeyuki
Crystal structure of the 2'-5' RNA ligase from Thermus thermophilus HB8.
Journal of molecular biology 2003;329(5):903-11.
2003: Kobayashi Takatsugu; Nureki Osamu; Ishitani Ryuichiro; Yaremchuk Anna; Tukalo Michael; Cusack Stephen; Sakamoto Kensaku; Yokoyama Shigeyuki
Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion.
Nature structural biology 2003;10(6):425-32.
2003: Kaminishi Tatsuya; Sakai Hiroaki; Takemoto-Hori Chie; Terada Takaho; Nakagawa Noriko; Maoka Nobuko; Kuramitsu Seiki; Shirouzu Mikako; Yokoyama Shigeyuki
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: Ishitani Ryuichiro; Nureki Osamu; Nameki Nobukazu; Okada Norihiro; Nishimura Susumu; Yokoyama Shigeyuki
Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme.
Cell 2003;113(3):383-94.
2003: Suenaga Atsushi; Hatakeyama Mariko; Ichikawa Mio; Yu Xiaomei; Futatsugi Noriyuki; Narumi Tetsu; Fukui Kazuhiko; Terada Takaho; Taiji Makoto; Shirouzu Mikako; Yokoyama Shigeyuki; Konagaya Akihiko
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: Mitsui Tsuneo; Kitamura Aya; Kimoto Michiko; To Taiko; Sato Akira; Hirao Ichiro; Yokoyama Shigeyuki
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: Fujikawa Norie; Kurumizaka Hitoshi; Nureki Osamu; Terada Takaho; Shirouzu Mikako; Katayama Tsutomu; Yokoyama Shigeyuki
Structural basis of replication origin recognition by the DnaA protein.
Nucleic acids research 2003;31(8):2077-86.
2003: Yoshimasu Masatoshi; Aihara Hideki; Ito Yutaka; Rajesh Sundaresan; Ishibe Satoko; Mikawa Tsutomu; Yokoyama Shigeyuki; Shibata Takehiko
An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes.
Nucleic acids research 2003;31(6):1735-43.
2003: Sekine Shun-Ichi; Nureki Osamu; Dubois Daniel Y; Bernier Stéphane; Chênevert Robert; Lapointe Jacques; Vassylyev Dmitry G; Yokoyama Shigeyuki
ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding.
The EMBO journal 2003;22(3):676-88.
2003: Yokoyama Shigeyuki
Protein expression systems for structural genomics and proteomics.
Current opinion in chemical biology 2003;7(1):39-43.
2003: Someya Tatsuhiko; Nameki Nobukazu; Hosoi Haruko; Suzuki Sakura; Hatanaka Hideki; Fujii Michiko; Terada Takaho; Shirouzu Mikako; Inoue Yorinao; Shibata Takehiko; Kuramitsu Seiki; Yokoyama Shigeyuki; Kawai Gota
Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus.
FEBS letters 2003;535(1-3):94-100.
2003: Fukai Shuya; Nureki Osamu; Sekine Shun-Ichi; Shimada Atsushi; Vassylyev Dmitry G; Yokoyama Shigeyuki
Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase.
RNA (New York, N.Y.) 2003;9(1):100-11.
2003: Fujikawa Norie; Kurumizaka Hitoshi; Yamazoe Mitsuyoshi; Hiraga Sota; Yokoyama Shigeyuki
Identification of functional domains of the Escherichia coli SeqA protein.
Biochemical and biophysical research communications 2003;300(3):699-705.
2003: Kishida Hiroyuki; Wada Takashi; Unzai Satoru; Kuzuyama Tomohisa; Takagi Motoki; Terada Takaho; Shirouzu Mikako; Yokoyama Shigeyuki; Tame Jeremy R H; Park Sam-Yong
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.
2003: Yokoyama Hiroshi; Kurumizaka Hitoshi; Ikawa Shukuko; Yokoyama Shigeyuki; Shibata Takehiko
Holliday junction binding activity of the human Rad51B protein.
The Journal of biological chemistry 2003;278(4):2767-72.
2003: Endo Makoto; Shirouzu Mikako; Yokoyama Shigeyuki
The Cdc42 binding and scaffolding activities of the fission yeast adaptor protein Scd2.
The Journal of biological chemistry 2003;278(2):843-52.
2003: Tanaka Takanori; Kuroda Yutaka; Yokoyama Shigeyuki
Characteristics and prediction of domain linker sequences in multi-domain proteins.
Journal of structural and functional genomics 2003;4(2-3):79-85.
2003: Takada Kazuma; Hori-Takemoto Chie; Kawazoe Masahito; Lee SungGa; Shirouzu Mikako; Yokoyama Shigeyuki; Muto Akira; Himeno Hyouta
In vitro analysis of the initial steps of trans-translation.
Nucleic acids research. Supplement (2001) 2003;(3):287-8.
