特任教授　石谷　隆一郎（いしたに　りゅういちろう）

学歴 ↑

1998年

東京大学理学部生物化学科卒業

1998年

同 大学院理学系研究科生物化学専攻修士課程入学

2000年

同 博士課程進学

2003年

博士（理学）（東京大学）取得

職歴 ↑

2003年

東京大学理学部 生物情報科学 特任教員（助手相当）

2004年

東京大学 農学生命科学研究科 産学官連携研究員

2005年

東京大学 農学生命科学研究科 農学生命情報科学ユニット 特任助手

2006年

東京工業大学 生命理工学研究科 生命情報専攻 助手

2008年

東京大学 医科学研究所 基礎医科学部門 染色体制御分野 准教授

2010年

東京大学大学院 理学系研究科 生物化学専攻 准教授

2018年

株式会社Preferred Networks Researcher

2019年

東京大学大学院 理学系研究科 生物化学専攻 特任教授（兼任）

2024年

東京医科歯科大学 難治疾患研究所 教授

現在に至る

学位論文 ↑

tRNA修飾酵素 アーケオシンtRNAグアニントランスグリコシラーゼの機能･構造解析

PDFファイル [4MBytes]

研究業績 ↑

1. "Crystal structures of the TRIC trimeric intracellular cation channel orthologues."
   Kasuya G, Hiraizumi M, Maturana AD, Kumazaki K, Fujiwara Y, Liu K, Nakada-Nakura Y, Iwata S, Tsukada K, Komori T, Uemura S, Goto Y, Nakane T, Takemoto M, Kato HE, Yamashita K, Wada M, Ito K, Ishitani R, Hattori M, Nureki O,
   Cell Res, (2016).
2. "Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide."
   Omura H, Oikawa D, Nakane T, Kato M, Ishii R, Ishitani R, Tokunaga F, Nureki O,
   Sci Rep, (2016).
3. "Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA."
   Matsumoto N, Nishimasu H, Sakakibara K, Nishida KM, Hirano T, Ishitani R, Siomi H, Siomi MC, Nureki O,
   Cell, (2016).
4. "Structural and functional insights into IZUMO1 recognition by JUNO in mammalian fertilization"
   Kato K, Satouh Y, Nishimasu H, Kurabayashi A, Morita J, Fujihara Y, O,
   Nat Commun, 7 12198 (2016).
5. "Crystal structure of the plant receptor-like kinase TDR in complex with the TDIF peptide."
   Morita J, Kato K, Nakane T, Kondo Y, Fukuda H, Nishimasu H, Ishitani ,
   Nat Commun, 7 12383 (2016).
6. "LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae."
   Kusakizako T, Tanaka Y, Hipolito CJ, Kuroda T, Ishitani R, Suga H, Nureki O,
   Acta Crystallogr F Struct Biol Commun, (2016).
7. "Structural basis for amino acid export by DMT superfamily transporter YddG."
   Tsuchiya H, Doki S, Takemoto M, Ikuta T, Higuchi T, Fukui K, Usuda Y, Tabuchi E, Nagatoishi S, Tsumoto K, Nishizawa T, Ito K, Dohmae N, Ishitani R, Nureki O,
   Nature, 534 417-20 (2016).
   PubMed: link
8. "Data processing pipeline for serial femtosecond crystallography at SACLA."
   Nakane T; Joti Y; Tono K; Yabashi M; Nango E; Iwata S; Ishitani R; Nureki O,
   J Appl Crystallogr, (2016).
9. "Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA."
   Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O,
   Cell, (2016).
10. "Structural basis for specific inhibition of Autotaxin by a DNA aptamer."
    Kato K, Ikeda H, Miyakawa S, Futakawa S, Nonaka Y, Fujiwara M, Okudaira S, Kano K, Aoki J, Morita J, Ishitani R, Nishimasu H, Nakamura Y, Nureki O,
    Nat Struct Mol Biol, (2016).
11. "Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9."
    Hirano S, Nishimasu H, Ishitani R, Nureki O,
    Mol Cell, (2016).
12. "Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase"
    Morita J, Kano K, Kato K, Takita H, Sakagami H, Yamamoto Y, Mihara E, Ueda H, Sato T, Tokuyama H, Arai H, Asou H, Takagi J, Ishitani R, Nishimasu H, Nureki O, Aoki J,
    Sci Rep., 6 20995 (2016).
    PubMed: link Open access, PDB: 5EGE 5EGH
13. "Structure and Engineering of Francisella novicida Cas9"
