Elucidation of reaction mechanism for post-transcriptional modification at tRNA anticodon region

2010 Fiscal Year Final Research Report

• Project/Area Number: 20687007
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Structural biochemistry
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: NUMATA Tomoyuki National Institute of Advanced Industrial Science and Technology, バイオメディカル研究部門, 研究員 (10401564)
• Project Period (FY): 2008 – 2010
• Keywords: tRNA / 転写後修飾 / RNA修飾酵素 / 結晶構造解析

Research Abstract

The uridine at the first position of the tRNA anticodon (U34) in tRNA^<Glu>UUC, tRNA^<Lys>UUU, tRNA^<Gln>UUG is modified to 5-carboxymethylaminomethyl-2-thiouridine (cmnm^5s^2U), which is crucial for the precise decoding of the genetic code. In eubacteria, two conserved proteins, GidA and MnmE, are responsible for adding the cmnm5 group to the 5-position of U34. Here we report the crystal structures of GidA and MnmE. Together with the mutational study, we propose a novel mechanism for the cmnm^5U modification process.

Research Products

• [Journal Article] Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. (2010)
  • Author(s): Ikeuchi, Y., Kimura, S., Numata, T., Nakamura, D., Yokogawa, T., Ogata, T., Wada, T., Suzuki, T., Suzuki, T.
  • Journal Title: Nat.Chem.Biol. 6 Pages: 277-282
  • Peer Reviewed
• [Journal Article] Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon. (2009)
  • Author(s): Osawa, T., Ito, K., Inanaga, H., Nureki, O., Tomita, K., Numata, T.
  • Journal Title: Structure* : Corresponding author 17 Pages: 713-724
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of the tRNA-modification enzyme GidA from Aquifex aeolicus. (2009)
  • Author(s): Osawa, T., Inanaga, H., Numata, T.
  • Journal Title: Acta Crystallogr.Sect.* : Corresponding author F 65 Pages: 508-511
  • Peer Reviewed
• [Presentation] アーキアtRNA^Ileのアンチコドン領域に見られる新規RNA修飾塩基の生合成機構解明 (2010)
  • Author(s): 大澤拓生、寺坂尚紘、木村聡、鈴木勉、沼田倫征
  • Organizer: 第34回蛋白質と酵素の構造と機能に関する九州シンポジウム
  • Place of Presentation: 福岡
  • Year and Date: 20100900
• [Presentation] tRNA揺らぎ塩基の5-カルボキシメチルアミノメチル化修飾に関わる酵素GidAおよびMnmEの構造機能解析 (2010)
  • Author(s): 大澤拓生、稲永英子、沼田倫征
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌
  • Year and Date: 20100600
• [Presentation] tRNA揺らぎ塩基の5-カルボキシメチルアミノメチル化修飾に関わる酵素MnmEの結晶構造解析 (2009)
  • Author(s): 大澤拓生、伊藤耕一、稲永英子、沼田倫征
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 20090500
• [Presentation] tRNAアンチコドンの修飾に関わる酵素GidAにおいて保存されているシステインは5-カルボキシメチルアミノメチルウリジン生合成に不可欠である (2009)
  • Author(s): 大澤拓生、伊藤耕一、稲永英子、沼田倫征
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 20090500
• [Presentation] tRNA揺らぎ塩基の修飾に関わる酵素の構造機能解析(1) (2009)
  • Author(s): 大澤拓生、伊藤耕一、稲永英子、沼田倫征
  • Organizer: 日本農芸化学会2009年度大会
  • Place of Presentation: 福岡
  • Year and Date: 20090300
• [Presentation] tRNA揺らぎ塩基の修飾に関わる酵素の構造機能解析(2) (2009)
  • Author(s): 大澤拓生、伊藤耕一、稲永英子、沼田倫征
  • Organizer: 日本農芸化学会2009年度大会
  • Place of Presentation: 福岡
  • Year and Date: 20090300
• [Book] 入門構造生物学-放射光X線と中性子で最新の生命現象を読み解く- (2010)
  • Author(s): 富田耕造、沼田倫征
  • Total Pages: 111-119
  • Publisher: 「第4章生命現象の理解に迫る構造生物学研究、4.3翻訳」共立出版