Structural and functional studies on biological macromolecules involved in the flow of genetic information and the cellular signal transduction.

2007 Fiscal Year Final Research Report Summary

• Project/Area Number: 15107002
• Research Category: Grant-in-Aid for Scientific Research (S)
• Allocation Type: Single-year Grants
• Research Field: Structural biochemistry
• Research Institution: The University of Tokyo
• Principal Investigator: YOKOYAMA Shigeyuki The University of Tokyo, Graduate School of Science, Professor (00159229)
• Project Period (FY): 2003 – 2007
• Keywords: Crystallography / Translation / Transcription / Intermolecular interaction / Artificial genetic code / tRNA

Research Abstract

To understand in detail the systems of genetic expression and cellular signal transduction, which consist of cascades of macromolecular interactions, molecular interactions involved in the cascades were analyzed at atomic resolutions by crystallography. We targeted post-transcriptional tRNA processing and modification enzymes and aminoacyl-tRNA synthetases, which are responsible for accurate joining tRNA and amino acid during translation, and performed structural analyses of their complexes with tRNAs, other substrates, and/or inhibitors. We also determined the crystal structure of Vasa, an RNA helicase involved in the differentiation of Drosophila germline, and elucidated structural basis of the RNA double strand resolution by a DEAD-box RNA helicase. Furthermore, we succeeded in crystal structure determination of RNA polymerase and Dmc1, which play central roles in transcription and homologous recombination in meiosis, respectively. The structural information was applied to develop the artificial genetic code system to incorporate a useful, natural or non-natural amino acid into a specific position of any protein. We have established systems to incorporate tyrosine or lysine derivatives, and thus opened a way to the technology that facilitates incorporating an amino acid possessing fluorescent, reactive, or heavy-atom containing groups.

Research Products

• [Journal Article] Crystal structure of archaeal tRNA (m(1)G37) methyltransferase aTrm5 (2008)
  • Author(s): Goto-Ito, S.
  • Journal Title: Proteins (In press)
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA (2008)
  • Author(s): Kuratani, M.
  • Journal Title: J Mol Biol 375 Pages: 1064-75
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of histone demethylase LSDI and tranylcypromine at 2.25 A (2008)
  • Author(s): Mimasu, S.
  • Journal Title: Biochem Biophys Res Commun 366 Pages: 15-22
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Alteration of enzymatic properties of cell-surface antigen CD38 by agonistic anti-CD38 antibodies that prolong B cell survival and induce activation (2008)
  • Author(s): Hara-Yokoyama, M.
  • Journal Title: Int Immunopharmacol 8 Pages: 59-70
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase (2008)
  • Author(s): Yanagisawa, T.
  • Journal Title: J Mol Biol (In press)
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2^1-O-methylcytidine at position 56 of tRNA (2008)
  • Author(s): Kuratani, M., Bessho, Y., Nishimoto, M., Grosjean, H., Yokoyama, S.
  • Journal Title: J Mol Biol 375(4) Pages: 1064-1075
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A (2008)
  • Author(s): Mimasu, S., Sengoku, T, Fukuzawa, S., Umehara, T., Yokoyama, S.
  • Journal Title: Biochem Biophys Res Commun 366(1) Pages: 15-22
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Alteration of enzymatic properties of cell-surface antigen CD38 by agonistic anti-CD38 antibodies that prolong B cell survival and induce activation (2008)
  • Author(s): Hara-Yokoyama, M., Kimura, T., Kaku, H., Wakiyama, M., Kaitsu, Y., Inoue, M., Kusano, S., Shirou, M., Yokoyama, S., katada, T., Hirabayashi, Y., Takatsu, K., Yanagishita, M.
  • Journal Title: Int Immunopharmacol 8(1) Pages: 59-70
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase (2008)
  • Author(s): Yanagisawa, T., Ishii, R., Fukunaga, R., Kobayashi, T., Sakamoto, K., Yokoyama, S.
  • Journal Title: j Mol Biol in press
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea (2007)
  • Author(s): Fukunaga, R.
  • Journal Title: Nat Struct Mol Biol 14 Pages: 272-9
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray crystallographic study of alanyl-tRNA synthetase from the archaeon Archaeoglobus fulgidus (2007)
  • Author(s): Fukunaga, R.
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun 63 Pages: 224-8
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The C-terminal domain of the archaeal leucyl-tRNA synthetase prevents misediting of isoleucyl-tRNA (Ile) (2007)
  • Author(s): Fukunaga, R.
  • Journal Title: Biochemistry 46 Pages: 4985-96
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA: Cys-tRNA synthase from Archaeoglobus fulgidus (2007)
  • Author(s): Fukunaga, R.
  • Journal Title: J Mol Biol 370 Pages: 128-41
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii (2007)
  • Author(s): Fukunaga, R.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 63 Pages: 390-40
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye base biosynthesis (2007)
  • Author(s): Goto-Ito, S.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 63 Pages: 1059-68
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Site-specific incorporation of non-natural amino acids into proteins in mammalian cells with an expanded genetic code (2007)
  • Author(s): Hino, N.
  • Journal Title: Nat Protoc 1 Pages: 2957-62
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes (2007)
  • Author(s): Ishii, R.
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun 63 Pages: 637-41
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis of the initial binding of tRNA (Ile) lysidine synthetase TilS with ATP and L-lysine (2007)
  • Author(s): Kuratani, M.
  • Journal Title: Structure 15 Pages: 1642-53
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA (2007)
  • Author(s): Bessho, Y.
  • Journal Title: Proc Natl Acad Sci USA 104 Pages: 8293-8
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors (2007)
  • Author(s): Connell. S. R.
  • Journal Title: Mol Cell 25 Pages: 751-64
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural aspects of RbfA action during small ribosomal subunit assembly (2007)
  • Author(s): Datta, P. P.