    Hirano H, Gootenberg JS, Horii T, Abudayyeh OO, Kimura M, Hsu PD, Nakane T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O,
    Cell., 164 950-961 (2016).
    PubMed: link Open access, PDB: 3B2Q 3B2P 3B2O 4OO8 5CZZ
14. "Structural Insights into Divalent Cation Modulations of ATP-Gated P2X Receptor Channels"
    Kasuya G, Fujiwara Y, Takemoto M, Dohmae N, Nakada-Nakura Y, Ishitani R, Hattori M, Nureki O,
    Cell Rep., 14 932-944 (2016).
    PubMed: link Open access
15. "Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State"
    Tanaka Y, Sugano Y, Takemoto M, Mori T, Furukawa A, Kusakizako T, Kumazaki K, Kashima A, Ishitani R, Sugita Y, Nureki O, Tsukazaki T.,
    Cell Rep., 13 1561-1568 (2015).
    PubMed: link Open access, PDB: 5AWW 5CH4
16. "Outward- and inward-facing structures of a putative bacterial transition-metal transporter with homology to ferroportin"
    Taniguchi R, Kato HE, Font J, Deshpande CN, Wada M, Ito K, Ishitani R, Jormakka M, Nureki O.,
    Nat. Commun., 6 8545 (2015).
    PubMed: link Open access, PDB: 5AXW 5CZZ
17. "Crystal Structure of Staphylococcus aureus Cas9."
    Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B, Li Y, Kurabayashi A, Ishitani R, Zhang F, Nureki O.,
    Cell, 162 1113-1126 (2015).
    PubMed: link Open access, PDB: 4LD0 4OGE 4OO8 4UN3
18. "Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening."
    Takemoto M, Kato HE, Koyama M, Ito J, Kamiya M, Hayashi S, Maturana AD, Deisseroth K, Ishitani R, Nureki O.,
    PLoS One, 10 0131094 (2015).
    PubMed: link Open access
19. "Atomistic design of microbial opsin-based blue-shifted optogenetics tools."
    Kato HE, Kamiya M, Sugo S, Ito J, Taniguchi R, Orito A, Hirata K, Inutsuka A, Yamanaka A, Maturana AD, Ishitani R, Sudo Y, Hayashi S, Nureki O.,
    Nat. Commun., 6 7177 (2015).
    PubMed: link Open access
20. "Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK."
    Fukuda M, Takeda H, Kato HE, Doki S, Ito K, Maturana AD, Ishitani R, Nureki O.,
    Nat. Commun., 6 7097 (2015).
    PubMed: link Open access, PDB: 4U4T 4U4V 4U4W
21. "Crystal Structure and Activity of the Endoribonuclease Domain of the piRNA Pathway Factor Maelstrom."
    Matsumoto, N., Sato, K., Nishimasu, H., Namba, Y., Miyakubi, K., Dohmae, N., Ishitani, R., Siomi, H., Siomi, M. C., Nureki, O.,
    Cell Rep, 11 366-375 (2015).
    PubMed: link Open access, PDB: 4YBG
22. "Structural Basis for the Catalytic Mechanism of DncV, Bacterial Homolog of Cyclic GMP-AMP Synthase."
    Kato, K., Ishii, R., Hirano, S., Ishitani, R., Nureki, O.,
    Structure, 23 843-50 (2015).
    PubMed: link, PDB: 3WT0 4XJ1 4XJ3 4XJ4 4XJ5 4XJ6
23. "Structural basis for Na transport mechanism by a light-driven Na pump."
    Kato, H. E., Inoue, K., Abe-Yoshizumi, R., Kato, Y., Ono, H., Konno, M., Hososhima, S., Ishizuka, T., Hoque, M. R., Kunitomo, H., Ito, J., Yoshizawa, S., Yamashita, K., Takemoto, M., Nishizawa, T., Taniguchi, R., Kogure, K., Maturana, A. D., Iino, Y., Yawo, H., Ishitani, R., Kandori, H., Nureki, O.,
    Nature, 521 48-53 (2015).
    PubMed: link Open access, PDB: 3X3B 3X3C
24. "Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter."
    Lee, Y., Nishizawa, T., Yamashita, K., Ishitani, R., Nureki, O.,
    Nat Commun, 6 6112 (2015).
    PubMed: link Open access, PDB: 4X5M 4X5N
