Structure of RNA and RNP

• Project/Area Number: 14035205
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The University of Tokyo
• Principal Investigator: YOKOYAMA Shigeyuki The University of Tokyo, Graduate School of Science, Professor (00159229)
• Co-Investigator(Kenkyū-buntansha): KAWAI Gota Chiba Institute of Technology, Faculty of Engineering, Professor (70211860)
• Project Period (FY): 2002 – 2006
• Project Status: Completed (Fiscal Year 2006)
• Budget Amount: ¥73,700,000 (Direct Cost: ¥73,700,000); Fiscal Year 2006: ¥14,200,000 (Direct Cost: ¥14,200,000); Fiscal Year 2005: ¥14,200,000 (Direct Cost: ¥14,200,000); Fiscal Year 2004: ¥15,100,000 (Direct Cost: ¥15,100,000); Fiscal Year 2003: ¥15,100,000 (Direct Cost: ¥15,100,000); Fiscal Year 2002: ¥15,100,000 (Direct Cost: ¥15,100,000)
• Keywords: X-ray Crystallography / NMR / 3D structure / RNA / Intermolecular interaction / RNA-binding protein / アミノアシルtRNA合成酵素 / LINE / RNA修飾酵素 / tmRNA / SRP / RNAポリメラーゼ / リボゾーム / RNAポリメーゼ

Research Abstract

X-ray crystallography: By crystallography of RNA-protein complexes, structural details of their interactions and roles of RNA in activities were analyzed. We determined crystal structures of aminoacyl-tRNA synthetases, which are responsible for joining corresponding tRNAs and amino acids during translation. It revealed that tRNAs play positive roles in both aminoacylation and proofreading reactions by modulating protein structures. To analyze structural bases of pre-tRNA maturation, structural studies have been done on enzymes responsible for the pre-tRNA processing and modifications. The structure of tRNA complexed with ArcTGT revealed that the modification is achieved via a step including a transitional tRNA structure "λ form". We also determined the crystal structure of Vasa, an RNA helicase involved in the differentiation of germ cells, and elucidated structural basis of the RNA double strand resolution by a DEAD-box RNA helicase.
NMR: (1) Solution structures of helix 6 stem-loop RNA of SRP RNA from human and Pyrococcus furiosus were determined and the difference in recognition by SRP19 was discussed. (2) Solution structure of SmpB from Thermus thermophilus HB8 was determined and the interaction between tmRNA and SmpB was analyzed. It was found that the structure of SmpB changed upon binding of tmRNA. (3) Solution structures of stem-loop RNAs derived from UnaL2 RNA were determined. The GNRNA motif in the penta loop was found to be required for the recognition by the LINE reverse transcriptase and the flexibility of the bulged stem was found to be important for the retrotransposition initiation reaction. (4) A classification system for RNA structures, CSNA, was developed and applied for RNA structure determination by NMR.

Research Products

• [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: 272-279
  • 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: 224-228
  • 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 preventsmisediting of isoleucyl-tRNA(Ile) (2007)
  • Author(s): Fukunaga, R.
  • Journal Title: Biocb emis try 46 Pages: 4985-4996
  • 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 cysteinebiosyn thesis in archaea : crystal structure of Sep-tRNA : Cys・tRNA synthasefrom 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: Ada Crystallogr D Biol Crystallogr 63 Pages: 390-400
  • 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: Ada 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] The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes (2007)
  • Author(s): Ishii, R.
  • Journal Title: Ada 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 TilSwith 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 U S A 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] Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding (2007)
  • Author(s): Dawson, W. K.
  • Journal Title: PLoS ONE 2
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [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: 272-9
  • 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: 224-8
  • 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(Ile). (2007)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: Biochemistry 46(17) Pages: 4985-96
  • 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: 128-41
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of the AlaX-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 (Pt10) Pages: 1059-68
  • 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: 637-41
  • 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: 1642-53
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Stmctural 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., Kuramitsu, S., Yokoyama, S.
  • Journal Title: Proc Natl Acad Sci U S A 104(20) Pages: 8293-8
  • 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 regions of GTP-bound elongation factors. (2007)
  • Author(s): Connell, S. R., Takemoto, C, Wilson, D. N., Wang, H., Murayama, K., Terada, 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: 751-64
  • 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: 434-45
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A snapshot of the 30S ribosomal 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: 289-97
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding. (2007)
  • Author(s): Dawson, W. K., Fujiwara, K., Kawai, G.
