論文

• Vipul Gupta, Shujie Liu, Hideki Ando, Ryohei Ishii, Shumpei Tateno, Yuki Kaneko, Masato Yugami, Satoshi Sakamoto, Yuki Yamaguchi, Osamu Nureki, Hiroshi Handa. Salicylic acid induces mitochondrial injury by inhibiting ferrochelatase heme biosynthesis activity, Mol. Pharmacol., Vol. 84, No. 6, pp. 824-833, Nov. 2013.
• T. Sengoku, O. Nureki, A. Nakamura, S. Kobayashi, S. Yokoyama. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa, Cell, Vol. 125, pp. 287-300, 2006.
• K. Tomita, R. Ishitani, S. Fukai, O. Nureki. Complete crystallographic analysis of the dynamics of CCA-addition, Nature, Vol. 443, pp. 956-960, 2006.
• K. Watanabe K, O. Nureki, S. Fukai, Y. Endo, H. Hori. Functional categorization of the conserved basic amino acid residues in TrmH [tRNA (Gm18) methyltansferase] enzymes, J. Biol. Chem., Vol. 281, pp. 34630-34639, 2006.
• T. Numata, Y. Ikeuchi, S. Fukai, H. Adachi, H. Matsumura, K. Takano, S. Murakami, T. Inoue, Y. Mori, T. Sasaki, T. Suzuki, O. Nureki. Crystallization and preliminary X-ray analysis of tRNA thiolation enzyme MnmA from Escherichia coli complexed with tRNA^Glu, Acta Crystallographica F, Vol. 62, pp. 368-371, 2006.
• T. Yanagisawa, R. Ishii, R. Fukunaga, O. Nureki, S. Yokoyama. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of pyrrolysyl-tRNA synthetase from the methanogenic archaeon Methanosarcina mazei, Acta. Crystallograph. Sect. F Struct. Biol. Cryst. Commun., Vol. 62, pp. 1031-1033, 2006.
• K. Suto, Y. Shimizu, K. Watanabe, T. Ueda, S. Fukai, O. Nureki, K. Tomita. Crystal structure of leucyl/phenylalanyl-tRNA-protein transferase and its complex with aminoacyl-tRNA analog, EMBO J., Vol. 13, pp. 5942-5950, 2006.
• T. Numata, Y. Ikeuchi, S. Fukai, T. Suzuki, O. Nureki. Snapshots of tRNA sulfuration via an adenylated intermediate, Nature, Vol. 442, pp. 419-424, 2006.
• T. Numata, S. Fukai, Y. Ikeuch, T. Suzuki, O. Nureki. Structural basis for sulfur relay to RNA mediated by heterohexametric TusBCD complex, Structure, Vol. 14, pp. 357-366, 2006.
• H. Oshikane, K. Sheppard, S. Fukai, Y. Nakamura, R. Ishitani, T. Numata, L. R. Sherrer, L. Feng, E. Schmitt, M. Panvert, S. Blanquet, Y. Mechulam, D. Söll, O. Nureki. Structural basis of RNA-dependent recruitment of glutamine to the genetic code, Science, Vol. 312, pp. 1950-1954, 2006.
• T. Tsukazaki, H. Mori., S. Fukai, T. Numata, A. Perederina, H. Adachi, H. Matsumura, K. Takano, S. Murakami., T. Inoue., Y. Mori., T. Sasaki., D. G. Vassylyev., O. Nureki, K. Ito. Purification, crystallization and preliminary X-ray diffraction of SecDF, a translocon-associated membrane protein, from Thermus thermophilus, Acta Crystallographica F, Vol. 62, pp. 376-380, 2006.
• R. Fukunaga, R. Ishitani, O. Nureki, S. Yokoyama. Crystallization of leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii, Acta Crystallographica F, Vol. 61, pp. 30-32, 2005.
• K. Watanabe, O. Nureki, S. Fukai, R. Ishii, H. Okamoto, S. Yokoyama, Y. Endo, H. Hori. Roles of conserved amino acid sequence motifs in the SpoU (TrmH) RNA methyltransferase family, J Biol Chem., Vol. 280, pp. 10368-10377, 2005.
