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

Research Project

Project/Area Number 20687007
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field Structural biochemistry
Research InstitutionNational 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
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥25,740,000 (Direct Cost: ¥19,800,000、Indirect Cost: ¥5,940,000)
Fiscal Year 2010: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
Fiscal Year 2009: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
Fiscal Year 2008: ¥10,920,000 (Direct Cost: ¥8,400,000、Indirect Cost: ¥2,520,000)
KeywordstRNA / 転写後修飾 / RNA修飾酵素 / 結晶構造解析 / 揺らぎ塩基 / アンチコドン / 古細菌 / ポリアミン / ミトコンドリア病 / 遺伝暗号翻訳 / アンチコト゛ン
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.

Report

(4 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (18 results)

All 2011 2010 2009 2008

All Journal Article (10 results) (of which Peer Reviewed: 10 results) Presentation (6 results) Book (2 results)

  • [Journal Article] Mechanism for the alteration of the substrate specificities of template-independent RNA polymerases2011

    • Author(s)
      Toh, et al.
    • Journal Title

      Structure

      Volume: 19 Pages: 232-243

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure and mode of action of a class V chitinase from Nicotiana tabacum2011

    • Author(s)
      Ohnuma, et al.
    • Journal Title

      Plant Mol.Biol.

      Volume: 75 Pages: 291-304

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization and preliminary X-ray diffraction analysis of a class V chitinase from Nicotiana tabacum2010

    • Author(s)
      Ohnuma, et al.
    • Journal Title

      Acta Crystallogr.Sect.F

      Volume: 66 Pages: 1599-1601

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea2010

    • Author(s)
      Yoshiho Ikeuchi, et al.
    • Journal Title

      Nat.Chem.Biol. 6

      Pages: 277-282

    • Related Report
      2009 Annual Research Report
    • 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

    • Related Report
      2010 Final Research Report
    • 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

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization and preliminary X-ray diffraction analysis of the tRNA-modification enzyme GidA from Aquifex aeolicus2009

    • Author(s)
      Takuo Osawa, et al.
    • Journal Title

      Acta Crystallogr.Sect.F 65

      Pages: 508-511

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Conserved cystein residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon2009

    • Author(s)
      Takuo Osawa, et al.
    • Journal Title

      Structure 17

      Pages: 713-724

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme2008

    • Author(s)
      Yukimatsu Toh, et al.
    • Journal Title

      EMBO J. 27

      Pages: 1944-1952

    • Related Report
      2008 Annual Research Report
    • 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
    • Related Report
      2010 Final Research Report
  • [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
    • Related Report
      2010 Annual Research Report 2010 Final Research Report
  • [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
    • Related Report
      2010 Final Research Report
  • [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
    • Related Report
      2010 Final Research Report
  • [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
    • Related Report
      2010 Final Research Report
  • [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
    • Related Report
      2010 Final Research Report
  • [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
    • 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
    • Related Report
      2010 Final Research Report
  • [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」,第4章 生命現象の理解に迫る構造生物学研究 4.3 翻訳2010

    • Author(s)
      富田耕造、沼田倫征
    • Publisher
      共立出版
    • Related Report
      2010 Annual Research Report

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Published: 2008-04-01   Modified: 2016-04-21  

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