  • Journal Title: PLoS ONE 2(9)
  • 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: 272-279
• [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] 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 U S A 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 andactivation 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] 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: Ada Crystallogr Sect F Struct Biol Cryst Commu 62 Pages: 1031-3
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Solution structure and functional importance of a conserved RNA hairpin of eelLINE UnaL2 (2006)
  • Author(s): Nomura, Y.
  • Journal Title: Nucleic Acids Res. 34 Pages: 5184-5193
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus (2006)
  • Author(s): Okada, K.
  • Journal Title: Nucleosides, Nucleotides and Nucleic Acids 25 Pages: 383-395
  • 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: 901-12
  • 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 Mol Biol 360(2) Pages: 329-42
  • 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: 14744-9
  • 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: 1791-9
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis for RNA unwinding by the DEADbox 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] 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: 1031-3
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2. (2006)
  • Author(s): Nomura, Y., Kajikawa, M., Baba, S., Nakazato, S., Imai, T., Sakamoto, T., Okada, N., Kawai, G.
  • Journal Title: Nucleic Adds Res. 34 Pages: 5184-5193
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus (2006)
  • Author(s): Okada, K., Takahashi, M., Sakamoto, T., Nakamura, K., Kanai, A., Kawai, G.
  • Journal Title: Nucleosides, Nucleotides and Nucleic Acids 25 Pages: 383-395
  • 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.
  • Journal Title: Structure 14 Pages: 1791-1799
• [Journal Article] Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA (2006)
  • Author(s): Sasaki, H.M.
  • Journal Title: Proc. Natl. Acad. Sci. USA 103 Pages: 14744-14749
• [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: 329-342
• [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
• [Journal Article] Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2 (2006)
  • Author(s): Nomura, Y.
  • Journal Title: Nucleic Acids Res 34 Pages: 5184-5193
• [Journal Article] Structural basis for RNA unwinding by the DEAD-box protein Drosop (2006)
  • Author(s): Sengoku, T.
  • Journal Title: Cell (In press)
• [Journal Article] Crystal structures of tyrosyl-tRNA synthetases from Archaea (2006)
  • Author(s): Kuratani, M.
  • Journal Title: J.Mol.Biol. 355 Pages: 395-408
• [Journal Article] Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus (2006)
  • Author(s): Okada, K.
  • Journal Title: Nucleotides and Nucleic Acids (In press)
• [Journal Article] Crystallization of leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii (2005)
  • Author(s): Fukunaga, R.
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun 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 tRNA Leu 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 tRNA 3' processing endoribonuclease tRNase Z from Thermotoga 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 a mino acid recognition by an engineeredaminoacyl-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 acidactivation 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] 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 Kl at 1.7 A resolution (2005)
  • Author(s): Murayama, K.
  • Journal Title: Ada 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] Interaction analysis between tmRNA and SmpB from Thermus Thermophilus (2005)
  • Author(s): Nameki, N.
  • Journal Title: J. Biochem. 138 Pages: 729-739
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A (2005)
  • Author(s): Sakamoto, T.
  • Journal Title: Nucl. Acids Res. 33 Pages: 745-754
  • 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: 30-2
  • 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 Mol Biol 12(10) Pages: 915-22
  • 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: 29937-45
  • 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 Biol 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 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: 14138-44
  • 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: 1366-71
  • 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: 105-17
  • 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: 16002-8
  • 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: 923-30
  • 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 (TrmH) RNA methyltransferase family. (2005)
  • Author(s): Watanabe, K., Nureki, O., Fukai, S., Ishii, R., Okamoto, H., Yokoyama, S., Endo, Y., Hori, H.
  • Journal Title: J Biol Chem 280(11) Pages: 10368-77
  • 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: 26-9
  • 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: 319-29
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Interaction analysis between tmRNA and SmpB from Thermus Thermophilus. (2005)
  • Author(s): Nameki, N., Someya, T., Okano, S., Suemasa, R., Kimoto, M., Hanawa-Suetsugu, K., Terada, T., Shirouzu, M., Hirao, I., Takaku, H., Himeno, H., Muto, A., Kuramitsu, S., Yokoyama, S., Kawai, G.