2003: Moriyama Kei; Kimoto Michiko; Mitsui Tsuneo; Yokoyama Shigeyuki; Hirao Ichiro
Simple preparation of biotinylated RNA by transcription via an unnatural base pair.
Nucleic acids research. Supplement (2001) 2003;(3):277-8.
2003: Hirao Ichiro; Mitsui Tsuneo; Kimoto Michiko; Harada Yoko; Yokoyama Shigeyuki
An unnatural base pair for efficient incorporation of nucleotide analogs into RNAs.
Nucleic acids research. Supplement (2001) 2003;(3):215-6.
2002: Sakamoto Kensaku; Hayashi Akiko; Sakamoto Ayako; Kiga Daisuke; Nakayama Hiroshi; Soma Akiko; Kobayashi Takatsugu; Kitabatake Makoto; Takio Koji; Saito Kazuki; Shirouzu Mikako; Hirao Ichiro; Yokoyama Shigeyuki
Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells.
Nucleic acids research 2002;30(21):4692-9.
2002: Akanuma Satoshi; Kigawa Takanori; Yokoyama Shigeyuki
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: Furukawa Hiroyasu; Hamada Toshiyuki; Hayashi Mariko K; Haga Tatsuya; Muto Yutaka; Hirota Hiroshi; Yokoyama Shigeyuki; Nagasawa Kazuo; Ishiguro Masaji
Conformation of ligands bound to the muscarinic acetylcholine receptor.
Molecular pharmacology 2002;62(4):778-87.
2002: Ogiso Hideo; Ishitani Ryuichiro; Nureki Osamu; Fukai Shuya; Yamanaka Mari; Kim Jae-Hoon; Saito Kazuki; Sakamoto Ayako; Inoue Mio; Shirouzu Mikako; Yokoyama Shigeyuki
Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains.
Cell 2002;110(6):775-87.
2002: Kagawa Wataru; Kurumizaka Hitoshi; Ishitani Ryuichiro; Fukai Shuya; Nureki Osamu; Shibata Takehiko; Yokoyama Shigeyuki
Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form.
Molecular cell 2002;10(2):359-71.
2002: Fukushima Kay; Kikuchi Jun; Koshiba Seizo; Kigawa Takanori; Kuroda Yutaka; Yokoyama Shigeyuki
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: Kiga Daisuke; Sakamoto Kensaku; Kodama Koichiro; Kigawa Takanori; Matsuda Takayoshi; Yabuki Takashi; Shirouzu Mikako; Harada Yoko; Nakayama Hiroshi; Takio Koji; Hasegawa Yoshinori; Endo Yaeta; Hirao Ichiro; Yokoyama Shigeyuki
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: Nureki Osamu; Shirouzu Mikako; Hashimoto Kyoko; Ishitani Ryuichiro; Terada Takaho; Tamakoshi Masatada; Oshima Tairo; Chijimatsu Masao; Takio Koji; Vassylyev Dmitry G; Shibata Takehiko; Inoue Yorinao; Kuramitsu Seiki; Yokoyama Shigeyuki
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: Ohtani Naoto; Nakagawa Noriko; Hoseki Jun; Ebihara Akio; Satoh Shinya; Agari Yoshihiro; Kobayashi Shin-ichiro; Agari Kazuko; Maoka Nobuko; Masui Ryoji; Miki Kunio; Yokoyama Shigeyuki; Kuramitsu Seiki
[An exhaustive overproduction of bacterial proteins]
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 2002;47(8 Suppl):1009-13.
2002: Kitabatake Makoto; Ali Kamilah; Demain Arnold; Sakamoto Kensaku; Yokoyama Shigeyuki; Söll Dieter
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: Ishitani Ryuichiro; Nureki Osamu; Fukai Shuya; Kijimoto Teiya; Nameki Nobukazu; Watanabe Masakatsu; Kondo Hisao; Sekine Mitsuo; Okada Norihiro; Nishimura Susumu; Yokoyama Shigeyuki
Crystal structure of archaeosine tRNA-guanine transglycosylase.
Journal of molecular biology 2002;318(3):665-77.
2002: Kikuchi Jun; Iwahara Junji; Kigawa Takanori; Murakami Yota; Okazaki Tsuneko; Yokoyama Shigeyuki
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: Kitamura Aya; Muto Yutaka; Watanabe Satoru; Kim Insil; Ito Takuhiro; Nishiya Yoichi; Sakamoto Kensaku; Ohtsuki Takashi; Kawai Gota; Watanabe Kimitsuna; Hosono Kazumi; Takaku Hiroshi; Katoh Etsuko; Yamazaki Toshimasa; Inoue Tan; Yokoyama Shigeyuki
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: Terada Takaho; Nureki Osamu; Ishitani Ryuichiro; Ambrogelly Alexandre; Ibba Michael; Söll Dieter; Yokoyama Shigeyuki
Functional convergence of two lysyl-tRNA synthetases with unrelated topologies.
Nature structural biology 2002;9(4):257-62.