  • Journal Title: Mol Cell 28 Pages: 434-45
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction (2007)
  • Author(s): Kaminishi, T.
  • Journal Title: Structure 15 Pages: 289-97
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Site-specific functionalization of proteins by organopalladium reactions (2007)
  • Author(s): Kodama, K.
  • Journal Title: Chembiochem 8 Pages: 232-8
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Curved EFC/F-BAR-domain dimers are joined end to end into a filament for membrane invagination in endocytosis (2007)
  • Author(s): Shimada, A
  • Journal Title: Cell 129 Pages: 761-72
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The putative DNA-binding protein Sto12a from the thermoacidophilic archaeon Sulfolobus tokodaii contains intrachain and interchain disulfide bonds (2007)
  • Author(s): Shinkai, A.
  • Journal Title: J Mol Biol 372 Pages: 1293-304
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Analysis of the role of Aurora B on the chromosomal targeting of condensin I (2007)
  • Author(s): Takemoto, A.
  • Journal Title: Nucleic Acids Res 35 Pages: 2403-12
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Let-7 microRNA-mediated mRNA deadenylation and translational repression in amammalian cell-free system (2007)
  • Author(s): Wakiyama, M.
  • Journal Title: Genes Dev 21 Pages: 1857-62
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] TAF4-homology domain from the corepressor ETO is a docking platform for positive and negative regulators of transcription (2007)
  • Author(s): Wei, Y.
  • Journal Title: Nat Struct Mol Biol 14 Pages: 653-61
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5 (2007)
  • Author(s): Goto-lto, S., Ito, T., Ishii, R., Muto, Y., Bessho, Y., Yokoyama, S.
  • Journal Title: Proteins (In press)
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea (2007)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: Nat Struct Mol Biol 14(4) Pages: 272-279
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystallization and preliminary X-ray crystallographic study of alanyl-tRNA synthetase from the archaeon Archaeoglobus fulgidus (2007)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun 63(Pt 3) Pages: 224-228
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The C-terminal domain of the archaeal leucyl-tRNA synthetase prevents misediting of isoleucyl-tRNA(lle) (2007)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: Biochemistry 46(17) Pages: 4985-4996
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea : crystal structure of Sep-tRNA : Cys-tRNA synthase from Archaeoglobus fulgidus (2007)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: J Mol Biol 370(1) Pages: 128-141
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of the AIaX-M trans-editing enzyme from Pyrococcus horikoshii (2007)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 63(Pt 3) Pages: 390-400
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis (2007)
  • Author(s): Goto-Ito, S., Ishii, R, Ito, T., Shibata, R, Fusatomi, E., Sekine, S. I., Bessho, Y., Yokoyama, S.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 63(Pt 10) Pages: 1059-1068
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Site-specific incorporation of non-natural amino acids into proteins in mammalian cells with an expanded genetic code (2007)
  • Author(s): Hino, N., Hayashi, A., Sakamoto, K., Yokoyama, S.
  • Journal Title: Nat Protoc 1(6) Pages: 2957-2962
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes (2007)
  • Author(s): Ishii, R., Minagawa, A., Takaku, H., Takagi, M., Nashimoto, M., Yokoyama, S
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun 63(Pt 8) Pages: 637-641
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine (2007)
  • Author(s): Kuratani, M., Yoshikawa, Y., Bessho, Y., Higashijima, K., Ishii, T., Shibata, R, Takahashi, S., Yutani, K., Yokoyama, S.
  • Journal Title: Structure 15(12) Pages: 1642-1653
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA (2007)
  • Author(s): Bessho, Y., Shibata, R., Sekine, S., Murayama, K., Higashijima, K., Hori-Takemoto, C., Shirouzu, M., Kuramistsu, S., Yokoyama, S.
  • Journal Title: Proc Natl Acad Sci U S A 104(20) Pages: 8293-8298
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis for interaction of the ribosome with the switch reginons of GTP-bound elongation factors (2007)
  • Author(s): Connell, S. R., Takemoto, C., Wlison, D. N Wang, H., Murayama, K., Teraka, T., Shirouzu, M., Rost, M., Schuler, M., Giesebrecht, J., Dabrowski, M., Mielke, T., Fucini, P., Yokoyama, S., Spahn, C. M.
  • Journal Title: Mol Cell 25(5) Pages: 751-764
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural aspects of RbfA action during small ribosomal subunit assembly (2007)
  • Author(s): Datta, P. P., Wilson, D. N., Kawazoe, M., Swami, N, K., Kaminishi, T., Sharma, M. R., Booth, T. M., Takemoto, C., Fucini, P., Yokoyama, S., Agrawal, R. K.
  • Journal Title: Mol Cell 28(3) Pages: 434-445
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A snapshot of the 30S ribosomal subusomal subunit capturing mRNA via the Shine-Dalgarno interaction (2007)
  • Author(s): Kaminishi, T., Wilson, D. N., Takemoto, C., Harms, J. M., Kawazoe, M., Schluenzen, F., Hanawa-Suetsugu, K., Shirouzu, M., Fucini, P., Yokoyama, S.
  • Journal Title: Structure 15(3) Pages: 289-297
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Site-specific functionalization of proteins by organopalladium reactions (2007)
  • Author(s): Kodama, K., Fukuzawa, S., Nakayama, H., Sakamoto, K., Kigawa, T., Yabuki, T., Matsuda, N., Shirouzu, M., Takio, K., Yokoyama, S., Tachibana, K.
  • Journal Title: Chenbiochem 8(2) Pages: 232-238
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Curved EFC/F-BAR-domain dimers are joined end to end into a filament for membrane invagination in endocytosis (2007)
  • Author(s): Shimada, A., Niwa, H., Tsujita, K., Suetsugu, S., Nitta, K., Hanawa-Suetsugu, K., Akasaka, R., Nishino, Y., Toyama, M., Chen, L., Liu, Z. J., Wang, B. C., Yamamoto, M., Terada, T., Miyazawa, A., Tanaka, A., Sugano, S., Shirouzu, M., Nagayama, K., Takenawa, T., Yokoyama, S.
