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

• 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
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥19,110,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥4,410,000); Fiscal Year 2011: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000); Fiscal Year 2010: ¥7,020,000 (Direct Cost: ¥5,400,000、Indirect Cost: ¥1,620,000); Fiscal Year 2009: ¥8,710,000 (Direct Cost: ¥6,700,000、Indirect Cost: ¥2,010,000)
• 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 / X線結晶解析

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 Issue: 38 Pages: 15235-15240
  • DOI: 10.1073/pnas.1213795109
  • Peer Reviewed
• [Journal Article] The binding mechanism of eIF2β with its partner proteins, eIF5 and eIF2Bε, Biochem (2012)
  • Author(s): Gai Z, Kitagawa Y, Tanaka Y, Shimizu N, Komoda K, Tanaka I, Yao M
  • Journal Title: Biophys. Res. Commun Volume: 423 Issue: 3 Pages: 515-519
  • 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 Issue: 42 Pages: 17957-17961
  • DOI: 10.1073/pnas.1000601107
  • NAID: 120002911946
  • Peer Reviewed
• [Journal Article] Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition, Nucl (2010)
  • Author(s): Nakamura A, Sheppard K, Yamane J, Yao M, Soll D, Tanaka I
  • Journal Title: Acid Res Volume: 38 Issue: 2 Pages: 672-682
  • DOI: 10.1093/nar/gkp955
  • Peer Reviewed
• [Journal Article] Crystal Structures of the Multidrug Binding Repressor Corynebacterium glutamicum CgmR in Complex with Inducers and with an Operator (2010)
  • Author(s): Itou H, Watanabe N, Yao M, Shirakihara Y, Tanaka I
  • Journal Title: J. Mol. Biol Volume: 2010 Issue: 2 Pages: 174-184
  • DOI: 10.1016/j.jmb.2010.07.042
  • Peer Reviewed
• [Journal Article] Crystal Structures of the Multidrug Binding Repressor Corynebacterium glutamicum CgmR in Complex with Inducers and with an Operator (2010)
  • Author(s): H.Itou
  • Journal Title: J.Mol.Biol Volume: 403 Pages: 174-184
  • Peer Reviewed
• [Journal Article] Structure of bacterial cellulose synthase subunit D octamer with fourinner passageways (2010)
  • Author(s): S.-Q.Hu
  • Journal Title: Proc.Natl.Acad.Sci. Volume: 107 Pages: 17957-17961
  • Peer Reviewed
• [Journal Article] Two distinct regions in Staphylococcus aureus GatCAB guaranteeaccurate tRNA recognition (2010)
  • Author(s): Akiyoshi Nakamura
  • Journal Title: Nucleic Acids Research 38 Pages: 672-682
  • Peer Reviewed
• [Journal Article] The structure of alanyl-tRNA synthetase with editing domain, Proc (2009)
  • Author(s): Sokabe M, Ose T, Nakamura A, Tokunaga K, Nureki O, Yao M, Tanaka I
  • Journal Title: Natl. Acad. Sci. USA Volume: 106 Issue: 27 Pages: 11028-11033
  • 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 Issue: 9 Pages: 1362-1373
  • DOI: 10.1038/emboj.2009.69
  • Peer Reviewed
• [Journal Article] Snapshots of Dynamics in Synthesizing N6-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 Issue: 23 Pages: 5057-5065
  • DOI: 10.1021/bi900337d
  • Peer Reviewed
• [Journal Article] Snapshots of Dynamics in Synthesizing N^6-Isopentenyladenosine at the tRNA Anticodon (2009)
  • Author(s): Sarin Chimnaronk
  • Journal Title: Biochemistry 48 Pages: 5057-5065
  • Peer Reviewed
• [Journal Article] The structure of alany-tRNA synthetase with editing domain (2009)
  • Author(s): Masaaki Sokabe
  • Journal Title: Proc.Natl.Acad.Sci. 106 Pages: 11028-11033
  • Peer Reviewed
• [Journal Article] RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon (2009)
  • Author(s): Sarin Chimnaronk
  • Journal Title: The EMBO Journal 28 Pages: 1362-1373
  • 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)
• [Presentation] The Recognition Mechanism of eIF2β for its partner proteins eIF5 and eIF2Bε (2011)
  • Author(s): Zuoqi Gai
  • 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）
• [Presentation] 古細菌型GatCABと真正細菌型GatCABの比較 (2010)
  • Author(s): 周倩
  • 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(大阪)
  • Year and Date: 2010-12-05
• [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
  • Organizer: 第12回日本RNA学会年会
  • Place of Presentation: 一橋記念講堂(東京)
  • Year and Date: 2010-07-27
• [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)
• [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)
• [Presentation] Structural basis for translation factor recruitment to the eukaryotic/archaeal ribosomes (2009)
  • Author(s): Min Yao
  • Organizer: Taiwan-Japan Joint Seminar on Crystallography and IPR Seminar
  • Place of Presentation: 大阪大学蛋白質研究所(吹田市)
  • Year and Date: 2009-12-07
• [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)
• [Remarks]
  • URL: http://altair.sci.hokudai.ac.jp/g6/
• [Remarks] 北海道大学 大学院先端生命科学研究院 X線構造生物学研究室
  • URL: http://altair.sci.hokudai.ac.jp/g6/