2002: Kurumizaka Hitoshi; Ikawa Shukuko; Nakada Maki; Enomoto Rima; Kagawa Wataru; Kinebuchi Takashi; Yamazoe Mitsuyoshi; Yokoyama Shigeyuki; Shibata Takehiko
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: Hirao Ichiro; Ohtsuki Takashi; Fujiwara Tsuyoshi; Mitsui Tsuneo; Yokogawa Tomoko; Okuni Taeko; Nakayama Hiroshi; Takio Koji; Yabuki Takashi; Kigawa Takanori; Kodama Koichiro; Yokogawa Takashi; Nishikawa Kazuya; Yokoyama Shigeyuki
An unnatural base pair for incorporating amino acid analogs into proteins.
Nature biotechnology 2002;20(2):177-82.
2002: Kimoto Michiko; Shirouzu Mikako; Mizutani Shin; Koide Hiroshi; Kaziro Yoshito; Hirao Ichiro; Yokoyama Shigeyuki
Anti-(Raf-1) RNA aptamers that inhibit Ras-induced Raf-1 activation.
European journal of biochemistry / FEBS 2002;269(2):697-704.
2002: Mitsui Tsuneo; Kimoto Michiko; Harada Yoko; Sato Akira; Kitamura Aya; To Taiko; Hirao Ichiro; Yokoyama Shigeyuki
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: Hirao Ichiro; Kimoto Michiko; Mitsui Tsuneo; Harada Yoko; Fujiwara Tsuyoshi; Sato Akira; Yokoyama Shigeyuki
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: Miyazaki Satoshi; Kuroda Yutaka; Yokoyama Shigeyuki
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: Kigawa Takanori; Yamaguchi-Nunokawa Emi; Kodama Koichiro; Matsuda Takayoshi; Yabuki Takashi; Matsuda Natsuko; Ishitani Ryuichiro; Nureki Osamu; Yokoyama Shigeyuki
Selenomethionine incorporation into a protein by cell-free synthesis.
Journal of structural and functional genomics 2002;2(1):29-35.
2002: Koshiba Seizo; Kigawa Takanori; Kikuchi Akira; Yokoyama Shigeyuki
Solution structure of the epsin N-terminal homology (ENTH) domain of human epsin.
Journal of structural and functional genomics 2002;2(1):1-8.
2001: Kurimoto K; Fukai S; Nureki O; Muto Y; Yokoyama S
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: Kiga D; Sakamoto K; Sato S; Hirao I; Yokoyama S
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: Tanaka Y; Nureki O; Kurumizaka H; Fukai S; Kawaguchi S; Ikuta M; Iwahara J; Okazaki T; Yokoyama S
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: Nakama T; Nureki O; Yokoyama S
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: Shimada A; Nureki O; Goto M; Takahashi S; Yokoyama S
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: Ishitani R; Nureki O; Kijimoto T; Watanabe M; Kondo H; Nameki N; Okada N; Nishimura S; Yokoyama S
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: Kagawa W; Kurumizaka H; Ikawa S; Yokoyama S; Shibata T
Homologous pairing promoted by the human Rad52 protein.
The Journal of biological chemistry 2001;276(37):35201-8.
2001: Fujiwara T; Kimoto M; Sugiyama H; Hirao I; Yokoyama S
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: Shibata T; Nishinaka T; Mikawa T; Aihara H; Kurumizaka H; Yokoyama S; Ito Y
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: Yokoyama S; Tachibana K; Nakanishi H; Yamamoto Y; Irie K; Mandai K; Nagafuchi A; Monden M; Takai Y
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: Kurumizaka H; Ikawa S; Nakada M; Eda K; Kagawa W; Takata M; Takeda S; Yokoyama S; Shibata T
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: Sakisaka T; Taniguchi T; Nakanishi H; Takahashi K; Miyahara M; Ikeda W; Yokoyama S; Peng Y F; Yamanishi K; Takai Y
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: Shimada A; Nureki O; Dohmae N; Takio K; Yokoyama S
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: Itoh T; Koshiba S; Kigawa T; Kikuchi A; Yokoyama S; Takenawa T
Role of the ENTH domain in phosphatidylinositol-4,5-bisphosphate binding and endocytosis.
Science (New York, N.Y.) 2001;291(5506):1047-51.
2001: Kawaguchi S; Müller J; Linde D; Kuramitsu S; Shibata T; Inoue Y; Vassylyev D G; Yokoyama S
The crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus.
The EMBO journal 2001;20(3):562-9.
2001: Terada T; Shirouzu M; Fukumori Y; Fujimori F; Ito Y; Kigawa T; Yokoyama S; Uchida T
Solution structure of the human parvulin-like peptidyl prolyl cis/trans isomerase, hPar14.
Journal of molecular biology 2001;305(4):917-26.
2001: Asanuma H; Tamaru D; Yoshida T; Yamazawa A; Mitsui T; Okuni T; Kimoto M; Hirao I; Yokoyama S; Komiyama M
Photo-regulation of RNA polymerase reaction by use of modified DNA carrying an azobenzene.