25. "Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase."
    Kumazaki K, Kishimoto T, Furukawa A, Mori H, Tanaka Y, Dohmae N, Ishitani R, Tsukazaki T, Nureki O,
    Sci Rep, 4 7299 (2014).
    PubMed: link, PDB: 3WVF
26. "Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg(2+) channel MgtE."
    Takeda H, Hattori M, Nishizawa T, Yamashita K, Shah ST, Caffrey M, Maturana AD, Ishitani R, Nureki O.,
    Nat Commun, 5 5374 (2014).
    PubMed: link Open access, PDB: 4U9L 4U9N 4WIB
27. "Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation."
    Kobayashi K, Suzuki T, Dohmae N, Ishitani R, Nureki O.,
    Acta Crystallogr F Struct Biol Commun, 70 1236-1239 (2014).
    PubMed: link
28. "Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase from Bacillus halodurans."
    Kumazaki K, Tsukazaki T, Nishizawa T, Tanaka Y, Kato HE, Nakada-Nakura Y, Hirata K, Mori Y, Suga H, Dohmae N, Ishitani R, Nureki O.,
    Acta Crystallogr F Struct Biol Commun, 70 1056-1060 (2014).
    PubMed: link
29. "Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP."
    Tominaga T, Kobayashi K, Ishii R, Ishitani R, Nureki O.,
    Acta Crystallogr F Struct Biol Commun, 70 1009-1014 (2014).
    PubMed: link
30. "Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp6."
    Morita J, Kato K, Mihara E, Ishitani R, Takagi J, Nishimasu H, Aoki J, Nureki O.,
    Acta Crystallogr F Struct Biol Commun, 70 794-799 (2014).
    PubMed: link
31. "Crystal structure of a claudin provides insight into the architecture of tight junctions."
    Suzuki H, Nishizawa T, Tani K, Yamazaki Y, Tamura A, Ishitani R, Dohmae N, Tsukita S, Nureki O, Fujiyoshi Y.,
    Science, 344 304-307 (2014).
    PubMed: link, PDB: 4P79
32. "Structural basis of Sec-independent membrane protein insertion by YidC."
    Kumazaki K, Chiba S, Takemoto M, Furukawa A, Nishiyama K, Sugano Y, Mori T, Dohmae N, Hirata K, Nakada-Nakura Y, Maturana AD, Tanaka Y, Mori H, Sugita Y, Arisaka F, Ito K, Ishitani R, Tsukazaki T, Nureki O.,
    Nature, 509 516-520 (2014).
    PubMed: link, PDB: 3WO6 3WO7
33. "Crystal structure of Saccharomyces cerevisiae mitochondrial GatFAB reveals a novel subunit assembly in tRNA-dependent amidotransferases."
    Araiso Y, Huot JL, Sekiguchi T, Frechin M, Fischer F, Enkler L, Senger B, Ishitani R, Becker HD, Nureki O.,
    Nucleic Acids Res, 42 6052-6063 (2014).
    PubMed: link, PDB: 4N0I
34. "Crystal structure of Cas9 in complex with guide RNA and target DNA."
    Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O.,
    Cell, 156 935-949 (2014).
    PubMed: link, PDB: 4OO8
35. "Structural Basis for Potent Inhibition of SIRT2 Deacetylase by a Macrocyclic Peptide Inducing Dynamic Structural Change."
    Yamagata, K., Goto, Y., Nishimasu, H., Morimoto, J., Ishitani, R., Dohmae, N., Takeda, N., Nagai, R., Komuro, I., Suga, H., Nureki, O.,
    Structure, 22 345-352 (2013).
    PubMed: link, PDB: 4L3O
36. "Conformational variation of the translocon enhancing chaperone SecDF."
    Mio, K., Tsukazaki, T., Mori, H., Kawata, M., Moriya, T., Sasaki, Y., Ishitani, R., Ito, K., Nureki, O., Sato, C.,
    J Struct Funct Genomics, (2013).
    PubMed: link
37. "Structural and Functional Analyses of DNA-Sensing and Immune Activation by Human cGAS."
