The study on the multi-molecular reaction mechanism of transamidosome for Gln-tRNA(Gln) synthesis

2011 Fiscal Year Final Research Report

• Project/Area Number: 21370041
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Hokkaido University
• Principal Investigator: YAO Min 北海道大学, 大学院・先端生命科学研究院, 教授 (40311518)
• Co-Investigator(Renkei-kenkyūsha): TANAKA Isao 北海道大学, 大学院・先端生命科学研究院, 特任教授 (70093052)
• Project Period (FY): 2009 – 2011
• Keywords: X 線結晶解析 / 多段階反応の協調 / トランスアミドソーム / GatCAB / tRNA / GluRS / AspRS / 多分子協調機構

Research Abstract

In order to elucidate the multi-molecular reaction mechanism of transamidosome in the indirect synthetic pathway of aminoacyl tRNA (Gln-tRNA^Gln, Asn-tRNA^Asn), we over-expressed, purified 6 components of 2 transamidosomes from S. aureus and P. aeruginosa, respectively, and formed 2 transamidosomes in vitro. We succeeded in the structural analysis of Asn-tRNA^Asn transamidosomes of P.aeruginosa. The structure of Asn-tRNA^Asn transamidosomes consisted of tRNA^Asn, ND-AspRS and GatCAB with a rate of 2:2:2, according with the result of the biochemistry experiment. The structure shown that acceptor stem of tRNA^Asn was located in the active site of ND-AspRS, representing a tRNA-binding situation before aminoacylation (mischarge) of the tRNA^Asn. After the aminoacylation, the acceptor stem of tRNAAsn flipped toward the active site of GatCAB for transamidation.

Research Products

• [Journal Article] Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH (2012)
  • Author(s): Englert M, Xia S, Okada C, Nakamura A, Tanavde V, Yao M, Eom S-H, Konigsberg W-H, Soll D, Wang J
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 109 Pages: 15235-15240
  • DOI: doi:10.1073/pnas.1213795109
  • Peer Reviewed
• [Journal Article] The binding mechanism of eIF2ss with its partner proteins, eIF5 and eIF2Bε (2012)
  • Author(s): Gai Z, Kitagawa Y, Tanaka Y, Shimizu N, Komoda K, Tanaka I, Yao M
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 423 Pages: 515-519
  • DOI: doi:10.1016/j.bbrc.2012.05.155
  • Peer Reviewed
• [Journal Article] Structure of bacterial cellulose synthase subunit D octamer with four inner passageways (2010)
  • Author(s): Hu S-Q, Gao Y-G, Tajima K, Sunagawa N, Zhou Y, Kawano S, Fujiwara T, Yoda T, Shimura D, Satoh Y, Munekata M, Tanaka I, Yao M
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 107 Pages: 17957-17961
  • DOI: doi:10.1073/pnas.1000601107/-/DCSupplemental
  • Peer Reviewed
• [Journal Article] Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition (2010)
  • Author(s): Nakamura A, Sheppard K, Yamane J, YaoM, Soll D, Tanaka I
  • Journal Title: Nucl. Acid Res Volume: 38 Pages: 672-682
  • DOI: doi:10.1093/nar/gkp955
  • Peer Reviewed
• [Journal Article] The structure of alanyl-tRNA synthetase with editing domain (2009)
  • Author(s): Sokabe M, Ose T, Nakamura A, Tokunaga K, Nureki O, Yao M, Tanaka I
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 106 Pages: 11028-11033
  • DOI: doi:10.1073/pnas.0904645106
  • Peer Reviewed
• [Journal Article] RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon (2009)
  • Author(s): Chimnaronk S, Suzuki T, Manita T, Ikeuchi Y, Yao M, Suzuki T, Tanaka I
  • Journal Title: The EMBO J Volume: 28 Pages: 1362-1373
  • DOI: doi:10.1038/emboj.2009.69
  • Peer Reviewed
• [Journal Article] Snapshots of Dynamics in Synthesizing N^6-Isopentenyladenosine at the tRNA Anticodon (2009)
  • Author(s): Chimnaronk S, Forouhar F, Sakai J, Yao M, Tron C-M, Atta M, Fontecave M, Hunt J- F, Tanaka I
  • Journal Title: Biochemistry Volume: 48 Pages: 5057-5065
  • DOI: doi:10.1021/bi900337d
  • Peer Reviewed
• [Journal Article] Crystal Structures of the Multidrug Binding Repressor Corynebacterium glutamicum CgmR in Complex with Inducers and with an Operator
  • Author(s): Itou H, Watanabe N, Yao M, Shirakihara Y, Tanaka I
  • Journal Title: J. Mol. Biol Volume: 2010 Pages: 174-184
  • DOI: doi:10.1016/j.jmb.2010.07.042
  • Peer Reviewed
• [Presentation] The Recognition Mechanism of eIF2ss for its partner proteins eIF5 and eIF2Bε (2011)
  • Author(s): 蓋作啓,北川侑未枝,姚閔,尾瀬農之,田中良和,田中勲
  • Organizer: 第49回日本生物物理学会年会
  • Place of Presentation: 兵庫県立大学姫路書写キャンパス(姫路市)
  • Year and Date: 20110916-18
• [Presentation] 古細菌型GatCABと真正細菌型GatCABの比較 (2010)
  • Author(s): 周倩,中村彰良,朝野希美,姚閔,田中勲
  • Organizer: 第60回日本結晶学会年会
  • Place of Presentation: 大阪大学コンベンションセンター(吹田市)
  • Year and Date: 20101203-5
• [Presentation] 真正細菌型GatCABと古細菌型GatCABの構造比較 (2010)
  • Author(s): 中村彰良,周倩,朝野希美,姚閔,田中勲
  • Organizer: 第12回日本RNA学会年会
  • Place of Presentation: 一橋記念講堂(東京都千代田区)
  • Year and Date: 20100727-29
• [Presentation] Structural basis for translation factor recruitment to the eukaryotic/archaeal ribosomes (2009)
  • Author(s): Yao M
  • Organizer: Taiwan-Japan Joint Seminar on Crystallography and IPR Seminar
  • Place of Presentation: Osaka University (Suita, Japan)
  • Year and Date: 20091207-9
• [Remarks]
  • URL: http://altair.sci.hokudai.ac.jp/g6/