Nucleic acids research. Supplement (2001) 2001;(1):55-6.
2001: Hirao I; Mitsui T; Fujiwara T; Kimoto M; To T; Okuni T; Sato A; Harada Y; Yokoyama S
Efforts toward creating unnatural base pairs for an expanded genetic code.
Nucleic acids research. Supplement (2001) 2001;(1):17-8.
2001: Nureki O; Fukai S; Sekine S; Shimada A; Terada T; Nakama T; Shirouzu M; Vassylyev D G; Yokoyama S
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: Kuroda Y; Tani K; Matsuo Y; Yokoyama S
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: Peng Y F; Mandai K; Sakisaka T; Okabe N; Yamamoto Y; Yokoyama S; Mizoguchi A; Shiozaki H; Monden M; Takai Y
Ankycorbin: a novel actin cytoskeleton-associated protein.
Genes to cells : devoted to molecular & cellular mechanisms 2000;5(12):1001-8.
2000: Fukai S; Nureki O; Sekine S; Shimada A; Tao J; Vassylyev D G; Yokoyama S
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: Yokoyama S; Hirota H; Kigawa T; Yabuki T; Shirouzu M; Terada T; Ito Y; Matsuo Y; Kuroda Y; Nishimura Y; Kyogoku Y; Miki K; Masui R; Kuramitsu S
Structural genomics projects in Japan.
Nature structural biology 2000;7 Suppl():943-5.
2000: Yasuda T; Ohtsuka T; Inoue E; Yokoyama S; Sakisaka T; Kodama A; Takaishi K; Takai Y
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: Kim I; Muto Y; Watanabe S; Kitamura A; Futamura Y; Yokoyama S; Hosono K; Kawai G; Takaku H; Dohmae N; Takio K; Saskamoto H; Shimura Y
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: Satoh A; Takai K; Ouchi R; Yokoyama S; Takaku H
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: Sakamoto K; Gouzu H; Komiya K; Kiga D; Yokoyama S; Yokomori T; Hagiya M
Molecular computation by DNA hairpin formation.
Science (New York, N.Y.) 2000;288(5469):1223-6.
2000: Inoue M; Muto Y; Sakamoto H; Yokoyama S
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: Kanda T; Takai K; Yokoyama S; Takaku H
Specific inactivation of Escherichia coli tRNA(Phe) by antisense DNA-treatment under Mg2+-deficient conditions.
Bioorganic & medicinal chemistry 2000;8(3):675-9.
2000: Hirao I; Madin K; Endo Y; Yokoyama S; Ellington A D
RNA aptamers that bind to and inhibit the ribosome-inactivating protein, pepocin.
The Journal of biological chemistry 2000;275(7):4943-8.
2000: Kanda T; Takai K; Yokoyama S; Takaku H
An easy cell-free protein synthesis system dependent on the addition of crude Escherichia coli tRNA.
Journal of biochemistry 2000;127(1):37-41.
2000: Hirao I; Fujiwara T; Kimoto M; Mitsui T; Okuni T; Ohtsuki T; Yokoyama S
Unnatural base pairs between 2-amino-6-(2-thienyl)purine and the complementary bases.
Nucleic acids symposium series 2000;(44):261-2.
2000: Fujiwara T; Sugiyama H; Hirao I; Yokoyama S
Synthesis of 6-(2-thienyl)purine nucleoside derivatives toward the expansion of the genetic code.
Nucleic acids symposium series 2000;(44):43-4.
1999: Kamei T; Matozaki T; Sakisaka T; Kodama A; Yokoyama S; Peng Y F; Nakano K; Takaishi K; Takai Y
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: Sakamoto K; Kiga D; Komiya K; Gouzu H; Yokoyama S; Ikeda S; Sugiyama H; Hagiya M
State transitions by molecules.
Bio Systems 1999;52(1-3):81-91.
1999: Ito T; Muto Y; Green M R; Yokoyama S
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: Kurumizaka H; Aihara H; Kagawa W; Shibata T; Yokoyama S
Human Rad51 amino acid residues required for Rad52 binding.
Journal of molecular biology 1999;291(3):537-48.
1999: Aihara H; Ito Y; Kurumizaka H; Yokoyama S; Shibata T
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: Handa N; Nureki O; Kurimoto K; Kim I; Sakamoto H; Shimura Y; Muto Y; Yokoyama S
Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein.
Nature 1999;398(6728):579-85.
1999: Sekine S; Nureki O; Tateno M; Yokoyama S
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: Takai K; Takaku H; Yokoyama S
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: Takai K; Okumura S; Hosono K; Yokoyama S; Takaku H
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: Koshiba S; Yokoyama S
[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: Yokoyama S; Shirataki H; Sakisaka T; Takai Y
Three splicing variants of tomosyn and identification of their syntaxin-binding region.
Biochemical and biophysical research communications 1999;256(1):218-22.