    Kato, K., Ishii, R., Goto, E., Ishitani, R., Tokunaga, F., Nureki, O.,
    PLoS One, 8 e76983 (2013).
    PubMed: link, PDB: 4MKP
38. "Structural biology of ubiquitin signaling."
    Nishimasu, H., Ishitani, R., Nureki, O.,
    Seikagaku, 85 423-429 (2013).
    PubMed: link
39. "Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT."
    Doki S, Kato HE, Solcan N, Iwaki M, Koyama M, Hattori M, Iwase N, Tsukazaki T, Sugita Y, Kandori H, Newstead S, Ishitani R, Nureki O.,
    Proc Natl Acad Sci U S A, 110 11343-8 (2013).
    PubMed: link, PDB: 4IKV 4IKW 4IKX 4IKY 4IKZ
40. "Structural Basis for the Counter-Transport Mechanism of a H+/Ca2+ Exchanger."
    Nishizawa T, Kita S, Maturana AD, Furuya N, Hirata K, Kasuya G, Ogasawara S, Dohmae N, Iwamoto T, Ishitani R, Nureki O.,
    Science, 341 168-72 (2013).
    PubMed: link, PDB: 4KPP
41. "Screening and X-Ray Crystal Structure-based Optimization of Autotaxin (ENPP2) Inhibitors, Using a Newly Developed Fluorescence Probe."
    Kawaguchi M, Okabe T, Okudaira S, Nishimasu H, Ishitani R, Kojima H, Nureki O, Aoki J, Nagano T.,
    ACS Chem Biol, 8 1713-21 (2013).
    PubMed: link
42. "Structural basis for the drug extrusion mechanism by a MATE multidrug transporter."
    Tanaka Y, Hipolito CJ, Maturana AD, Ito K, Kuroda T, Higuchi T, Katoh T, Kato HE, Hattori M, Kumazaki K, Tsukazaki T, Ishitani R, Suga H, Nureki O.,
    Nature, 496 247-251 (2013).
    PubMed: link, PDB: 3W4T 3VVS 3VVR 3VVP 3VVO 3VVN 3WBN
43. "Crystal structure of Cex1p reveals the mechanism of tRNA trafficking between nucleus and cytoplasm."
    Nozawa K, Ishitani R, Yoshihisa T, Sato M, Arisaka F, Kanamaru S, Dohmae N, Mangroo D, Senger B, Becker HD, Nureki O.,
    Nucleic Acids Res, 41 3901-3914 (2013).
    PubMed: link, PDB: 3VWA
44. "Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling."
    Kato K, Nishimasu H, Okudaira S, Mihara E, Ishitani R, Takagi J, Aoki J, Nureki O,
    Proc Natl Acad Sci U S A., (2012).
    PubMed: link, PDB: 4GTW 4GTX 4GTY 4GTZ
45. "Molecular Dynamics Simulation of Autotaxin: Roles of the Nuclease-like Domain and the Glycan Modification."
    Koyama M, Nishimasu H, Ishitani R, Nureki O,
    J Phys Chem B., 116 11798–11808 (2012).
    PubMed: link
46. "Specific recognition of linear polyubiquitin by A20 zinc finger 7 is involved in NF-κB regulation."
    Tokunaga F, Nishimasu H, Ishitani R, Goto E, Noguchi T, Mio K, Kamei K, Ma A, Iwai K, Nureki O,
    EMBO J., 31 3856-3870 (2012).
    PubMed: link, PDB: 3VUW 3VUX 3VUY
47. "Simplification of the genetic code: restricted diversity of genetically encoded amino acids."
    Kawahara-Kobayashi A, Masuda A, Araiso Y, Sakai Y, Kohda A, Uchiyama M, Asami S, Matsuda T, Ishitani R, Dohmae N, Yokoyama S, Kigawa T, Nureki O, Kiga D,
    Nucleic Acids Res., (2012).
    PubMed: link, PDB: 3UFZ 3UG0
48. "Structural basis for translation termination by archaeal RF1 and GTP-bound EF1α complex."
    Kobayashi K, Saito K, Ishitani R, Ito K, Nureki O,
    Nucleic Acids Res., 40 9319-9328 (2012).
    PubMed: link, PDB: 3VMF
49. "Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp1."
    Kato K, Nishimasu H, Mihara E, Ishitani R, Takagi J, Aoki J, Nureki O,
    Acta Crystallogr Sect F Struct Biol Cryst Commun., 68(Pt 7) 778-782 (2012).
    PubMed: link