  • Journal Title: Cell 129(4) Pages: 761-772
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The putative DNA-binding protein Stol2a from the thermoacidophilic archaeon Sulfolobus tokodaii contains intrachain and interchain disulfide bonds (2007)
  • Author(s): Shinkai, A., Sekine, S., Urushibata, A., Terada, T., Shirouzu, M., Yokoyama, S.
  • Journal Title: J Mol Biol 372(5) Pages: 1293-1304
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Analysis of the tole of Aurora B on the chromosomal targeting of condensin I (2007)
  • Author(s): Takemoto, A., Murayama, A., Katano, M., Urano, T., Furukawa, K., Yokoyama, S., Yanagisawa, J., Hanaoka, F., Kimura, K.
  • Journal Title: Nucleic Acids Res 35(7) Pages: 2403-2412
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] let-7microRNA-mediated mRNA deadenylation and translationla repression in a mammalian cell-free system (2007)
  • Author(s): Wakiyama, M., Takimoto, K., Ohata, O., Yokoyama, S.
  • Journal Title: Genes Dev 21(15) Pages: 1857-1862
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A TAF4-homology domain from the corepressor ETO is a docking platform for positive and negative regulators of transcription (2007)
  • Author(s): Wei, Y., Liu, S., Lausen, J., Woodrell, C., Cho, S., Biris, N., Kobayashi, N., Wei, Y., Yokoyama, S., Werner, M. H.
  • Journal Title: Nat Struct Mol Biol 14(7) Pages: 653-661
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase (2006)
  • Author(s): Fukunaga, R.
  • Journal Title: J Mol Biol 359 Pages: 901-12
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of the single-domain rhodanese homologue TTHA0613 from The rmus thermophilus HB8 (2006)
  • Author(s): Hattori, M.
  • Journal Title: Proteins 64 Pages: 284-7
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins (2006)
  • Author(s): Hiyama, T. B.
  • Journal Title: J Struct Funct Genomics 7 Pages: 119-29
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase (2006)
  • Author(s): Iwasaki, W.
  • Journal Title: J Mol Biol 360 Pages: 329-42
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structures of tyrosyl-tRNA synthetases from Archaea (2006)
  • Author(s): Kuratani, M.
  • Journal Title: J Mol Biol 355 Pages: 395-408
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase (2006)
  • Author(s): Sasaki, H. M.
  • Journal Title: Proc Natl Acad Sci USA 103 Pages: 14744-9
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase (2006)
  • Author(s): Sekine, S.
  • Journal Title: Structure 14 Pages: 1791-9
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa (2006)
  • Author(s): Sengoku, T.
  • Journal Title: Cell 125 Pages: 287-300
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA (2006)
  • Author(s): Hirao, I.
  • Journal Title: Nat Methods 3 Pages: 729-35
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Regioselective carbon-carbon bond formation in proteins with palladium catalysis; new protein chemistry by organometallic chemistry (2006)
  • Author(s): Kodama, K.
  • Journal Title: Chembiochem 7 Pages: 134-9
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] A new protein engineering approach combining chemistry and biology, part I; site-specific incorporation of 4-iodo-L-phenylalanine in vitro by using misacylated soppressor tRNAPhe (2006)
  • Author(s): Kodama, K.
  • Journal Title: Chembiochem 7 Pages: 1577-81
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Tbmperature-dependent biosynthesis of 2-thioribothymidine of Thermus thermophilus tRNA (2006)
  • Author(s): Shigi, N.
  • Journal Title: J Biol Chem 281 Pages: 2104-13
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The RAC binding domain/IRSp53-MIM homology domain of IRSp53 induces RAC-dependent membrane deformation (2006)
  • Author(s): Suetsugu, S.
  • Journal Title: J Biol Chem 281 Pages: 35347-58
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Negative regulation of condensin I by CK2-mediated phosphorylation (2006)
  • Author(s): Takemoto, A.
  • Journal Title: EMBO J 25 Pages: 5339-48
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of pyrrolysyl-tRNA synthetase from the methanogenic archaeon Methanosarcina mazei (2006)
  • Author(s): Yanagisawa, T.
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun 62 Pages: 1031-3
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase (2006)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: J Mol Biol 359(4) Pages: 901-912
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structure of the single-domain rhodanese homologue TTHA0613 from Thermus thermophilus HB8 (2006)
  • Author(s): Hattori, M., Mizohata, E., Tatsuguchi, A., Shibata, R, Kishishita, S., Murayama, K., Terada, T., Kuramitsu, S., Shirouzu, M., Yokoyama, S.
  • Journal Title: Proteins 64(1) Pages: 284-287
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins (2006)
  • Author(s): Hiyama, T. B., Zhao, M., Kitago, Y., Yao, M., Sekine, S., Terada, T., Kuroishi, C., Liu, Z. J., Rose, J. P., Kuramitsu, S., Shirouzu, M., Watanabe, N., Yokoyama, S., Tanaka, I., Wang, B. C.
  • Journal Title: J Struct Funct Genomics 7(3-4) Pages: 119-129
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase (2006)
  • Author(s): Iwasaki, W, Sekine, S., Kuroishi, C., Kuramitsu, S., Shirouzu, M., Yokoyama, S.
  • Journal Title: J Mot Biol 360(2) Pages: 329-342
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structures of tyrosyl-tRNA synthetases from Archaea (2006)
  • Author(s): Kuratani, M., Sakai, H., Takahashi, M., Yanagisawa, T., Kobayashi, T., Murayama, K., Chen, L., Liu, Z. J., Wang, B. C., Kuroishi, C., Kuramitsu, S., Terada, T., Bessho, Y., Shirouzu, M., Sekine, S., Yokoyama, S.