1999: Terada T; Ito Y; Shirouzu M; Tateno M; Hashimoto K; Kigawa T; Ebisuzaki T; Takio K; Shibata T; Yokoyama S; Smith B O; Laue E D; Cooper J A
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: Koshiba S; Kigawa T; Iwahara J; Kikuchi A; Yokoyama S
Solution structure of the Eps15 homology domain of a human POB1 (partner of RalBP1).
FEBS letters 1999;442(2-3):138-42.
1999: Kigawa T; Yabuki T; Yoshida Y; Tsutsui M; Ito Y; Shibata T; Yokoyama S
Cell-free production and stable-isotope labeling of milligram quantities of proteins.
FEBS letters 1999;442(1):15-9.
1999: Horie N; Yamaizumi Z; Kuchino Y; Takai K; Goldman E; Miyazawa T; Nishimura S; Yokoyama S
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: Kim I; Muto Y; Hosono K; Kitamura A; Watanabe S; Ohtsuki T; Kawai G; Takaku H; Watanabe K; Sakamoto H; Shimura Y; Yokoyama S
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: Kitamura A; Muto Y; Watanabe S; Kim I; Ito T; Nishiya Y; Ohtsuki T; Kawai G; Watanabe K; Hosono K; Takaku H; Katoh E; Yamazaki T; Inoue T; Yokoyama S
The guanosine binding mechanism of the Tetrahymena group I intron.
Nucleic acids symposium series 1999;(42):191-2.
1998: Kigawa T; Endo M; Ito Y; Shirouzu M; Kikuchi A; Yokoyama S
Solution structure of the Ras-binding domain of RGL.
FEBS letters 1998;441(3):413-8.
1998: Kimoto M; Sakamoto K; Shirouzu M; Hirao I; Yokoyama S
RNA aptamers that specifically bind to the Ras-binding domain of Raf-1.
FEBS letters 1998;441(2):322-6.
1998: Kanda T; Takai K; Yokoyama S; Takaku H
Knocking out a specific tRNA species within unfractionated Escherichia coli tRNA by using antisense (complementary) oligodeoxyribonucleotides.
FEBS letters 1998;440(3):273-6.
1998: Kim J H; Shirouzu M; Kataoka T; Bowtell D; Yokoyama S
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: Fujita Y; Shirataki H; Sakisaka T; Asakura T; Ohya T; Kotani H; Yokoyama S; Nishioka H; Matsuura Y; Mizoguchi A; Scheller R H; Takai Y
Tomosyn: a syntaxin-1-binding protein that forms a novel complex in the neurotransmitter release process.
Neuron 1998;20(5):905-15.
1998: Asano K; Niimi T; Yokoyama S; Mizobuchi K
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: Nureki O; Vassylyev D G; Tateno M; Shimada A; Nakama T; Fukai S; Konno M; Hendrickson T L; Schimmel P; Yokoyama S
Enzyme structure with two catalytic sites for double-sieve selection of substrate.
Science (New York, N.Y.) 1998;280(5363):578-82.
1998: Kiga D; Futamura Y; Sakamoto K; Yokoyama S
An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition.
Nucleic acids research 1998;26(7):1755-60.
1998: Iwahara J; Kigawa T; Kitagawa K; Masumoto H; Okazaki T; Yokoyama S
A helix-turn-helix structure unit in human centromere protein B (CENP-B).
The EMBO journal 1998;17(3):827-37.
1997: Hosono K; Gozu H; Hosaka H; Sakamoto K; Yokoyama S; Takai K; Takaku H
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: Aihara H; Ito Y; Kurumizaka H; Terada T; Yokoyama S; Shibata T
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: Inoue M; Muto Y; Sakamoto H; Kigawa T; Takio K; Shimura Y; Yokoyama S
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: Kinoshita T; Shirouzu M; Kamiya A; Hashimoto K; Yokoyama S; Miyajima A
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: Ito Y; Yamasaki K; Iwahara J; Terada T; Kamiya A; Shirouzu M; Muto Y; Kawai G; Yokoyama S; Laue E D; Wälchli M; Shibata T; Nishimura S; Miyazawa T
Regional polysterism in the GTP-bound form of the human c-Ha-Ras protein.
Biochemistry 1997;36(30):9109-19.
1997: Koshiba S; Kigawa T; Kim J H; Shirouzu M; Bowtell D; Yokoyama S
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: Kim I; Muto Y; Inoue M; Watanabe S; Kitamura A; Yokoyama S; Hosono K; Takaku H; Ono A; Kainosho M; Sakamoto H; Shimura Y
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: Kanda T; Takai K; Yokoyama S; Takaku H
Removing tRNA from a cell-free protein synthesis system for use in protein production.
Nucleic acids symposium series 1997;(37):319-20.
1997: Shirakura H; Hosono K; Kawai G; Takai K; Ohtsuki T; Watanabe K; Sakamoto K; Yokoyama S; Takaku H
Study on site specific cleavage of RNA.