  • Journal Title: J. Biochem. 138 Pages: 729-739
  • NAID: 10017348907
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A. (2005)
  • Author(s): Sakamoto, T., Oguro, A., Kawai, G., Ohtsu, T., Nakamura, Y.
  • Journal Title: Nucl. Acids Res. 33 Pages: 745-754
  • 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 (DjVLGB) protein (2005)
  • Author(s): Kurimoto, K.
  • Journal Title: J.Struct.Biol. 150 Pages: 58-68
• [Journal Article] Crystal structure of the RNA 2'-phosphotransferase from Aeropyrum pernix K1 (2005)
  • Author(s): Kato-Murayama, M.
  • Journal Title: J.Mol.Biol. 348 Pages: 295-305
• [Journal Article] Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus (2005)
  • Author(s): Kuratani, M.
  • Journal Title: J.Biol.Chem. 280 Pages: 16002-16008
• [Journal Article] Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima (2005)
  • Author(s): Ishii, R.
  • Journal Title: J.Biol.Chem. 280 Pages: 14138-14144
• [Journal Article] Structural oasis 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: 29937-29945
• [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: 319-329
• [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: 915-922
• [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. 112 Pages: 923-930
• [Journal Article] Interaction analysis between tmRNA and SmpB from Thermus Thermophilus (2005)
  • Author(s): Nameki, N.
  • Journal Title: J.Biochem. 138 Pages: 729-739
• [Journal Article] Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima (2005)
  • Author(s): Ishii R.
  • Journal Title: J.Biol.Chem. (in press)
• [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
• [Journal Article] NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A (2005)
  • Author(s): Sakamoto, T.
  • Journal Title: Nucl.Acids Res. 33 Pages: 745-754
• [Journal Article] Crystal structures of the CPl domain from Thermus thermophilus isoleucvl-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: 1900-2
  • 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: Ada 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] 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] 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: Ada 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] Crystal structure of elongation factor P from Thermus thermophilus HB8 (2004)
  • Author(s): Hanawa-Suetsugu, K.
  • Journal Title: Proc Natl Acad Sci U S A 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: 545-8
  • 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 byT7 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] 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] 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] Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription factor DksA from Escherichia coli (2004)
  • Author(s): Vassylyeva, M. N.
  • Journal Title: Ada Crystallogr D Biol Crystallogr 60 Pages: 1611-3
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2 (2004)
  • Author(s): Baba, S.
  • Journal Title: RNA 10 Pages: 1380-1387
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Analysis of local convergence in NMR structure calculation for RNA by a classification system for nucleic acid structure, CSNA (2004)
  • Author(s): Someya, T.
  • Journal Title: Nucleosides, Nucleotides and Nucleic Acids 23 Pages: 691-700
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [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: 8396-402
  • Description: 「研究成果報告書概要(欧文)」より
• [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., Yokoyama, S.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 60(Pt 10) Pages: 1900-2
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystallization and preliminary Xray crystallographic study of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii. (2004)
  • Author(s): Fukunaga, R., Yokoyama, S.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 60(Pt10) Pages: 1916-8
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Deep knot structure for construction of active site and cofactor binding site 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., Sekine, S., Yokoyama, S., Soll, D., Jahn, D.
  • Journal Title: J Biol Chem 279(33) Pages: 34931-7
  • Description: 「研究成果報告書概要(欧文)」より
• [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., Nureki, O., Dohmae, N., Nakamura, A., Yokoyama, S.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 60(Pt2) Pages: 320-2
  • Description: 「研究成果報告書概要(欧文)」より
• [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] 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: 9595-600
  • 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 resemble 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: 3214-21
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Solution structure of a BolA-like protein from Mus musculus. (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: 545-8
  • 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] 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] Structural basis for substrate selection by t7 RNA polymerase. (2004)
  • Author(s): Temiakov, D., Patlan, V., Anikin, M., McAllister, W. T., Yokoyama, S., Vassylyev, D. G.
  • Journal Title: Cell 116(3) Pages: 381-91
  • 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(Pt9) Pages: 1611-3
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2. (2004)
  • Author(s): Baba, S., Kajikawa, K., Okada, N., Kawai, G.