• K. Nakanishi, Y. Ogiso, S. Fukai, O. Nureki. Structural basis for anticodon recognition by methionyl-tRNA synthetase, Nat. Struct. Mol. Biol, Vol. 12, pp. 931-932, 2005.
• K. Nakanishi, S. Fukai, Y. Ikeuchi, A. Soma, Y. Sekine, T. Suzuki, O. Nureki. Structural basis for lysidine formation by ATP pyrophosphatase accompanied with a lysine-specific loop and a tRNA-recognition domain, Proc. Natl. Acad.Sci. USA, Vol. 21, pp. 7487-7492, 2005.
• K. Nakanishi, O. Nureki. Recent progress of structural biology of tRNA processing and modification, Mol. Cells, Vol. 19, pp. 157-166, 2005.
• N. Fujikawa, H. Kurumizaka, O. Nureki, Y. Tanaka, M. Yamazoe, S. Hiraga, S. Yokoyama. Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein, Nucleic Acids Res., Vol. 32, pp. 82-92, 2004.
• K. Tomita, S. Fukai, R. Ishitani, T. Ueda, N. Takeuchi, D. G. Vassylyev, O. Nureki. Structural basis for template-independent RNA polymerization, Nature, Vol. 430, pp. 700-704, 2004.
• O. Nureki, K. Watanabe, S. Fukai, R. Ishii, Y. Endo, H. Hori, S. Yokoyama. Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme, Structure, Vol. 12, pp. 593-602, 2004.
• T. Sengoku, O. Nureki, N. Dohmae, A. Nakamura, Yokoyama S. Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue., Acta Crystallographica D, Vol. 60, pp. 320-322, 2004.
• R. Fukunaga, S. Fukai, R. Ishitani, O. Nureki, S. Yokoyama. Crystal structures of the CP1 domain from thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine, J. Biol. Chem., Vol. 279, pp. 8396-8402, 2004.
• Y. Kise, S. W. Lee, S. G. Park, S. Fukai, T. Sengoku, R. Ishii, S. Yokoyama, S. Kim, O. Nureki. A short peptide insertion crucial for angiostatic activity of human tryptophanyl–tRNA synthetase, Nature Struct. & Mol. Biol., Vol. 11, pp. 149-156, 2004.
• S. Fukai, O. Nureki, S. Skine, A. Shimada, D. G. Vassylyev, S. Yokoyama. Mechanism of molecular interactions for tRNA^Val recognition by valyl-tRNA synthetase, RNA, Vol. 8, pp. 100-111, 2003.
• R. Ishitani, O. Nureki, N. Nameki, N. Okada, S. Nishimura, S. Yokoyama. Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme., Cell, Vol. 113, pp. 383-394, 2003.
• N. Fujikawa, H. Kurumizaka, O. Nureki, T. Terada, M. Shirouzu, T. Katayama, S. Yokoyama. Structural basis of the replication origin recognition by the DnaA protein, Nucleic Acids Res., Vol. 31, pp. 2077-2086, 2003.
• T. Kobayashi, O. Nureki, R. Ishitani, A. Yaremchuk, M. Tukalo, S. Cusack, K. Sakamoto, S. Yokoyama. Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetses for genetic-code expansion, Nature Struct. Biol., Vol. 10, pp. 425-432, 2003.
• R. Ishii, O. Nureki, S. Yokoyama. Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus, J. Biol. Chem., Vol. 278, pp. 32397-32404, 2003.
• K. Saito, H. Ogiso, R. Ishitani, O. Nureki, S. Fukai, M. Yamanaka, J.-H. Kim, M. Shirouzu, S. Yokoyama. The Activation Mechanisu of the Epidermal Growth Factor Reseptor, The Japnese Peptide Society, pp. 93-96, 2003.
• Y. Katsura., M. Shirouzu, H. Yamaguchi., R. Ishitani., O. Nureki, S. Kuramitsu., H. Hayashi., S. Yokoyama. The Crystal Structure of a Putative Aspartate Aminotransferase Belonging to Subgroup IV, Proteins, Vol. 55, pp. 487-492, 2003.