Nucleic acids symposium series 1997;(37):217-8.
1997: Satoh A; Takai K; Yokoyama S; Takaku H
Codon recognition by artificial tRNA molecules with modified nucleosides in the anticodon.
Nucleic acids symposium series 1997;(37):117-8.
1997: Ouchi R; Takai K; Yokoyama S; Takaku H
Codon reading properties of tRNA variants substituted within the anticodon loop.
Nucleic acids symposium series 1997;(37):115-6.
1996: Miyaguchi H; Narita H; Sakamoto K; Yokoyama S
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: Takai K; Takaku H; Yokoyama S
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: Shinkai M; Masuda T; Kariya K; Tamada M; Shirouzu M; Yokoyama S; Kataoka T
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: Sakamoto K; Kawai G; Watanabe S; Niimi T; Hayashi N; Muto Y; Watanabe K; Satoh T; Sekine M; Yokoyama S
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: Watanabe S; Kawai G; Muto Y; Watanabe K; Inoue T; Yokoyama S
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: Sekine S; Nureki O; Sakamoto K; Niimi T; Tateno M; Go M; Kohno T; Brisson A; Lapointe J; Yokoyama S
Major identity determinants in the "augmented D helix" of tRNA(Glu) from Escherichia coli.
Journal of molecular biology 1996;256(4):685-700.
1996: Akasaka K; Tamada M; Wang F; Kariya K; Shima F; Kikuchi A; Yamamoto M; Shirouzu M; Yokoyama S; Kataoka T
Differential structural requirements for interaction of Ras protein with its distinct downstream effectors.
The Journal of biological chemistry 1996;271(10):5353-60.
1995: Tateno M; Nureki O; Sekine S; Kaneda K; Go M; Yokoyama S
A three-dimensional structure model of the complex of glutamyl-tRNA synthetase and its cognate tRNA.
FEBS letters 1995;377(1):77-81.
1995: Hu C D; Kariya K; Tamada M; Akasaka K; Shirouzu M; Yokoyama S; Kataoka T
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: Kigawa T; Muto Y; Yokoyama S
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: Taguchi T; Kitajima K; Niimi T; Muto Y; Yokoyama S; Inoue S; Inoue Y
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: Nureki S; Yokoyama S
[Mechanism of tRNA-recognition by aminoacyl-tRNA synthetases]
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 1995;40(10):1609-19.
1995: Liu J; Gagnon Y; Gauthier J; Furenlid L; L'Heureux P J; Auger M; Nureki O; Yokoyama S; Lapointe J
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: Hatta T; Takai K; Yokoyama S; Nakashima H; Yamamoto N; Takaku H
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: Fujita-Yoshigaki J; Shirouzu M; Ito Y; Hattori S; Furuyama S; Nishimura S; Yokoyama S
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: Taguchi T; Kitajima K; Muto Y; Yokoyama S; Inoue S; Inoue Y
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: Nureki O; Vassylyev D G; Katayanagi K; Shimizu T; Sekine S; Kigawa T; Miyazawa T; Yokoyama S; Morikawa K
Architectures of class-defining and specific domains of glutamyl-tRNA synthetase.
Science (New York, N.Y.) 1995;267(5206):1958-65.
1995: Yamamoto-Honda R; Tobe K; Kaburagi Y; Ueki K; Asai S; Yachi M; Shirouzu M; Yodoi J; Akanuma Y; Yokoyama S
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: Okumura S; Takai K; Yokoyama S; Takaku H
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: Kim I; Watanabe S; Muto Y; Hosono K; Takai K; Takaku H; Kawai G; Watanabe K; Yokoyama S
Selective deuteration of RNA for NMR signal assignment.
Nucleic acids symposium series 1995;(34):123-4.
1994: Hosaka H; Sakabe I; Sakamoto K; Yokoyama S; Takaku H
Sequence-specific cleavage of oligoribonucleotide capable of forming a stem and loop structure.
The Journal of biological chemistry 1994;269(31):20090-4.
1994: Hosaka H; Sakabe I; Sakamoto K; Niimi T; Yokoyama S; Takaku H
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: Shirouzu M; Koide H; Fujita-Yoshigaki J; Oshio H; Toyama Y; Yamasaki K; Fuhrman S A; Villafranca E; Kaziro Y; Yokoyama S
Mutations that abolish the ability of Ha-Ras to associate with Raf-1.
Oncogene 1994;9(8):2153-7.
1994: Koide H; Yokoyama S; Katayama Y; Muto Y; Kigawa T; Kohno T; Takusari H; Oishi M; Takahashi S; Tsukumo K
Receptor-binding affinities of human epidermal growth factor variants having unnatural amino acid residues in position 23.
Biochemistry 1994;33(23):7470-6.
1994: Takai K; Horie N; Yamaizumi Z; Nishimura S; Miyazawa T; Yokoyama S
Recognition of UUN codons by two leucine tRNA species from Escherichia coli.
