石谷 隆一郎

准教授 石谷 隆一郎(いしたに りゅういちろう)

学歴

1993年
香川県立丸亀高校卒業
1993年
東京大学教養学部理科I類入学
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

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

職歴

平成15年
東京大学理学部 生物情報科学 特任教員(助手相当)
平成16年
東京大学 農学生命科学研究科 産学官連携研究員
平成17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
平成18年
エーキューブ・インコーポレーティッド社 顧問
平成18年
東京工業大学 生命理工学研究科 生命情報専攻 助手
平成19年
東京工業大学 生命理工学研究科 生命情報専攻 助教
平成20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
平成22年
東京大学大学院 理学系研究科 生物化学専攻 准教授
平成30年
株式会社Preferred Networks Researcher
令和元年
東京大学大学院 理学系研究科 生物化学専攻 特任教授
令和6年
東京医科歯科大学 難治疾患研究所 教授
現在に至る

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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    38. "Structural biology of ubiquitin signaling."
      Nishimasu, H., Ishitani, R., Nureki, O.,
      Seikagaku, 85 423-429 (2013).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    53. "A 3D view of autotaxin."
      Nishimasu H, Ishitani R, Aoki J, Nureki O,
      Trends Pharmacol Sci., 33 138-145 (2012).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    71. "Pyrrolysyl-tRNA synthetase tRNAPyl 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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    82. "Crystal structure of the MgtE Mg2+ transporter."
      Hattori M, Tanaka Y, Fukai S, Ishitani R and Nureki O.,
      Nature, 448 1072-1075 (2007).
    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).
    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).
    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).
    86. "Complete crystallographic analysis of the dynamics of CCA sequence addition."
      Tomita K, Ishitani R, Fukai S, Nureki O.,
      Nature, 7114 956-960 (2006).
    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).
    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).
    89. "Crystallization of leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii"
      Fukunaga R, Ishitani R, Nureki O, Yokoyama S.,
      Acta Crystallogr., F61 30-32 (2005).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).
    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).


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