• M. S. Tawaramoto, S. Y. Park, Y. Tanaka, O. Nureki, H. Kurumizaka, S. Yokoyama. Crystal structure of the human CENP-B dimerization domain at 1.65 A resolution, J. Biol. Chem., Vol. 278, pp. 51454-51461, 2003.
• N. Ito, O. Nureki, M. Shirouzu, S. Yokoyama, F. Hanaoka. Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis, Genes Cells, Vol. 8, pp. 913-923, 2003.
• M. Okabe, K. Tomita, R. Ishitani, R. Ishii, N. Takeuchi, F. Arisaka, O. Nureki*, S. Yokoyama (*corresponding author). Divergent evolution of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure, EMBO J., Vol. 22, pp. 5918-5927, 2003.
• C. Polyvarpo, A. Ambrogelly, B. Ruan, D. Tumbla-Hansen, S. F. Ataide, R. Tshitani, S. Yokoyama, O. Nureki, M. Ibba, D. Söll. Activation of the pyrrolysine suppressor tRNA requires formation of ternary complex with class I and class II lysyl-tRNA synthetases, Mol. Cell., Vol. 12, pp. 287-294, 2003.
• S. Sekine, O. Nureki, S. Bernier, R. Chênevert, J. Lapointe, D. G. Vassylyev, S. Yokoyama. ATP-binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding, EMBO J., Vol. 23, pp. 1-13, 2003.
• W. Kagawa, H. Kurumizaka, S. Fukai, R. Ishitani, O. Nureki, T. Shibata, S. Yokoyama. Crystal structure of the human Rad52 protein and its implications for homologous recombination, Mol. Cell, Vol. 10, pp. 359-371, 2002.
• T. L. Hendrickson, T. K. Nomanbhoy, V. Crécy-Lagard, S. Fukai, O. Nureki, S. Yokoyama, P. Schimmel. Mutation Separation of two pathways for editing by a class I tRNA synthetase, Mol. Cell, Vol. 9, pp. 353-362, 2002.
• R. Ishitani, O. Nureki, S. Fukai, T. Kijimoto, N. Nameki, M. Watanabe, H. Kondo, M. Sekine, N. Okada, S. Nishimura, S. Yokoyama. Crystal structure of archaeosine tRNA-guanine transglycosylase, J. Mol. Biol., Vol. 318, pp. 665-677, 2002.
• T. Terada*, O. Nureki*, R. Ishitani, A. Amblogelly, M. Ibba, D. Söll, S. Yokoyama (*equal contribution). Functional convergence of two lysyl-tRNA synthetases with unrelated topologies, Nature Struct. Biol., Vol. 9, pp. 257-262, 2002.
• O. Nureki, M. Shiruuzu, K. Hashimoto, R. Ishitani, T. Terada, M. Tamakoshi, T. Oshima, M. Chijimatsu, K. Takio, D. G. Vassylyev, T. Shibata, Y. Inoue, S. Kuramitsu, S. Yokoyama. An enzyme with a deep trefoil knot for the active-site architecture, Acta Crystallographica D, Vol. 58, pp. 1129-1137, 2002.
• H. Ogiso, R. Ishitani, O. Nureki, S. Fukai, M. Yamanaka, J. ﾐH. Kim, K. Saito, M. Shirouzu, S. Yokoyama. Crystal structure of human epidermal growth factor in complex with the extracellular domains of the receptor, Cell, Vol. 110, pp. 775-787, 2002.
• Y. Tanaka*, O. Nureki*, H. Kurumizaka*, S. Fukai, S. Kawaguchi, M. Ikuta, J. Iwahara, T. Okazaki, S. Yokoyama (*equal contribution). DNA kink at the contact site with an arginine-rich helix of human centromere protein B, EMBO J., Vol. 20, pp. 6612-6618, 2001.
• T. Nakama, O. Nureki, S. Yokoyama. Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase, J. Biol. Chem., Vol. 276, pp. 47387-47393, 2001.
• A. Shimada, O. Nureki, M. Goto, S. Takahashi, S. Yokoyama. Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase, Proc. Natl. Acad.Sci. USA, Vol. 98, pp. 13537-13542, 2001.