FEBS letters 1994;344(1):31-4.
1994: Nureki O; Yokoyama S
[Aminoacyl-tRNA synthetase]
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 1994;39(7):1215-25.
1994: Nureki O; Niimi T; Muramatsu T; Kanno H; Kohno T; Florentz C; Giegé R; Yokoyama S
Molecular recognition of the identity-determinant set of isoleucine transfer RNA from Escherichia coli.
Journal of molecular biology 1994;236(3):710-24.
1994: Yamasaki K; Shirouzu M; Muto Y; Fujita-Yoshigaki J; Koide H; Ito Y; Kawai G; Hattori S; Yokoyama S; Nishimura S
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: Yajima S; Muto Y; Morikawa S; Nakamura H; Yokoyama S; Masaki H; Uozumi T
The three-dimensional structure of the colicin E3 immunity protein by distance geometry calculation.
FEBS letters 1993;333(3):257-60.
1993: Sakamoto K; Kawai G; Niimi T; Satoh T; Sekine M; Yamaizumi Z; Nishimura S; Miyazawa T; Yokoyama S
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: Hatta T; Kim S G; Nakashima H; Yamamoto N; Sakamoto K; Yokoyama S; Takaku H
Mechanisms of the inhibition of reverse transcription by unmodified and modified antisense oligonucleotides.
FEBS letters 1993;330(2):161-4.
1993: Nureki O; Kohno T; Sakamoto K; Miyazawa T; Yokoyama S
Chemical modification and mutagenesis studies on zinc binding of aminoacyl-tRNA synthetases.
The Journal of biological chemistry 1993;268(21):15368-73.
1993: Hiwasa T; Fujita-Yoshigaki J; Shirouzu M; Koide H; Sawada T; Sakiyama S; Yokoyama S
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: Muto Y; Yamasaki K; Ito Y; Yajima S; Masaki H; Uozumi T; Wälchli M; Nishimura S; Miyazawa T; Yokoyama S
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: Tanaka H; Hosaka H; Takahashi R; Imamura Y; Takai K; Yokoyama S; Takaku H
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: Niimi T; Kawai G; Takayanagi M; Noguchi T; Hayashi N; Kohno T; Muto Y; Watanabe K; Miyazawa T; Yokoyama S
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: Hatta T; Kim S; Yokoyama S; Takaku H
Mechanisms of the inhibition of reverse transcription by unmodified and modified antisense oligonucleotides.
Nucleic acids symposium series 1993;(29):67-8.
1992: Fujita-Yoshigaki J; Ito Y; Yamasaki K; Muto Y; Miyazawa T; Nishimura S; Yokoyama S
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: Kim S G; Tsukahara S; Yokoyama S; Takaku H
The influence of oligodeoxyribonucleotide phosphorothioate pyrimidine strands on triplex formation.
FEBS letters 1992;314(1):29-32.
1992: Fujita-Yoshigaki J; Yokoyama S; Shindo-Okada N; Nishimura S
Azatyrosine inhibits neurite outgrowth of PC12 cells induced by oncogenic Ras.
Oncogene 1992;7(10):2019-24.
1992: Yajima S; Muto Y; Yokoyama S; Masaki H; Uozumi T
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: Koide S; Yokoyama S; Matsuzawa H; Miyazawa T; Ohta T
Conformational equilibrium of an enzyme catalytic site in the allosteric transition.
Biochemistry 1992;31(23):5362-8.
1992: Shirouzu M; Fujita-Yoshigaki J; Ito Y; Koide H; Nishimura S; Yokoyama S
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: Nureki O; Suzuki K; Hara-Yokoyama M; Kohno T; Matsuzawa H; Ohta T; Shimizu T; Morikawa K; Miyazawa T; Yokoyama S
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: Kohno T; Koide H; Yokoyama S; Miyazawa T
[Alloprotein]
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 1992;37(3 Suppl):646-53.
1992: Kawai G; Yamamoto Y; Kamimura T; Masegi T; Sekine M; Hata T; Iimori T; Watanabe T; Miyazawa T; Yokoyama S
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: Yamasaki K; Muto Y; Ito Y; Wälchli M; Miyazawa T; Nishimura S; Yokoyama S
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: Fujita-Yoshigaki J; Shirouzu M; Koide H; Nishimura S; Yokoyama S
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: Hosaka H; Ogawa T; Sakamoto K; Yokoyama S; Takaku H
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: Kigawa T; Yokoyama S
A continuous cell-free protein synthesis system for coupled transcription-translation.
Journal of biochemistry 1991;110(2):166-8.
1991: Kanou M; Ohomori H; Nagai K; Yokoyama S; Suhadolnik R J; Sobol R; Takaku H
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: Nureki O; Muramatsu T; Suzuki K; Kohda D; Matsuzawa H; Ohta T; Miyazawa T; Yokoyama S
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: Nureki O; Tateno M; Niimi T; Kohno T; Muramatsu T; Kanno H; Muto Y; Giege R; Yokoyama S
Mechanisms of molecular recognition of tRNAs by aminoacyl-tRNA synthetases.