  • Journal Title: RNA 10 Pages: 1380-1387
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Analysis of local convergence in NMR structure calculation for RNA by a classification system for nucleic acid structure, CSNA. (2004)
  • Author(s): Someya, T., Sakamoto, T., Takasu, A., Kawai, G.
  • Journal Title: Nucleosides, Nucleotides and Nucleic Acids 23 Pages: 691-700
  • Description: 「研究成果報告書概要(欧文)」より
• [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: 1900-1902
• [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: 1916-1918
• [Journal Article] Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8 (2004)
  • Author(s): Wang H.
  • Journal Title: Protein Sci. 13 Pages: 2806-2810
• [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
• [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: 9595-9600
• [Journal Article] Structural basis for transcription regulation by alarmone ppGpp (2004)
  • Author(s): Artsimovitch I.
  • Journal Title: Cell 117 Pages: 299-310
• [Journal Article] Effects of Escherichia coil ribosomal protein S12 mutations on cell-free protein synthesis (2004)
  • Author(s): Chumpolkulwong N.
  • Journal Title: Eur.J.Biochem. 271 Pages: 1127-1134
• [Journal Article] Structural basis for substrate selection by T7 RNA polymerase (2004)
  • Author(s): Temiakov D.
  • Journal Title: Cell 116 Pages: 381-391
• [Journal Article] Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus (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] Crystallization and preliminary X-ray diffraction analysis of ribosomal protein Lll methvltransferase 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] Alternative Tertiary Structure of tRNA for Recognition by a Posttranscriptional Modification Enzyme (2003)
  • Author(s): Ishitani, R.
  • Journal Title: Cell 113 Pages: 383-394
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Mechanism of Molecular Interactions for tRNA^<Val> Recognition by Valyl-tRNA Synthetase (2003)
  • Author(s): Fukai, S.
  • Journal Title: RNA 9 Pages: 100-111
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] ATP Binding by Glutamyl-tRNA Synthetase Is Switched to the Productive Mode by tRNA Binding (2003)
  • Author(s): Sekine, S.
  • Journal Title: EMBO J. 23 Pages: 676-688
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural Basis for Orthogonal tRNA Specificities of Tyrosyl-tRNA Synthetases for Genetic Code Expansion (2003)
  • Author(s): Kobayashi, T.
  • Journal Title: Nat. Struct. Biol. 10 Pages: 425-432
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal structure of the 2'-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 aternary complex with class l and class II lvsvl-tRNA svnthetases (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] Role of the Zinc Fingers of HIV-1 Nucleocapsid Protein for Maturation of Genomic RNA (2003)
  • Author(s): Baba, S.
  • Journal Title: J. Biochem. 134 Pages: 637-639
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus (2003)
  • Author(s): Someya, T.
  • Journal Title: FEBS lett. 535 Pages: 94-100
  • 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 aeolicus. (2003)
  • Author(s): Ishii, R., Nureki, 0., Yokoyama, S.
  • Journal Title: J Biol Chem 278(34) Pages: 32397-404
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystallization and preliminary 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: 930-2
  • 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: 5918-27
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. (2003)
  • Author(s): Ishitani, R., Nureki, O., Nameki, N., Okada, N., Nishimura, S., Yokoyama, S.
  • Journal Title: Cell 113(3) Pages: 383-94
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase. (2003)
  • Author(s): Fukai, S., Nureki, O., Sekine, S., Shimada, A., Vassylyev, D. G., Yokoyama, S.
  • Journal Title: RNA 9(1) Pages: 100-11
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. (2003)
  • Author(s): Sekine, S., Nureki, 0., Dubois, D. Y., Bernier, S., Chenevert, R., Lapointe, J., Vassylyev, D. G., Yokoyama, S.
  • Journal Title: EMBO J 22(3) Pages: 676-88
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. (2003)
  • Author(s): Kobayashi, T., Nureki, 0., Ishitani, R., Yaremchuk, A., Tukalo, M., Cusack, S., Sakamoto, K., Yokoyama, S.
  • Journal Title: Nat Struct Biol 10(6) Pages: 425-32
  • NAID: 110001158009
  • 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 thermophilus 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: 903-11
  • 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., Soil, D.
  • Journal Title: Mol Cell 12(2) Pages: 287-94
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Role of the Zinc Fingers of HIV-1 Nucleocapsid Protein for Maturation of Genomic RNA. (2003)
  • Author(s): Baba, S., Takahashi, K., Koyanagi, Y., Yamamoto, N., Takaku, H., Gorelick, R. J., Kawai, G.