50. "Spatial distribution of cytoplasmic domains of the Mg(2+)-transporter MgtE, in a solution lacking Mg(2+), revealed by paramagnetic relaxation enhancement."
    Imai S, Maruyama T, Osawa M, Hattori M, Ishitani R, Nureki O, Shimada I,
    Biochim Biophys Acta., 1824 1129-1135 (2012).
    PubMed: link
51. "Backbone resonance assignments for the cytoplasmic region of the Mg(2+) transporter MgtE in the Mg (2+)-unbound state."
    Maruyama T, Imai S, Osawa M, Hattori M, Ishitani R, Nureki O, Shimada I,
    Biomol NMR Assign., (2012).
    PubMed: link
52. "Structure of a dominant-negative helix-loop-helix transcriptional regulator suggests mechanisms of autoinhibition."
    Ishii R, Isogaya K, Seto A, Koinuma D, Watanabe Y, Arisaka F, Yaguchi SI, Ikushima H, Dohmae N, Miyazono K, Miyazawa K, Ishitani R, Nureki O,
    EMBO J., 31 2541-2552 (2012).
    PubMed: link, PDB: 3AY5
53. "A 3D view of autotaxin."
    Nishimasu H, Ishitani R, Aoki J, Nureki O,
    Trends Pharmacol Sci., 33 138-145 (2012).
    PubMed: link
54. "Crystal structure of the channelrhodopsin light-gated cation channel."
    Kato HE, Zhang F, Yizhar O, Ramakrishnan C, Nishizawa T, Hirata K, Ito J, Aita Y, Tsukazaki T, Hayashi S, Hegemann P, Maturana AD, Ishitani R, Deisseroth K, Nureki O,
    Nature, 482 369-374 (2012).
    PubMed: link, PDB: 3UG9
55. "Omnipotent role of archaeal elongation factor 1 alpha (EF1α) in translational elongation and termination, and quality control of protein synthesis."
    Saito K, Kobayashi K, Wada M, Kikuno I, Takusagawa A, Mochizuki M, Uchiumi T, Ishitani R, Nureki O, Ito K,
    Proc Natl Acad Sci U S A., 107 19242-19247 (2010).
    PubMed: link, PDB: 3AGK
56. "Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification."
    Kato M, Araiso Y, Noma A, Nagao A, Suzuki T, Ishitani R, Nureki O,
    Nucleic Acids Res., (2010).
    PubMed: link, PDB: 3AL5 3AL6
57. "Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex."
    Kobayashi K, Kikuno I, Kuroha K, Saito K, Ito K, Ishitani R, Inada T, Nureki O,
    Proc Natl Acad Sci U S A. , 107 17575-17579 (2010).
    PubMed: link, PDB: 3AGJ
58. "C-terminal domain of archaeal O-phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNASec."
    Sherrer RL, Araiso Y, Aldag C, Ishitani R, Ho JM, Söll D, Nureki O,
    Nucleic Acids Res., (2010).
    PubMed: link, PDB: 3AM1
59. "Expanding role of the Jumonji C domain as an RNA hydroxylase."
    Noma A, Ishitani R, Kato M, Nagao A, Nureki O, Suzuki T,
    J Biol Chem., (2010).
    PubMed: link
60. "Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation."
    Nureki O, O'Donoghue P, Watanabe N, Ohmori A, Oshikane H, Araiso Y, Sheppard K, S醇rll D, Ishitani R,
    Nucleic Acids Res., (2010).
    PubMed: link
61. "Molecular mechanisms underlying the early stage of protein translocation through the Sec translocon."
    Mori T, Ishitani R, Tsukazaki T, Nureki O, Sugita Y,
    Biochemistry, 49 945-950 (2010).
    PubMed: link
62. "Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase"
    Nakanishi K, Bonnefond L, Kimura S, Suzuki T, Ishitani R, Nureki O,
    Nature, 461 1144-1148 (2009).
    PubMed: link, PDB: 3A2K 3HJ7
63. "Structure of a tRNA-dependent kinase essential for selenocysteine decoding"
    Araiso Y, Sherrer RL, Ishitani R, Ho JM, S�ll D, Nureki O,