  • Journal Title: J Mol Biol 355(3) Pages: 395-408
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase (2006)
  • Author(s): Sasaki, H. M., Sekine, S., Sengoku, T., Fukunaga, R., Hattori, M., Utsunomiya, Y, Kuroishi, C., Kuramitsu, S., Shirouzu, M., Yokoyama, S.
  • Journal Title: Proc Natl Acad Sci U S A 103(40) Pages: 14744-14749
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase (2006)
  • Author(s): Sekine, S., Shichiri, M., Bernier, S., Chenevert, R., Lapointe, J., Yokoyama, S.
  • Journal Title: Structure 14(12) Pages: 1791-1799
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa (2006)
  • Author(s): Sengoku, T., Nureki, O., Nakamura, A., Kobayashi, S., Yokoyama, S.
  • Journal Title: Cell 125(2) Pages: 287-300
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] 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 (2006)
  • Author(s): Kodama, K., Fukuzawa, S., Sakamoto, K., Nakayama, H., Kigawa, T., Yabuki, T., Matsuda, N., Shirouzu, M., Takio, K., Tachibana, K., Yokoyama, S.
  • Journal Title: Chembiochem 7(10) Pages: 1577-1581
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Temperature-dependent biosynthesis of 2-thioribothymidine of Thermus thermophilus tRNA (2006)
  • Author(s): Shigi, N., Suzuki, T., Terada, T., Shirouzu, M., Yokoyama, S., Watanabe, K
  • Journal Title: J Biol Chem 281(4) Pages: 2104-2113
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The RAC binding domain/IRSp53-MIM homology domain of IRSp53 induces RAC-dependent membrane deformation (2006)
  • Author(s): Suetsugu, S., Murayama, K, Sakamoto, A., Hanawa-Suetsugu, K., Seto, A., Oikawa, T., Mishima, C., Shirouzu, M., Takenawa, T., Yokoyama, S.
  • Journal Title: J Biol Chem 281(46) Pages: 35347-35358
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Negative regulation of condensin I by CK2-mediated phosphorylation (2006)
  • Author(s): Takemoto, A., Kimura, K., Yanagisawa, J., Yokoyama, S., Hanaoka, F.
  • Journal Title: EMBO J 25(22) Pages: 5339-5348
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of pyrrolysyl-tRNA synthetase from the methanogenic archaeon Methanosarcina mazei (2006)
  • Author(s): Yanagisawa, T., Ishii, R., Fukunaga, R, Nureki, O., Yokoyama, S.
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun 62(Pt 10) Pages: 1031-1033
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] An unnatural hydrophobic base pair system : site-specific incopration of nucleotide analogs into DNA and RNA (2006)
  • Author(s): Hirao, I., Kimoto, M., Mitsui, T., Fujiwara, T., Kawai, R., Sato, A., Harada, Y., Yokoyama, S.
  • Journal Title: Nat Methods 3(9) Pages: 729-735
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] regioselective carbon-carbon bond formation in proteins with palladium catalysis; new protein chemistry by organometallic chemistry (2006)
  • Author(s): Kodama, K., Fukuzawa, S., Nakayama, H., Kigawa, T., Sakamoto, K., Yabuki, T., Matsuda, N., Shirouzu, M., Takio, K., Tachibana, K., Yokoyama, S.
  • Journal Title: Chembiochem 7(1) Pages: 134-139
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystallization of leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Ryrococcus horikoshii (2005)
  • Author(s): Fukunaga, R.
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commu 61 Pages: 30-2
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator-base recognition (2005)
  • Author(s): Fukunaga, R.
  • Journal Title: Nat Struct Mol Biol 12 Pages: 915-22
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain (2005)
  • Author(s): Fukunaga, R.
  • Journal Title: J Biol Chem 280 Pages: 29937-45
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation (2005)
  • Author(s): Fukunaga, R.
  • Journal Title: J Mol Biol 346 Pages: 57-71
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8 (2005)
  • Author(s): Hattori, M.
  • Journal Title: Proteins 61 Pages: 1117-20
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid (2005)
  • Author(s): Hino, N.
  • Journal Title: Nat Methods 2 Pages: 201-6
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of the tRNA 3′ processing endoribonuclease tRNase Z from The rmotoga maritima (2005)
  • Author(s): Ishii, R.
  • Journal Title: J Biol Chem 280 Pages: 14138-44
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion (2005)
  • Author(s): Kobayashi, T.
  • Journal Title: Proc Natl Acad Sci U S A 102 Pages: 1366-71
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase (2005)
  • Author(s): Kobayashi, T.
  • Journal Title: J Mol Biol 346 Pages: 105-17
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus (2005)
  • Author(s): Kuratani, M.
  • Journal Title: J Biol Chem 280 Pages: 16002-8
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation (2005)
  • Author(s): Tukalo, M.
  • Journal Title: Nat Struct Mol Biol 12 Pages: 923-30
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Roles of conserved amino acid sequence motifs in the SpoU(TrmH) RNA methyltransferase family (2005)
  • Author(s): Watanabe, K.
  • Journal Title: J Biol Chem 280 Pages: 10368-77
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Role of the N-terminal domain of the human DMC1 protein in octamer formation and DNA binding (2005)
  • Author(s): Kinebuchi, T.
  • Journal Title: J Biol Chem 280 Pages: 28382-7
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of the N-terminal RecA-like domain of a DEAD-box RNA helicase, the Dugesia japonica vasa-like gene B protein (2005)
  • Author(s): Kurimoto, K.
  • Journal Title: J Struct Biol 150 Pages: 58-68
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 A resolution (2005)
  • Author(s): Murayama, K.