  • Journal Title: J. Biochem. 134 Pages: 637-639
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus. (2003)
  • Author(s): Someya, T., Nameki, N., Hosoi, H., Suzuki, S., Hatanaka, H., Fujii, M, Terada, T., Shirouzu, ML, Inoue, Y., Shibata, T., Kuramitsu, S., Yokoyama, S., Kawai, G.
  • Journal Title: FEBS lett. 535 Pages: 94-100
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] An Engineered Escherichia coli Tyrosyl-tRNA Synthetase for Site-specific Incorporation of an Unnatural Amino Acid into Proteins in Eukaryotic Translation and Its Application in a Wheat Germ Cell-free System (2002)
  • Author(s): Kiga, D.
  • Journal Title: Proc Natl Acad Sci U S A 99 Pages: 9715-9720
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Purification, Crystallization and Initial Crystallographic Analysis of RNA Polymerase Holoenzyme from Thermus thermophilus (2002)
  • Author(s): Vassylyeva. M. N.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 58 Pages: 1497-1500
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structure of A T7 RNA Polymerase Elongation Complex at 2.9 A Resolution (2002)
  • Author(s): Tahirov, T. H.
  • Journal Title: Nature 420 Pages: 43-50
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system. (2002)
  • Author(s): Kiga, D., Sakamoto, K., Kodama, K., Kigawa, T., Matsuda, T., Yabuki, T., Shirouzu, M., Harada, Y., Nakayama, H., Takio, K., Hasegawa, Y., Endo, Y., Hirao, I., Yokoyama, S.
  • Journal Title: Proc Natl Acad Sci U S A 99(15) Pages: 9715-20
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus. (2002)
  • Author(s): Vassylyeva, M. N., Lee, J., Sekine, S. I., Laptenko, O., Kuramitsu, S., Shibata, T., Inoue, Y., Borukhov, S., Vassylyev, D. G., Yokoyama, S.
  • Journal Title: Acta Crystallogr D Biol Crystallogr 58(Pt9) Pages: 1497-500
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution. (2002)
  • Author(s): Tahirov, T. H., Temiakov, D., Anikin, M., Patlan, V., McAllister, W. T., Vassylyev, D. G., Yokoyama, S.
  • Journal Title: Nature 420(6911) Pages: 43-50
  • Description: 「研究成果報告書概要(欧文)」より
• [Presentation] RIKEN structural genomics/proteomics initiative (2006)
  • Author(s): Yokoyama, S.
  • Organizer: International Conference on Aminoacyl-tRNA Synthetases : From the genetic Code to Human Disease & Medicine(AARS2006)
  • Place of Presentation: SanDiego, USA
  • Year and Date: 2006-10-22
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] RIKEN structural genomics/proteomics initiative. (2006)
  • Author(s): Yokoyama, S.
  • Organizer: International Conference on Aminoacyl-tRNA Synthetases : From the genetic Code to Human Disease & Medicine (AARS2006)
  • Place of Presentation: SanDiego, USA
  • Year and Date: 2006-10-22
  • 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 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(欧文)」より
• [Presentation] Structural basis for the non-cognate amino acid editing by isoleucyl-tRNA syntehtase (2004)
  • Author(s): 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(和文)」より
• [Presentation] Structural basis for the non-cognate amino acid editing by isoleucyl-tRNA syntehtase. (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.rna.it-chiba.ac.ip/csnatrial/
• [Publications] Temiakov, D.: "Structural Basis for Substrate Selection by T7 RNA Polymerase"Cell. 116. 381-391 (2004)
• [Publications] Kise, Y.: "A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase"Nat.Struct.Mol.Biol.. 11. 149-156 (2004)
• [Publications] Sengoku, T.: "Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue"Acta Crystallogr.D Biol Crystallogr.. 60. 320-322 (2004)
• [Publications] Hirao, I.: "In vitro selection of RNA aptamers that bind to colicin E3 and structurally resemble the decoding site of 16S ribosomal RNA"Biochem.. 279. 8396-8402 (2003)
• [Publications] Okabe, M.: "Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure"EMBO J.. 22. 5918-5927 (2003)