    Proc Natl Acad Sci U S A, 106 16215-16220 (2009).
    PubMed: link, PDB: 3A4N
64. "Mg²⁺-dependent gating of bacterial MgtE channel underlies Mg²⁺ homeostasis"
    Hattori M, Iwase N, Furuya N, Tanaka Y, Tsukazaki T, Ishitani R, Maguire ME, Ito K, Maturana A, Nureki O,
    EMBO J, 28 3602-3612 (2009).
    PubMed: link, PDB: 2ZY9
65. "Structural Basis of Novel Interactions Between the Small-GTPase and GDI-like Domains in Prokaryotic FeoB Iron Transporter."
    Hattori M, Jin Y, Nishimasu H, Tanaka Y, Mochizuki M, Uchiumi T, Ishitani R, Ito K, Nureki O.,
    Structure., 17 1345-55 (2009).
    PubMed: link, PDB: 3A1S 3A1T 3A1U 3A1V 3A1W
66. "Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2."
    Umitsu M, Nishimasu H, Noma A, Suzuki T, Ishitani R, Nureki O.,
    Proc Natl Acad Sci U S A., 106 15616-21 (2009).
    PubMed: link, PDB: 3A27 3A26 3A25
67. "Crystallization and preliminary X-ray diffraction analysis of the truncated cytosolic domain of the iron transporter FeoB."
    Jin Y, Hattori M, Nisimasu H, Ishitani R, Nureki O.,
    Acta Crystallogr Sect F Struct Biol Cryst Commun., 65(Pt 8) 784-7 (2009).
    PubMed: link
68. "Crystal structure of the cytosolic domain of the cation diffusion facilitator family protein."
    Higuchi T, Hattori M, Tanaka Y, Ishitani R, Nureki O.,
    Proteins, [Epub ahead of print] (2009).
    PubMed: link, PDB: 2ZZT
69. "Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase."
    Nishimasu H, Ishitani R, Yamashita K, Iwashita C, Hirata A, Hori H, Nureki O,
    Proc Natl Acad Sci U S A, [Epub ahead of print] (2009).
    PubMed: link, PDB: 3G5Q 3G5R 3G5S
70. "Structural basis of tRNA modification with CO₂ fixation and methylation by wybutosine synthesizing enzyme TYW4."
    Suzuki Y, Noma A, Suzuki T, Ishitani R, Nureki O,
    Nucleic Acids Res., [Epub ahead of print] (2009).
    PubMed: link, PDB: 2ZW9 2ZWA 2ZZK
71. "Pyrrolysyl-tRNA synthetase tRNA^Pyl structure reveals the molecular basis of orthogonality."
    Nozawa K, O'Donoghue P, Gundllapalli S, Araiso Y, Ishitani R, Umehara T, Soll D and Nureki O,
    Nature, 457(7233) 1163-1167 (2009).
    PubMed: link, PDB: 2ZNI 2ZNJ
72. "Crystallization and preliminary X-ray diffraction analysis of GCIP/HHM transcriptional regulator."
    Seto A, Ikushima H, Suzuki T, Sato Y, Fukai S, Yuki K, Miyazawa K, Miyazono K, Ishitani R and Nureki O,
    Acta Crystallogr Sect. F Struct. Biol. Cryst. Commun., 65(Pt 1) 21-24 (2009).
    PubMed: link
73. "Conformational transition of Sec machinery inferred from bacterial SecYE structures."
    Tsukazaki T, Mori H, Fukai S, Ishitani R, Mori T, Dohmae N, Perederina A, Sugita Y, Vassylyev D, Ito K and Nureki O,
    Nature, 455 988-991 (2008).
    PubMed: link, PDB: 2ZJS 2ZQP
74. "Mg²⁺-sensing mechanism of Mg²⁺ transporter MgtE probed by molecular dynamics study."
    Ishitani R, Sugita Y, Dohmae N, Furuya N, Hattori M and Nureki O.,
    Proc Natl Acad Sci U S A, 105(40) 15393-15398 (2008).
    PubMed: link
75. "Structure, dynamics, and function of RNA modification enzymes."
    Ishitani R, Yokoyama S and Nureki O.,
    Curr Opin Struct Biol., 18(3) 330-339. (2008).
    PubMed: link
76. "Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations."