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun 61 Pages: 26-9
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly (2005)
  • Author(s): Sharma, M.R.
  • Journal Title: Mol Cell 18 Pages: 319-29
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Human centromere protein B induces translational positioning of nucleosomes on alpha-satellite sequences (2005)
  • Author(s): Tanaka, Y.
  • Journal Title: J Biol Chem 280 Pages: 41609-18
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] CpG methylation of the CENP-B box reduces human CENP-B binding (2005)
  • Author(s): Tanaka, Y.
  • Journal Title: FEBS J 272 Pages: 282-9
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystallization of leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii (2005)
  • Author(s): Fukunaga, R., Ishitani, R., Nureki, O., Yokoyama, S.
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun 61(Pt 1) Pages: 30-32
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator-base recognition (2005)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: Nat Struct Mot Biol 12(10) Pages: 915-922
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain (2005)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: J Biol Chem 280(33) Pages: 29937-429945
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation (2005)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: J Mol Biot 346(1) Pages: 57-71
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8 (2005)
  • Author(s): Hattori, M., Mizohata, E., Manzoku, M., Bessho, Y., Murayama, K., Terada, T., Kuramitsu, S., Shirouzu, M., Yokoyama, S.
  • Journal Title: Proteins 61(4) Pages: 1117-1120
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid (2005)
  • Author(s): Hino, N., Okazaki, Y., Kobayashi, T., Hayashi, A., Sakamoto, K., Yokoyama, S.
  • Journal Title: Nat Methods 2(3) Pages: 201-206
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima (2005)
  • Author(s): Ishii, R., Minagawa, A., Takaku, H., Takagi, M., Nashimoto, M., Yokoyama, S.
  • Journal Title: J Biol Chem 280(14) Pages: 14138-14144
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion (2005)
  • Author(s): Kobayashi, T., Sakamoto, K., Takimura, T., Sekine, R., Kelly, V. P., Kamata, K., Nishimura, S., Yokoyama, S.
  • Journal Title: Proc Natl Acad Sci U S A 102(5) Pages: 1366-1371
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase (2005)
  • Author(s): Kobayashi, T., Takimura, T., Sekine, R., Kelly, V. P., Kamata, K., Sakamoto, K., Nishimura, S., Yokoyama, S.
  • Journal Title: J Mol Biol 346(1) Pages: 105-117
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus (2005)
  • Author(s): Kuratani, M., Ishii, R., Bessho, Y., Fukunaga, R., Sengoku, T., Shirouzu, M., Sekine, S., Yokoyama, S.
  • Journal Title: J Biol Chem 280(16) Pages: 16002-16008
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation (2005)
  • Author(s): Tukalo, M., Yaremchuk, A., Fukunaga, R., Yokoyama, S., Cusack, S.
  • Journal Title: Nat Struct Mol Biol 12(10) Pages: 923-930
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Role of the N-terminal domain of the human DMC1 protein in octamer formation and DNA binding (2005)
  • Author(s): Kinebuchi, T., Kagawa, W., Kurumizaka, H., Yokoyama, S.
  • Journal Title: J Biol Chem 280(31) Pages: 28382-28387
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structure of the N-terminal RecA-like domain of a DEAD-box RNA helicase, the Dugesia japonica vasa-like gene B protein (2005)
  • Author(s): Kurimoto, K., Muto, Y., Obayashi, N., Terada, T., Shirouzu, M., Yabuki, T., Aoki, M., Seki, E., Matsuda, T., Kigawa, T., Okumura, H., Tanaka, A., Shibata, N., Kashikawa, M., Agata, K., Yokoyama, S.
  • Journal Title: J Struct Biol 150(1) Pages: 58-68
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 A resolution (2005)
  • Author(s): Murayama., K, Kato-Murayama, M., Katsura, K, Uchikubo-Kamo, T., Yamaguchi-Hirafuji, M., Kawazoe, M., Akasaka, R., Hanawa-Suetsugu, K., Hori-Takemoto, C., Terada, T., Shirouzu, M., Yokoyama, S.
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun 61(Pt 1) Pages: 26-29
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly (2005)
  • Author(s): Sharma, M. R., Barat, C., Wilson, D. N., Booth, T. M., Kawazoe, M., Hori-Takemoto, C., Shirouzu, M., Yokoyama, S., Fucini, P., Agrawal, R., K.
  • Journal Title: Mol Cell 18(3) Pages: 319-329
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Human centromere protein B induces translational positioning of nucleosomes on alpha-satellite sequences (2005)
  • Author(s): Tanaka, Y., Tachiwana, H., Yoda, K., Masumoto, H., Okazaki, T., Kurumizaka, H., Yokoyama, S.
  • Journal Title: J Biol Chem 280(50) Pages: 41609-41618
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] "CpG methylation of the CENP-B box reduces human CENP-B binding (2005)
  • Author(s): Tanaka, Y., Kurumizaka, H., Yokoyama, S.
  • Journal Title: FEBS J 272(1) Pages: 282-289
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The Aminoacyl-tRNA Synthetases : Chapter7 & 8 (2005)
  • Author(s): Yokoyama, S.
  • Journal Title: The Aminoacyl-tRNA Synthetase Landes Bioscience
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Roles of conserved amino acid sequence motifs in the SpoU (TrmH0 RNA methyltransferase family (2005)
  • Author(s): Watanabe, K., Nureki, O., Fukai, S., Ishiii, Okamoto, H., Yokoyama, S., Endo, Y., Hori, H.
