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Ryohei Ishii

Research Profile

Procedures

X Ray Crystallography

Genes & Molecular Sequences

Amino Acid Sequences

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Chemicals & Drugs

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Protein Binding

Physiology

Aminoacylation

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Publications

TOP 3
Tatsuo Yanagisawa; Ryohei Ishii; Tomomi Sumida; Shigeyuki Yokoyama
A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site.
Ryohei Ishii; Ryuichiro Ishitani; Kazunobu Isogaya; Daizo Koinuma; Keiji Miyazawa; Kohei Miyazono; Fumio Arisaka; Naoshi Dohmae; Hiroaki Ikushima; Azusa Seto; Yuji Watanabe; So-ichi Yaguchi; Osamu Nureki
Structure of a dominant-negative helix-loop-helix transcriptional regulator suggests mechanisms of autoinhibition.
Jonathan Cooper; Hediye Erdjument-Bromage; Marco Giovannini; C Oliver Hanemann; Ryohei Ishii; Wei Li; Stephen Barstow Long; Angela Pepe-Caprio; Gaia Schiavon; Paul Tempst; Liru You; Lu Zhou; Pengbo Zhou; Filippo G Giancotti
Merlin/NF2 functions upstream of the nuclear E3 ubiquitin ligase CRL4DCAF1 to suppress oncogenic gene expression.