• S. Sekine, A. Shimada, O. Nureki, J. Cavarelli, D. Moras, D. G. Vassylyev, S. Yokoyama. Crucial role of the HIGH-loop lysine for the catalytic activity of arginyl-tRNA synthetase, J. Biol. Chem., Vol. 276, pp. 3723-3726, 2001.
• S. Sekine, O. Nureki, A. Shimada, D. G. Vassylyev, S. Yokoyama. Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase, Nature Struct. Biol., Vol. 8, pp. 203-206, 2001.
• R. Ishitani, O. Nureki, T. Kijimoto, M. Watanabe, H. Kondo, N. Nameki, N. Okada, S. Nishimura, S. Yokoyama. Crystallization and preliminary X-ray analysis of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii, Acta Crystallographica D, Vol. 57, pp. 1659-1662, 2001.
• N. Ito, O. Nureki, M. Shirouzu, S. Yokoyama, F. Hanaoka. Crystallization and preliminary X-ray analysis of a DNA primase from the hyperthermophilic archaeon, Pyrococcus horikoshii, J. Biochemistry, Vol. 130, pp. 727-730, 2001.
• T. Kigawa, E. Yamaguchi-Nunokawa, K. Kodama, T. Matsuda, T. Yabuki, Natsuko Matsuda, R. Ishitani, O. Nureki, S. Yokoyama. Selenomethionine incorporation into a protein by cell-free synthesis, J. Struc. Func. Gen., Vol. 2, pp. 87-104, 2001.
• K. Kurimoto, S. Fukai, O. Nureki, Y. Muto, S. Yokoyama. Crystal structure of human AUH protein, a single-stranded RNA-binding homologue of enoyl-CoA hydratase, Structure, Vol. 9, pp. 1253-1263, 2001.
• A. Shimada, O. Nureki, N. Dohmae, K. Takio, S. Yokoyama. Gene cloning, expression, crystallization, and preliminary X-ray analysis of Thermus thermophilus arginyl-tRNA synthetase, Acta Crystallographica D, Vol. 57, pp. 272-275, 2000.
• S. Fukai, O. Nureki, S. Sekine, A. Shimada, J. Tao, D. G. Vassylyev, S. Yokoyama. Structural basis for double-sieve discrimination of the cognate L-valine from L-isoleucine and L-threonine by the complex of tRNA^Val and valyl-tRNA synthetase, Cell, Vol. 103, pp. 793-803, 2000.
• I. Sugiura, O. Nureki, Y. Ugaji-Yoshikawa, S. Kuwabara, A. Shimada, M. Tateno, B. Lober, R. Giegé, D. Moras, S. Yokoyama, M. Konno. The 2.0 Å crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules, Structure, Vol. 8, pp. 197-208, 2000.
• M. Kukimoto, O. Nureki, M. Shirouzu, T. Katada, Y. Hirabayashi, H. Sugiya, S. Furuyama, S. Yokoyama, M. Hara-Yokoyam. Crystallization and preliminary X-ray diffraction analysis of the extracellular domain of the cell surface antigen CD38 complexed with ganglioside, J. Biochemistry, Vol. 127, pp. 181-184, 2000.
• O. Nureki, D. G. Vassylyev, M. Tateno, A. Shimada, T. Nakama, S. Fukai, M. Konno, T. L. Hendrickson, P. Schimmel, S. Yokoyama. Proofreading by isoleucyl-transfer RNA synthetase, Science, Vol. 283, pp. 459, 1999.
• S. Sekine, O. Nureki, M. Tateno, S. Yokoyama. The identity determinants required for the discrimination between tRNAGlu and tRNA^Asp by glutamyl-tRNA synthetase from Escherichia coli., Eur. J. Biochem., Vol. 261, pp. 354-360, 1999.
• N. Handa, O. Nureki, K. Kurimoto, I. Kim, H. Sakamoto, Y. Shimura, Y. Muto, S. Yokoyama. Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein, Nature, Vol. 398, pp. 579-585, 1999.