  • Journal Title: J Biol Chem 280(110 Pages: 10368-10377
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structures of the CPl domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine (2004)
  • Author(s): Fukunaga, R
  • Journal Title: J Biol Chem 279 Pages: 8396-402
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] 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 (2004)
  • Author(s): Fukunaga, R
  • Journal Title: Acta Crystallogr D Biol Crystallogr 60 Pages: 19002
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaeon pyrococcus horikoshii (2004)
  • Author(s): Fukunaga, R
  • Journal Title: Acta Crystallogr D Biol Crystallogr 60 Pages: 1916-8
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase (2004)
  • Author(s): Kise, Y.
  • Journal Title: Nat Struct Mol Biol 11 Pages: 149-56
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme (2004)
  • Author(s): Nureki, O.
  • Journal Title: Structure 12 Pages: 593-602
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] tRNA recognition by glutamyl-tRNA reductase (2004)
  • Author(s): Randau, L.
  • Journal Title: J Biol Chem 279 Pages: 34931-7
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] 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 (2004)
  • Author(s): Sakamoto, K.
  • Journal Title: J Bacteriol 186 Pages: 5899-905
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue (2004)
  • Author(s): Sengoku, T.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 60 Pages: 320-2
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis for transcription regulation by alarmone ppGpp (2004)
  • Author(s): Artsimovitch, I.
  • Journal Title: Cell 117 Pages: 299-310
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein (2004)
  • Author(s): Fujikawa, N.
  • Journal Title: Nucleic Acids Res 32 Pages: 82-92
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of elongation factor P from Thermus thermophilus HB8 (2004)
  • Author(s): Hanawa-Suetsugu, K
  • Journal Title: Proc Natl Acad Sci USA 101 Pages: 9595-600
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] In vitro selection of RNA aptamers that bind to colicin E3 and structurally resemble the decoding site of 16S ribosomal RNA (2004)
  • Author(s): Hirao, I.
  • Journal Title: Biochemistry 43 Pages: 3214-21
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Solution structure of a BolA-like protein from Mus musculus (2004)
  • Author(s): Kasai, T.
  • Journal Title: Protein Sci 13 Pages: 545-
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs (2004)
  • Author(s): Kimoto, M.
  • Journal Title: Chem Biol 11 Pages: 47-55
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmcl (2004)
  • Author(s): Kinebuchi, T.
  • Journal Title: Mol Cell 14 Pages: 363-74
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16) (2004)
  • Author(s): Maeda, T.
  • Journal Title: J Biol Chem 279 Pages: 13174-82
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Regulation through the secondary channel-structural framework for ppGpp-DksA synergism during transcription (2004)
  • Author(s): Perederina, A.
  • Journal Title: Cell 118 Pages: 297-309
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Cell cycle-dependent phosphorylation, nuclear localization, and activation of human condensin (2004)
  • Author(s): Takemoto, A.
  • Journal Title: J Biol Chem 279 Pages: 4551-9
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis for substrate selection by T7 RNA polymerase (2004)
  • Author(s): Temiakov, D.
  • Journal Title: Cell 116 Pages: 381-91
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Expression and purification of recombinant human histones (2004)
  • Author(s): Tanaka, Y
  • Journal Title: Methods 33 Pages: 3-11
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription factor DksA from Escherichia coli (2004)
  • Author(s): Vassylyeva, M. N.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 60 Pages: 1161-3
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis for transcription regulation by alarmone ppGpp (2004)
  • Author(s): Artsimovitch, I., Patlan, V., Sekine, S., Vassylyeva, M. N., Hosaka, T., Ochi, K., Yokoyama, S., Vassylyev, D. G.
  • Journal Title: Cell 117(3) Pages: 299-310
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural and biochemical analyses of hemimethylated DNA binding by the SegA protein (2004)
  • Author(s): Fujikawa, N., Kurumizaka, H., Nureki, O., Tanaka, Y., Yamazoe, M., Hiraga, S., Yokoyama, S.
  • Journal Title: Nucleic Acids Res 32(1) Pages: 82-92
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structure of elongation factor P from Thermus thermophilus HB8 (2004)
  • Author(s): Hanawa-Suetsugu, K., Sekine, S., Sakai, H., Hori-Takemoto, C., Terada, T., Unzai, S., Tame, J. R., Kuramitsu, S., Shirouzu, M., Yokoyama, S.
  • Journal Title: Proc Natl Acad Sci U S A 101(26) Pages: 9595-9600
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] In vitro selection of RNA aptamers that bind to colicin E3 and structurally tesemble the decoding site of 16S ribosomal RNA (2004)
  • Author(s): Hirao, I., Harada, Y., Nojima, T., Osawa, Y., Masaki, H., Yokoyama, S.
  • Journal Title: Biochemistry 43(11) Pages: 3214-3221
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Solution structure of a BolA-like protein from Musmusculus (2004)
  • Author(s): Kasai, T., Inoue, M., Koshiba, S., Yabuki, T., Aoki, M., Nunokawa, E., Seki, E., Matsuda, T., Matsuda, N., Tomo, Y., Shirouzu, M., Terada, T., Obayashi, N., Hamana, H., Shinya, N., Tatsuguchi, A., Yasuda, S., Yoshida, M., Hirota, H., Matsuo, Y., Tani, k., Suzuki, H., Arakawa, T., Carninci, P., Kawai, J., Hayashizaki, Y., Kigawa, T., Yokoyama, S
  • Journal Title: Protein Sci 13(2) Pages: 545-548
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs (2004)
  • Author(s): Kimoto, M., Endo, M., Mitsui, T., Okuni, T., Hirao, I., Yokoyama, S.
  • Journal Title: Chem Biol 11(1) Pages: 47-55
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmcl (2004)
  • Author(s): Kinebuchi, T., Kagawa, W., Enomoto, R., Tanaka, K., Miyagawa, K., Shibata, T., Kurumizaka, H., Yokoyama, S.