    Ishitani R, Terada T and Shimizu K.,
    Mol. Simul., 34 327–336 (2008).
77. "Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation."
    Araiso Y, Palioura S, Ishitani R, Sherrer RL, O'Donoghue P, Yuan J, Oshikane H, Domae N, Defranco J, Soll D and Nureki O.,
    Nucleic Acids Res., 36(4) 1187-1199. (2008).
    PubMed: link, PDB: 2Z67
78. "Animated crystallography of genetic code translation."
    Tomita K, Numata T, Fukai S, Ishitani R and Nureki O.,
    Nucleic Acids Symp. Ser. (Oxf), 51 101-102 (2007).
    PubMed: link
79. "Crystallization and preliminary X-ray diffraction analysis of the cytosolic domain of a cation diffusion facilitator family protein."
    Hattori M, Tanaka Y, Ishitani R and Nureki O.,
    Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 63(Pt 9) 771-773 (2007).
    PubMed: link
80. "Anticodon recognition and discrimination by the alpha-helix cage domain of class I lysyl-tRNA synthetase."
    Levengood JD, Roy H, Ishitani R, Söll D, Nureki O and Ibba M.,
    Biochemistry., 46(39) 11033-11038 (2007).
    PubMed: link
81. "Crystal Structure of the Radical SAM Enzyme Catalyzing Tricyclic Modified Base Formation in tRNA."
    Suzuki Y, Noma A, Suzuki T, Senda M, Senda T, Ishitani R and Nureki O.,
    J. Mol. Biol., 372(5) 1204-1214 (2007).
    PubMed: link, PDB: 2Z2U
82. "Crystal structure of the MgtE Mg²⁺ transporter."
    Hattori M, Tanaka Y, Fukai S, Ishitani R and Nureki O.,
    Nature, 448 1072-1075 (2007).
    PubMed: link, PDB: 2YVX 2YVY 2YVZ
83. "Crystallization and preliminary X-ray diffraction analysis of the full-length Mg²⁺ transporter MgtE."
    Hattori M, Tanaka Y, Fukai S, Ishitani R and Nureki O.,
    Acta Crystallograph Sect F Struct Biol Cryst Commun. , 63(Pt 8) 682-684 (2007).
    PubMed: link
84. "Crystallization and preliminary X-ray diffraction analysis of the cytosolic domain of the Mg²⁺ transporter MgtE."
    Tanaka Y, Hattori M, Fukai S, Ishitania R and Nureki O.,
    Acta Crystallograph Sect F Struct Biol Cryst Commun, 63(Pt 8) 678-681 (2007).
    PubMed: link
85. "Crystal structure of the Sec4p·Sec2p complex in the nucleotide exchanging intermediate state "
    Sato Y, Fukai S, Ishitani R and Nureki O,
    PNAS, 104 (19) 8305-8310 (2007).
    PubMed: link, PDB: 2EQB
86. "Complete crystallographic analysis of the dynamics of CCA sequence addition."
    Tomita K, Ishitani R, Fukai S, Nureki O.,
    Nature, 7114 956-960 (2006).
    PubMed: link
87. "Structural basis of RNA-dependent recruitment of glutamine to the genetic code"
    Oshikane H, Sheppard K, Fukai S, Nakamura Y, Ishitani R, Numata T, Sherrer RL, Feng L, Schmitt E, Panvert M, Blanquet S, Mechulam Y, Soll D, Nureki O.,
    Science, 312 1950-1954 (2006).
    PubMed: link
88. "Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides"
    Ishitani R, Shimizu K, Terada T.,
    J. Chem. Phys., 124 214902 (2006).
    PubMed: link
89. "Crystallization of leucyl-tRNA synthetase complexed with tRNA^Leu from the archaeon Pyrococcus horikoshii"
    Fukunaga R, Ishitani R, Nureki O, Yokoyama S.,
    Acta Crystallogr., F61 30-32 (2005).
    PubMed: link
90. "Structural basis for template-independent RNA polymerization"
    Tomita K, Fukai S, Ishitani R, Ueda T, Takeuchi N, Vassylyev DG, Nureki O.,
    Nature, 430 700-704 (2004).