• Y. Mechulam, E. Schmitt, L. Maveyraud, C. Zelwer, O. Nureki, S. Yokoyama, M. Konno, S. Blanquet. Crystal structure of Escherichia coli methionyl-tRNA synthetase highlights species-specific features, J. Mol. Biol., Vol. 294, pp. 1287-1297, 1999.
• O. Nureki, D. G. Vassylyev, M. Tateno, A. Shimada, T. Nakama, S. Fukai, M. Konno, T. L. Hendrickson, P. Schimmel, S. Yokoyama. Enzyme structure with two catalytic sites for double-sieve selection of substrate, Science, Vol. 280, pp. 578-582, 1998.
• S. Sekine, O. Nureki, K. Sakamoto, T. Niimi, M. Tateno, M. Go, T. Kohno, A. Brisson, J. Lapointe, S. Yokoyama. Major identity determinants in the "augmented D helix" of tRNAGlu from Escherichia coli, J. Mol. Biol., Vol. 256, pp. 685-700, 1996.
• O. Nureki, D. G. Vassylyev, K. Katayanagi, T. Shimizu, S. Sekine, T. Kigawa, T. Miyazawa, S. Yokoyama, K.Morikawa. Architectures of the class-defining and specific domains of glutamyl-tRNA synthetase, Science, Vol. 267, pp. 1958-1965, 1995.
• M. Tateno, O. Nureki, S. Sekine, K. Kaneda, M. Go, S. Yokoyama. A three-dimensional structure model of the complex of glutamyl-tRNA synthetase and its cognate tRNA, FEBS Lett., pp. 77-81, 1995.
• T. Niimi, O. Nureki, T. Yokogawa, N. Hayashi, K. Nishikawa, K. Watanabe, S. Yokoyama. Recognition of the anticodon loop of tRNA1Ile by isoleucyl-tRNA synthetase from Escherichia coli, Nucleosides and Nucleotides, Vol. 13, pp. 1231-1237, 1994.
• O. Nureki, T. Niimi, T. Muramatsu, H. Kanno, T. Kohno, C. Florentz, R. Giége, S. Yokoyama. Molecular recognition of the identity-determinant set of isoleucine transfer RNA from Escherichia coli, J. Mol. Biol., Vol. 236, pp. 710-724, 1994.
• O. Nureki, T. Kohno, K. Sakamoto, T. Miyazawa, S.Yokoyama. Chemical modification and mutagenesis studies on zinc binding of aminoacyl-tRNA synthetases, J. Biol.Chem., Vol. 268, pp. 15368-15373, 1993.
• O. Nureki, K. Suzuki, M. Hara-Yokoyama, T. Kohno, H.Matsuzawa, T. Ohta, T. Shimizu, K. Morikawa, T. Miyazawa, S. Yokoyama. Glutamyl-tRNA synthetase from Thermus thermophilus HB8, Eur. J. Biochem, Vol. 204, pp. 465-472, 1992.
• O. Nureki, T. Muramatsu, K. Suzuki, D. Kohda, H. Matsuzawa, T. Ohta, T. Miyazawa, S. Yokoyama. Methionyl-tRNA synthetase gene from an extreme thermophile, Thermus thermophilus HB8, J. Biol. Chem., Vol. 266, pp. 3268-3277, 1991.

国内会議発表 (査読なし・不明)

• 坂本 聡, Gupta Vipul, 劉 舒捷, 安藤秀樹, 舘野峻平, 金子裕生, 湯上真人, 石井亮平, 濡木 理, 山口雄輝, 半田 宏. 抗炎症薬サリチル酸が示す生体内作用メカニズムの解析, 日本化学会年第97春季年会, Mar. 2017.
• 坂本 聡, Vipul Gupta, 劉 舒捷, 安藤 秀樹, 舘野 峻平, 金子 裕生, 湯上 真人, 石井 亮平, 濡木 理, 山口 雄輝, 半田 宏. 抗炎症薬サリチル酸の生体内作用機構の解析, 日本ケミカルバイオロジー学会第９回年会, June 2014.

学位論文

• アミノアシルtRNA合成酵素によるtRNAの認識機構,  本文,  Doctor of Science,  The University of Tokyo,  1993/--/--, 

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