  • Journal Title: Mol Cell 14(3) Pages: 363-374
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125(MUC16) (2004)
  • Author(s): Maeda, T., Inoue, M., Koshiba, S., Yabuki, T., Aoki, M., Nunokawa, E., Seki, EMatsuda, T., Motoda, Y., Kobayashi, A., Hiroyasu, F., Shirouzu, M., Terada, T., Hayami, N., Ishizuka, Y., Shinya, N., Tatsuguchi, A., Yoshida, M., Hirota, H., Matsuo, Y., Tani, K., Arakawa, T., Carninci, P., Kawai, J., Hayashizaki, Y., Kigawa, T., Yokoyama, S.
  • Journal Title: J Biol Chem 279(13) Pages: 13174-13182
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Regulation through the secondary channel-structural framework for ppGpp-DksA synergism during transcription (2004)
  • Author(s): Perederina, A., Svetlov, V., Vassylyeva, M. N., Tahirov, T. H., Yokoyama, S., Artsimovitch, I., Vassylyev, D. G.
  • Journal Title: Cell 118(3) Pages: 297-309
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Cell cycle-dependent phosphorylation, nuclear localization, and activation of human condensin (2004)
  • Author(s): Takemoto, A., Kimura, K., Yokoyama, S., Hanaoka, F.
  • Journal Title: J Biol Chem 279(6) Pages: 4551-4559
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis for substrate selection by t7RNA polymerase (2004)
  • Author(s): Temiakov, D., Patlan, V., Anikin, M., McAllister, W. T., Yokoyama, S., Vassylyev, D. G.
  • Journal Title: Cell 116(3) Pages: 381-391
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Expression and purification of recombinant human histones (2004)
  • Author(s): Tanaka, Y., Tawaramoto-Sasanuma, M., Kawaguchi, S., Ohta, T., Yoda, K., Kurumizaka, H., Yokoyama, S.
  • Journal Title: Methods 33(1) Pages: 3-11
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription factor DksA from Escherichia coli (2004)
  • Author(s): Vassylyeva, M. N., Perederina, A. A., Svetlov, V., Yokoyama, S., Artsimovitch, I., Vassylyev, D. G.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 60(Pt 9) Pages: 1611-1613
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine (2004)
  • Author(s): Fukunaga, R., Fukai, S., Ishitani, R., Nureki, O., Yokoyama, S.
  • Journal Title: J Biol Chem 279(9) Pages: 8396-8402
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystallization and preliminary X-ray crystallographic study of leucy-tRNA synthetase from the archaeon Pyrococcus horikoshii (2004)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 60(Pt 10) Pages: 1900-1902
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaceon Pyrococcus horikoshii (2004)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: Nat Struct Mol Biol 11(2) Pages: 149-156
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase (2004)
  • Author(s): Kise, Y., lee, S. E., park, S. G., Fukai, S., Sengoku, T., Ishii, R., Yokoyama, S., Kim, S., Nureki, O.
  • Journal Title: Nat Struct Mol Biol 11(2) Pages: 149-156
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Deep knte of tRNA modification enzyme (2004)
  • Author(s): Nureki, O., Watanabe, K, Fukai, S., Ishii, R, Endo, Y, Hori, H., Yokoyama, S.
  • Journal Title: Structure 12(4) Pages: 593-602
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] tRNA recognition by glutamyl-tRNA reductase (2004)
  • Author(s): Randau, L., Schauer, S., Ambrogelly, A., Salazar, J. C., Moser, J., Aekine, S., Yokoyama, S., Soll, D., Jahn, D.
  • Journal Title: J Biol Chem 279(33) Pages: 34931-34937
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] 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 (2004)
  • Author(s): Sakamoto, K., Ishimaru, S., Kobayashi, T., Walker, J. R., Yokoyama, S.
  • Journal Title: J Bacteriol 186(17) Pages: 5899-5905
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystallization and preliminaty X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue (2004)
  • Author(s): Sengoku, T., Nureki, O., Dohmae, N., nakamura, A., Yokoyama, S.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 60(Pt 2) Pages: 320-322
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] An open-and-shut case? Recent insights into the activation of EGF/ErbB receptor (2003)
  • Author(s): Burgess, A.W.
  • Journal Title: Mol Cell 12 Pages: 541-52
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolic us (2003)
  • Author(s): Ishii, R.
  • Journal Title: J Biol Chem 278 Pages: 32397-404
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implic ations for the mechanism of primer synthesis (2003)
  • Author(s): Ito, N.
  • Journal Title: Genes Cells 8 Pages: 913-23
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of ribosomal protein L11 methyltransferase from Thermus thermophilus HB8 (2003)
  • Author(s): Kaminishi, T.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 59 Pages: 930-2
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure (2003)
  • Author(s): Okabe, M.
  • Journal Title: EMBO J 22 Pages: 5918-27
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis of replication origin recognition by the DnaA protein (2003)
  • Author(s): Fujikawa, N.
  • Journal Title: Nucleic Acids Res 31 Pages: 2077-8
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of the 2'一5'RNA ligase from Thermus thermophilus HB8 (2003)
  • Author(s): Kato, M.
  • Journal Title: J Mol Biol 329 Pages: 903-11
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Activation of the pyrrolysine suppressor tRNA requires formation of a ternary complex with class I and class II lysyl-tRNA synthetases (2003)
  • Author(s): Polycarpo, C.
  • Journal Title: Mol Cell 12 Pages: 287-94
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Reconstitution of Src-dependent phospholipase Cgamma phosphorylation and transient calcium release by using membrane rafts and cell-free extracts from Xenopus eggs (2003)
  • Author(s): Sato, K.
  • Journal Title: J Biol Chem 278 Pages: 38413-20
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons (2003)
  • Author(s): Takai, K.
  • Journal Title: Nucleic Acids Res 31 Pages: 6383-91
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of the human centromere protein B(CENP-B)dimerization dom ain at 1.65-A resolution (2003)
  • Author(s): Tawaramoto, M. S.