    PubMed: link
91. "Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl- tRNA synthetase and its complex with L-valine"
    Fukunaga R, Fukai S, Ishitani R, Nureki O, Yokoyama S.,
    J. Biol. Chem., 279 8396-8402 (2004).
    PubMed: link
92. "The Crystal Structure of a Putative Aspartate Aminotransferase Belonging to Subgroup IV"
    Katsura Y, Shirouzu M, Yamaguchi H, Ishitani R, Nureki O, Kuramitsu S, Hayashi H, Yokoyama S.,
    Proteins, 55 487-492 (2003).
    PubMed: link
93. "Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure."
    Okabe M, Tomita K, Ishitani R, Ishii R, Takeuchi N, Arisaka F, Nureki O, Yokoyama S.,
    EMBO J., 22 5918-5927 (2003).
    PubMed: link
94. "Activation of the pyrrolysine suppressor tRNA requires formation of a ternary complex with class I and class II lysyl-tRNA synthetases."
    Polycarpo C, Ambrogelly A, Ruan B, Tumbula-Hansen D, Ataide SF, Ishitani R, Yokoyama S, Nureki O, Ibba M, Soll D.,
    Mol. Cell, 12 287-294 (2003).
    PubMed: link
95. "Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic-code expansion"
    Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, Cusack S, Sakamoto K, Yokoyama S.,
    Nat. Struct. Biol., 10 425-432 (2003).
    PubMed: link
96. "Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme"
    Ishitani R, Nureki O, Nameki N, Okada N, Nishimura S, Yokoyama S.,
    Cell, 113 383-394 (2003).
    PubMed: link
97. "Crystal structure of human epidermal growth factor in complex with the extracellular domains of the receptor"
    H. Ogiso, R. Ishitani, O. Nureki, S. Fukai, M. Yamanaka, J.-H. Kim, K. Saito, M., Shirouzu, and S. Yokoyama,
    Cell, 110 775-787 (2002).
    PubMed: link
98. "Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form."
    Kagawa W, Kurumizaka H, Ishitani R, Fukai S, Nureki O, Shibata T, Yokoyama S.,
    Mol. Cell, 10 359-371 (2002).
    PubMed: link
99. "An enzyme with a deep trefoil knot for the active-site architecture"
    Nureki O, Shirouzu M, Hashimoto K, Ishitani R, Terada T, Tamakoshi M, Oshima T, Chijimatsu M, Takio K, Vassylyev DG, Shibata T, Inoue Y, Kuramitsu S, Yokoyama S.,
    Acta Crystallogr., D58 1129-1137 (2002).
    PubMed: link
100. "Functional convergence of two lysyl-tRNA synthetases with unrelated topologies"
     Terada T, Nureki O, Ishitani R, Ambrogelly A, Ibba M, Soll D, Yokoyama S.,
     Nat. Struct. Biol., 9 257-262 (2002).
     PubMed: link
101. "Crystal structure of archaeosine tRNA-guanine transglycosylase"
     Ishitani R, Nureki O, Fukai S, Kijimoto T, Nameki N, Watanabe M, Kondo H, Sekine M, Okada N, Nishimura S, Yokoyama S.,
     J. Mol. Biol., 318 665-677 (2002).
     PubMed: link
102. "Selenomethionine incorporation into a protein by cell-free synthesis"
     Kigawa T, Yamaguchi-Nunokawa E, Kodama K, Matsuda T, Yabuki T, Matsuda N, Ishitani R, Nureki O, Yokoyama S.,
     J. Struc. Func. Gen., 2 87-104 (2001).
     PubMed: link
103. "Crystallization and preliminary X-ray analysis of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii"
     Ishitani R, Nureki O, Kijimoto T, Watanabe M, Kondo H, Nameki N, Okada N, Nishimura S, Yokoyama S.,
     Acta Crystallogr., D57 1659-1662 (2001).
     PubMed: link




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