• [Publications] Polycarpo, C.: "Activation of the Pyrrolysine Suppressor tRNA Requires Formation of a Ternary Complex with Class I and Class II Lysyl-tRNA Synthetases"Mol.Cell. 12. 287-294 (2003)
• [Publications] Kato, M.: "Crystal structure of the 2'-5'RNA ligase from Thermus thermophilus HB8"J.Mol.Biol.. 329. 903-911 (2003)
• [Publications] Kobayashi, T.: "Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion"Nat.Struct.Biol.. 10. 425-432 (2003)
• [Publications] Ishii, R.: "Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus"J.Biol.Chem.. 278. 32397-32404 (2003)
• [Publications] Ishitani, R.: "by a posttr Alternative tertiary structure of tRNA for recognition anscriptional modification enzyme"Cel. 113. 383-394 (2003)
• [Publications] Kaminishi, T.: "Crystallization and preliminary X-ray diffraction analysis of ribosomal protein L11 methyltransferase from Thermus thermophilus HB8"Acta Crystallogr.D Biol Crystallogr.. 59. 930-932 (2003)
• [Publications] Baba, S.: "Role of the Zinc Fingers of HIV-1 Nucleocapsid Protein for Maturation of Genomic RNA"J.Biochem.. 134. 637-639 (2004)
• [Publications] Someya, T.: "Analysis of local convergence in NMR structure calculation for RNA by a classification system for nucleic acid structure, CSNA"Nucleosides, Nucleotides and Nucleic Acids. (in press). (2004)
• [Publications] Sekine, S.: "ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding"EMBO J.. 23. 676-688 (2003)
• [Publications] Someya, T.: "Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus"FEBS Lett.. 535. 94-100 (2003)
• [Publications] Fukai, S.: "Mechanism of molecular interactions for tRNA^<Val> recognition by valyl-tRNA synthetase"RNA. 9. 100-111 (2003)
• [Publications] Temiakov, D.: "Crystallization and preliminary crystallographic analysis of T7 RNA polymerase elongation complex"Acta Cryst.. D59. 185-187 (2003)
• [Publications] Tachirov, T.H.: "Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution"Nature. 420. 43-50 (2002)
• [Publications] Sakamoto, K.: "Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells"Nucleic Acids Res. 30. 4692-4699 (2002)
• [Publications] Vassylyeva, M.N.: "Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus"Acta Cryst.. D58. 1497-1500 (2002)
• [Publications] Kiga, D.: "An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system"Proc. Natl. Acad. Sci. U.S.A.. 99. 9715-9720 (2002)
• [Publications] Nureki, O.: "an enzyme with a deep trefoil knot for the active-site architecture"Acta Cryst.. D58. 1129-1137 (2002)
• [Publications] Vassylyev, D.G.: "Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution"Nature. 417. 712-719 (2002)
• [Publications] Kitamura, A.: "Solution structure of an RNA fragment with the P7/P9.0 region and the 3'-terminal guanosine of the tetrahymena group I intron"RNA. 8. 440-451 (2002)
• [Publications] Terada, T.: "Functional convergence of two lysyl-tRNA synthetases with unrelated topologies"Nature Struct. Biol.. 9. 257-262 (2002)
• [Publications] Kitabatake, M.: "Indolmycin resistance of Streptomyces coelicolor A3(2) by induced expression of one of its two tryptophanyl-tRNA synthetases"J. Biol. Chem.. 277. 23882-23887 (2002)
• [Publications] Hendrickson, T.L.: "Mutational separation of two pathways for editing by a class I tRNA synthetase"Mol. Cell. 9. 353-362 (2002)
• [Publications] Hirao, I.: "An unnatural base pair for incorporating amino acid analogs into proteins"Nature Biotechnol.. 20. 177-182 (2002)
• [Publications] Takasu, A.: "Analysis of Relative Positions of Ribonucleotide Bases in a Crystal Structure of Ribosome"Nucleotides and Nucleic Acids. 21. 449-462 (2002)
• [Publications] Takasu, A.: "Classification of RNA Structures Based on Hydrogen Bond and Base-Base Stacking Patterns : Application for NMR structures"J. Biochem.. 132. 211-215 (2002)
• [Publications] Sakamoto, T: "Solution structure of a SRP19 binding domain in human SRP RNA"J. Biochem.. 132. 177-182 (2002)