  • Journal Title: J Biol Chem 278 Pages: 51454-61
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis of replication origin recognition by the DnaA protein (2003)
  • Author(s): Fujikawa, N., Kurumizaka, H., Nureki, O., Terada, T., Shirouzu, M., Katayama, T., Yokoyama, S.
  • Journal Title: Nucleic Acids Ees 31(8) Pages: 2077-2086
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structure of the 2'-5' RNA ligase from Thermus thermopilus HB8 (2003)
  • Author(s): Kato, M., Shirouzu, M., Terada, T., Yamaguchi, H., Murayama, K., Sakai, H., Kuramitsu, S., Yokoyama, S.
  • Journal Title: J Mol Biol 329(5) Pages: 903-911
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Activation of the pyrrolysine suppressor tRNA requires formation of a ternary complex with class I and class II lysyl-tRNA synthetases (2003)
  • Author(s): Polycarpo, C., Ambrogelly, A., Ruan, B., Tumbula-Hansen, D., Ataide, S. F., Ishitani, R., Yokoyama, S., Nureki, O., Ibba, M., Soll, D.
  • Journal Title: Mol Cell 12(2) Pages: 287-294
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Reconstitution of Src-dependent phospholipase Cgamma phosphorylation and transient calcium release by using membrane rafts and cell-free extracts from Xenpus eggs (2003)
  • Author(s): Sato, K., Tokmakov, A. A., He, C. L., Kurokawa, M., Iwasaki, T., Shirouzu, M., Fissore, R. A., Yokoyama, S., Fukami, Y.
  • Journal Title: J Biol Chem 278(40) Pages: 38413-38420
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Roles of 5-substiutents of tRNA wobble uridines in the recognition of purine-ending codons (2003)
  • Author(s): Takai, K., Yokoyama, S.
  • Journal Title: Nucleic Acids Res 31(22) Pages: 6383-6391
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structure of the human centromere protein B(CENP-B) dimerization domain at 1.65-A resolution (2003)
  • Author(s): Tawaramoto, M. S., Park, S. Y., Tanaka, Nureki, O., Kurumizaka, H., Yokoyama, S.
  • Journal Title: J Biol Chem 278(51) Pages: 51454-51461
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] An open-and-shut case? Recent insights into the activation of EGF/ErbB receptors (2003)
  • Author(s): Burgess, A. W., Cho, H. S., Eigenbrot, C., Ferguson, K. M., Garrett, T. P., Leahy, D. J., Lemmon, M. A., Sliwkowski, M. X., Ward, C. W., Yokoyama, S.
  • Journal Title: Mol Cell 12(3) Pages: 541-542
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus (2003)
  • Author(s): Ishii, R., Nureki, O., Yokoyama, S.
  • Journal Title: J Biol Chem 278(34) Pages: 32397-32404
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex : implications for the mechanism of primase-UTP complex : implications for the mechanism of primer synthesis (2003)
  • Author(s): Ito, N., Nureki, O., Shirouzu, M., Yokoyama, S., Hanaoka, F.
  • Journal Title: Genes Cell 8(12) Pages: 913-923
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystallization and preliminaty X-ray diffraction analysis of ribosomal protein L11 methyltransferase from Thermus thermophilus HB8 (2003)
  • Author(s): Kaminishi, T., Sakai, H., Takemoto-Hori, C., Terada, T., Nakagawa, N., Maoka, N., Kuramitsu, S., Shirouzu, M., Yokoyama, S.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 59(Pt 5) Pages: 930-932
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure (2003)
  • Author(s): Okabe, M., Tomita, K., Ishitani, R., Ishii, R., Takeuchi, N., Arisaka, F., Nureki, O., Yokoyama, S.
  • Journal Title: EMBO J 22(21) Pages: 5981-5927
  • Description: 「研究成果報告書概要(欧文)」より
• [Presentation] Structural proteomics of transcription and translation proteins (2005)
  • Author(s): Yokoyama, S.
  • Organizer: 30th FEBS Congress and 9th IUBMB Conference
  • Place of Presentation: Budapest, Hungary
  • Year and Date: 2005-07-02
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] Structural basis for the noncognate amino acid editing by isoleucyl-tRNA syntehtase (2004)
  • Author(s): Yokoyama, S.
  • Organizer: 2004 International Conference on Aminoacyl-tRNA Synt hetases: Ancient Molecules for Future Biology and Medicine(ARS2004)
  • Place of Presentation: Seoul, SouthKorea
  • Year and Date: 2004-07-04
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] Structural basis for the non-cognate amino acid editing by isoleucyl-tRNA sntehtase (2004)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Organizer: 2004 International Conference on Aminoacyl-tRNA Synthetases : Ancient Molecules for Future Biology and Medicine (ARS2004)
  • Place of Presentation: Seoul, SouthKorea
  • Year and Date: 2004-07-04
  • Description: 「研究成果報告書概要(欧文)」より
• [Book] The Aminoacyl-tRNA Synthetases: Chapter 7 & 8 (2005)
  • Author(s): Yokoyama, S.
  • Total Pages: 14
  • Publisher: Landes Bioscience
  • Description: 「研究成果報告書概要(和文)」より
• [Remarks] 「研究成果報告書概要(和文)」より
  • URL: http://www.biochem.s.u-tokyo.ac.jp/yokoyama-lab/
• [Patent(Industrial Property Rights)] 変異体SepRS及びこれを用いるタンパク質への部位特異的ホスホセリン導入法 (2006)
  • Inventor(s): 横山茂之福永流也関根俊一
  • Industrial Property Rights Holder: 東京大学理化学研究所
  • Industrial Property Number: PCT/JP2007/063414
  • Filing Date: 2006-06-28
  • Description: 「研究成果報告書概要(和文)」より