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All Publications

2013: Tatsuo Yanagisawa; Ryohei Ishii; Tomomi Sumida; Shigeyuki Yokoyama
A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site.
Acta crystallographica. Section D, Biological crystallography 2013;69(Pt 1):5-15.
2012: Ryohei Ishii; Ryuichiro Ishitani; Kazunobu Isogaya; Daizo Koinuma; Keiji Miyazawa; Kohei Miyazono; Fumio Arisaka; Naoshi Dohmae; Hiroaki Ikushima; Azusa Seto; Yuji Watanabe; So-ichi Yaguchi; Osamu Nureki
Structure of a dominant-negative helix-loop-helix transcriptional regulator suggests mechanisms of autoinhibition.
The EMBO journal 2012;31(11):2541-52.
2011: Jonathan Cooper; Hediye Erdjument-Bromage; Marco Giovannini; C Oliver Hanemann; Ryohei Ishii; Wei Li; Stephen Barstow Long; Angela Pepe-Caprio; Gaia Schiavon; Paul Tempst; Liru You; Lu Zhou; Pengbo Zhou; Filippo G Giancotti
Merlin/NF2 functions upstream of the nuclear E3 ubiquitin ligase CRL4DCAF1 to suppress oncogenic gene expression.
Science signaling 2011;4(188):pt6.
2010: Tomomi Sumida; Tatsuo Yanagisawa; Ryohei Ishii; Shigeyuki Yokoyama
Crystallization and preliminary X-ray crystallographic study of GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, in complex with translation elongation factor P.
Acta crystallographica. Section F, Structural biology and crystallization communications 2010;66(Pt 9):1115-8.
2010: Tatsuo Yanagisawa; Tomomi Sumida; Ryohei Ishii; Chie Takemoto; Shigeyuki Yokoyama
A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.
Nature structural & molecular biology 2010;17(9):1136-43.
2010: Meiri Shida; Akihiko Arakawa; Ryohei Ishii; Seiichiro Kishishita; Tetsuo Takagi; Mutsuko Kukimoto-Niino; Sumio Sugano; Akiko Tanaka; Mikako Shirouzu; Shigeyuki Yokoyama
Direct inter-subdomain interactions switch between the closed and open forms of the Hsp70 nucleotide-binding domain in the nucleotide-free state.
Acta crystallographica. Section D, Biological crystallography 2010;66(Pt 3):223-32.
2010: Wei Li; Liru You; Jonathan Cooper; Gaia Schiavon; Angela Pepe-Caprio; Lu Zhou; Ryohei Ishii; Marco Giovannini; C Oliver Hanemann; Stephen Barstow Long; Hediye Erdjument-Bromage; Pengbo Zhou; Paul Tempst; Filippo G Giancotti
Merlin/NF2 suppresses tumorigenesis by inhibiting the E3 ubiquitin ligase CRL4(DCAF1) in the nucleus.
Cell 2010;140(4):477-90.
2009: Tomomi Sumida; Ryohei Ishii; Tatsuo Yanagisawa; Shigeyuki Yokoyama; Makoto Ito
Molecular cloning and crystal structural analysis of a novel beta-N-acetylhexosaminidase from Paenibacillus sp. TS12 capable of degrading glycosphingolipids.
Journal of molecular biology 2009;392(1):87-99.
2008: Tatsuo Yanagisawa; Ryohei Ishii; Ryuya Fukunaga; Takatsugu Kobayashi; Kensaku Sakamoto; Shigeyuki Yokoyama
Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification.
Chemistry & biology 2008;15(11):1187-97.
2008: Sakurako Goto-Ito; Takuhiro Ito; Ryohei Ishii; Yutaka Muto; Yoshitaka Bessho; Shigeyuki Yokoyama
Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.
Proteins 2008;72(4):1274-89.
2008: Asako Minagawa; Ryohei Ishii; Hiroaki Takaku; Shigeyuki Yokoyama; Masayuki Nashimoto
The flexible arm of tRNase Z is not essential for pre-tRNA binding but affects cleavage site selection.
Journal of molecular biology 2008;381(2):289-99.
2008: Tatsuo Yanagisawa; Ryohei Ishii; Ryuya Fukunaga; Takatsugu Kobayashi; Kensaku Sakamoto; Shigeyuki Yokoyama
Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase.
Journal of molecular biology 2008;378(3):634-52.
2007: Sakurako Goto-Ito; Ryohei Ishii; Takuhiro Ito; Rie Shibata; Emiko Fusatomi; Shun-ichi Sekine; Yoshitaka Bessho; Shigeyuki Yokoyama
Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis.
Acta crystallographica. Section D, Biological crystallography 2007;63(Pt 10):1059-68.
2007: Ryohei Ishii; Asako Minagawa; Hiroshi Takaku; Masamichi Takagi; Masayuki Nashimoto; Shigeyuki Yokoyama
The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes.
Acta crystallographica. Section F, Structural biology and crystallization communications 2007;63(Pt 8):637-41.
2006: Tatsuo Yanagisawa; Ryohei Ishii; Ryuya Fukunaga; Osamu Nureki; Shigeyuki Yokoyama
Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of pyrrolysyl-tRNA synthetase from the methanogenic archaeon Methanosarcina mazei.
Acta crystallographica. Section F, Structural biology and crystallization communications 2006;62(Pt 10):1031-3.
2006: Asako Minagawa; Hiroshi Takaku; Hirotaka S Shibata; Ryohei Ishii; Masamichi Takagi; Shigeyuki Yokoyama; Masayuki Nashimoto
Substrate recognition ability differs among various prokaryotic tRNase Zs.
Biochemical and biophysical research communications 2006;345(1):385-93.
2006: Asako Minagawa; Hiroshi Takaku; Ryohei Ishii; Masamichi Takagi; Shigeyuki Yokoyama; Masayuki Nashimoto
Identification by Mn2+ rescue of two residues essential for the proton transfer of tRNase Z catalysis.
Nucleic acids research 2006;34(13):3811-8.
2005: Mitsuo Kuratani; Ryohei Ishii; Yoshitaka Bessho; Ryuya Fukunaga; Toru Sengoku; Mikako Shirouzu; Shun-ichi Sekine; Shigeyuki Yokoyama
Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus.
The Journal of biological chemistry 2005;280(16):16002-8.
2005: Ryohei Ishii; Asako Minagawa; Hiroshi Takaku; Masamichi Takagi; Masayuki Nashimoto; Shigeyuki Yokoyama
Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima.
The Journal of biological chemistry 2005;280(14):14138-44.
2005: Kazunori Watanabe; Osamu Nureki; Shuya Fukai; Ryohei Ishii; Hironori Okamoto; Shigeyuki Yokoyama; Yaeta Endo; Hiroyuki Hori
Roles of conserved amino acid sequence motifs in the SpoU (TrmH) RNA methyltransferase family.
The Journal of biological chemistry 2005;280(11):10368-77.
2004: Osamu Nureki; Kazunori Watanabe; Shuya Fukai; Ryohei Ishii; Yaeta Endo; Hiroyuki Hori; Shigeyuki Yokoyama
Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme.
Structure (London, England : 1993) 2004;12(4):593-602.
2004: Christa Wiederkehr; R Basavaraj; Cyril Sarrauste de Menthière; Reinhold Koch; Ulrich Schlecht; Leandro Hermida; B Masdoua; Ryohei Ishii; V Cassen; M Yamamoto; C Lane; M Cherry; N Lamb; Michael Primig
Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation.
Bioinformatics (Oxford, England) 2004;20(5):808-11.
2004: Yoshiaki Kise; Sang Won Lee; Sang Gyu Park; Shuya Fukai; Toru Sengoku; Ryohei Ishii; Shigeyuki Yokoyama; Sunghoon Kim; Osamu Nureki
A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase.
Nature structural & molecular biology 2004;11(2):149-56.
2004: C Wiederkehr; R Basavaraj; C Sarrauste de Menthière; L Hermida; R Koch; U Schlecht; A Amon; S Brachat; M Breitenbach; P Briza; S Caburet; M Cherry; R Davis; A Deutschbauer; H G Dickinson; T Dumitrescu; M Fellous; A Goldman; J A Grootegoed; R Scott Hawley; Ryohei Ishii; B Jégou; Randal J Kaufman; F Klein; N Lamb; B Maro; K Nasmyth; A Nicolas; Terry L. Orr-Weaver; P Philippsen; C Pineau; K P Rabitsch; V Reinke; H Roest; W Saunders; M Schröder; T Schedl; M Siep; A Villeneuve; D J Wolgemuth; M Yamamoto; D Zickler; R E Esposito; Michael Primig
GermOnline, a cross-species community knowledgebase on germ cell differentiation.
Nucleic acids research 2004;32(Database issue):D560-7.
2003: Mayuko Okabe; Kozo Tomita; Ryuichiro Ishitani; Ryohei Ishii; Nono Takeuchi; Fumio Arisaka; Osamu Nureki; Shigeyuki Yokoyama
Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure.
The EMBO journal 2003;22(21):5918-27.
2003: Ryohei Ishii; Osamu Nureki; Shigeyuki Yokoyama
Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus.
The Journal of biological chemistry 2003;278(34):32397-404.