Nucleic acids symposium series 1991;(25):165-6.
1990: Kanamori A; Inoue S; Iwasaki M; Kitajima K; Kawai G; Yokoyama S; Inoue Y
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: Kanou M; Ohomori H; Takaku H; Yokoyama S; Kawai G; Suhadolnik R J; Sobol R
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: Haruki M; Matsumoto R; Hara-Yokoyama M; Miyazawa T; Yokoyama S
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: Kohno T; Kohda D; Haruki M; Yokoyama S; Miyazawa T
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: Muramatsu T; Yokoyama S
[Identity of tRNA]
Nippon rinsho. Japanese journal of clinical medicine 1990;48(3):639-46.
1990: Koide H; Yokoyama S; Miyazawa T
[Biosynthesis of alloprotein]
Nippon rinsho. Japanese journal of clinical medicine 1990;48(1):208-13.
1990: Komatsu H; Ichikawa T; Takaku H; Yokoyama S; Kawai G
Recognition by restriction endodeoxyribonuclease EcoRI of octadeoxyribonucleotides containing modified sugar and base moieties.
Nucleic acids symposium series 1990;(22):95-6.
1990: Nagai K; Yokoyama S; Kawai G; Shuhadlnik R J; Takaku H
Synthesis and biological activities of 8-substituted 2-5A analogues.
Nucleic acids symposium series 1990;(22):13-4.
1990: Muramatsu T; Nureki O; Kanno H; Niimi T; Tateno M; Kohno T; Kawai G; Miyazawa T; Muto Y; Yokoyama S
Recognition of tRNA identity determinants by aminoacyl-tRNA synthetases.
Nucleic acids symposium series 1990;(22):119-20.
1989: Hata-Tanaka A; Kawai G; Yamasaki K; Ito Y; Kajiura H; Ha J M; Miyazawa T; Yokoyama S; Nishimura S
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: Ha J M; Ito Y; Kawai G; Miyazawa T; Miura K; Ohtsuka E; Noguchi S; Nishimura S; Yokoyama S
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: Hiwasa T; Yokoyama S; Fujita J; Kominami E; Katunuma N; Sakiyama S
Potentiation of cysteine proteinase-inhibitor activity of full-length Ha-ras oncogene products by denaturation-renaturation.
Biochemistry international 1989;19(3):593-601.
1989: Yamasaki K; Kawai G; Ito Y; Muto Y; Fujita J; Miyazawa T; Nishimura S; Yokoyama S
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: Koide S; Yokoyama S; Matsuzawa H; Miyazawa T; Ohta T
Conformation of NAD+ bound to allosteric L-lactate dehydrogenase activated by chemical modification.
The Journal of biological chemistry 1989;264(15):8676-9.
1988: Muramatsu T; Nishikawa K; Nemoto F; Kuchino Y; Nishimura S; Miyazawa T; Yokoyama S
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: Kotani S; Ikai A; Kawai G; Maekawa S; Yokoyama S; Sakai H
Microtubule-assembly inhibitor protein. Its distribution, localization and physicochemical properties.
European journal of biochemistry / FEBS 1988;176(3):573-80.
1988: Koide H; Yokoyama S; Kawai G; Ha J M; Oka T; Kawai S; Miyake T; Fuwa T; Miyazawa T
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: Muramatsu T; Yokoyama S; Horie N; Matsuda A; Ueda T; Yamaizumi Z; Kuchino Y; Nishimura S; Miyazawa T
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: Hiwasa T; Sakiyama S; Yokoyama S; Ha J M; Noguchi S; Bando Y; Kominami E; Katunuma N
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: Hiwasa T; Sakiyama S; Yokoyama S; Ha J M; Fujita J; Noguchi S; Bando Y; Kominami E; Katunuma N
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: Kawai G; Yokoyama S; Hasegawa T; Murao K; Ishikura H; Nishimura S; Miyazawa T
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: Kohda D; Kawai G; Yokoyama S; Kawakami M; Mizushima S; Miyazawa T
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: Hiwasa T; Sakiyama S; Noguchi S; Ha J M; Miyazawa T; Yokoyama S
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: Hiwasa T; Yokoyama S; Ha J M; Noguchi S; Sakiyama S
c-Ha-ras gene products are potent inhibitors of cathepsins B and L.
FEBS letters 1987;211(1):23-6.
1987: Yokoyama S; Watanabe K; Miyazawa T
Dynamic structures and functions of transfer ribonucleic acids from extreme thermophiles.
Advances in biophysics 1987;23():115-47.
1986: Yokoyama S; Haruki M; Hara-Yokoyama M; Miyazawa T
Circular dichroism analyses of tRNA X protein interactions.
Nucleic acids symposium series 1986;(17):199-201.

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Shigeyuki Yokoyama

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