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2010 Fiscal Year Annual Research Report

中性子結晶解析法によるヒドロゲナーゼの水素活性化反応機構の解明

Research Project

Project/Area Number 22657031
Research InstitutionUniversity of Hyogo

Principal Investigator

樋口 芳樹  兵庫県立大学, 大学院・生命理学研究科, 教授 (90183574)

Keywordsヒドロゲナーゼ / 中性子結晶解析 / 反応機構 / Ni酵素 / プロトン経路
Research Abstract

本申請研究では,硫酸還元菌由来の水素酸化還元酵素・ヒドロゲナーゼのNi-Fe活性部位における水素活性化の反応中間体を,中性子結晶解析法により直接観察することを主目的とする.そのために最終的には分子中の全ての水素原子を重水素に置換した酵素試料を調製することを目指す.本酵素の基質は「水素および重水素」である.従って,構造中に(重)水素を「直接に精度良く見る」ことが可能な中性子結晶解析法は最適の研究手法である.中性子回折実験において,試料中の水素原子は,非干渉性散乱の割合が大きいためバックグラウンドを上げて回折データのS/N比に多大な悪影響を与える。
そこで,平成22年度は,通常の野生(水素)型ヒドロゲナーゼ試料を,重水中で,重水素化した沈殿剤(2-メチル-2,4-ペンタンジオール)を用いて結晶化したところ,約4mm^3の単結晶の調製に成功した.得られた結晶を,日本原子力開発研究機構の実験炉で得られる中性子線を用いて回折実験を行ったところ,7A分解能の回折パターンの取得に成功した.さらに,本結晶を最近開発された中性子回折実験用の試料凍結装置を用いて,100Kにて回折実験をしたところ,分解能は5A分解能まで到達した.現在,さらなる分解能の向上を目指して結晶化条件の改善を進めている.また,タンパク質の全水素原子を重水素にするため,重水中で重水素化培地を用いての硫酸還元菌の培養条件の検討を進めている.

  • Research Products

    (24 results)

All 2011 2010

All Journal Article (11 results) (of which Peer Reviewed: 11 results) Presentation (12 results) Book (1 results)

  • [Journal Article] How Coenzyme B12-dependent Ethanolamine Ammonialyase Deals with Both Enantiomers of 2-Amino-1-propanol as Substrates : Structure-based Rationalization2011

    • Author(s)
      N. Shibata, Y. Higuchi and T. Toraya
    • Journal Title

      Biochemistry

      Volume: 50 Pages: 591-598

    • DOI

      DOI:10.1021/bi101696h

    • Peer Reviewed
  • [Journal Article] A Functional Role of the Glycosylated N-terminal Domain of Chondromodulin-I2011

    • Author(s)
      J.Kondo, et al.
    • Journal Title

      J.Bone Miner.Metab.

      Volume: 29 Pages: 23-30

    • Peer Reviewed
  • [Journal Article] Positively Charged Domain Located Downstream of PIP Box, Together with TD Amino Acids within PIP Box, is Important for CRL4^<Cdt2>-mediated Proteolysis2011

    • Author(s)
      M.Michishita, et al.
    • Journal Title

      Gene to Cells

      Volume: 16 Pages: 12-22

    • Peer Reviewed
  • [Journal Article] Structure and Molecular Evolution of Multicopper Blue Proteins2010

    • Author(s)
      H. Komori and Y. Higuchi
    • Journal Title

      BIOMOLECULAR CONCEPTS

      Volume: 1 Pages: 31-40

    • DOI

      DOI:10.1515/BMC.2010.004

    • Peer Reviewed
  • [Journal Article] Enzymatic Synthesis of Nylon-6 units in Organic Solvent Contained Low-water : Structural Requirement of 6-aminohexanoate-dimer Hydrolase for Efficient Amide Synthesis2010

    • Author(s)
      Y.Kawashima, et al.
    • Journal Title

      J.Mol.Cat.B

      Volume: 64 Pages: 81-88

    • Peer Reviewed
  • [Journal Article] Expression, Crystallization and Preliminary X-ray Crystallographic Study of Ethanolamine Ammonia-lyase from Escherichia coli2010

    • Author(s)
      N.Shibata, et al.
    • Journal Title

      Acta Crystallogr.

      Volume: F66 Pages: 709-711

    • Peer Reviewed
  • [Journal Article] Crystal Structures of Ethanolamine Ammonia-lyase complexed with Coenzyme B_<12> Analogs and Substrates2010

    • Author(s)
      N.Shibata, et al.
    • Journal Title

      J.Biol.Chem.

      Volume: 285 Pages: 26484-26493

    • Peer Reviewed
  • [Journal Article] Cytochrome c polymerization by successive domain swapping at the C-terminal helix2010

    • Author(s)
      S.Hirota, et al.
    • Journal Title

      Proc.Natl.Acad.Sci.

      Volume: 107 Pages: 12854-12859

    • Peer Reviewed
  • [Journal Article] Purification, Crystallization and Preliminary X-ray Analysis of the Dis similatory Sulfite Reductase from Desulfovibrio vulgaris Miyazaki F2010

    • Author(s)
      H.Ogata, et al.
    • Journal Title

      Acta Crystallogr.

      Volume: F66 Pages: 1470-1472

    • Peer Reviewed
  • [Journal Article] Crystallization and Preliminary X-ray Analysis of Dimeric and Trimeric Cytochromes c from Horse Heart2010

    • Author(s)
      M.Taketa, et al.
    • Journal Title

      Acta Crystallogr.

      Volume: F66 Pages: 1477-1479

    • Peer Reviewed
  • [Journal Article] Crystal Structure Analysis of Bacillus subtilis Ferredoxin-NADP Oxid oreductase and the Structural Basis for Its Substrate Selectivity2010

    • Author(s)
      H.Komori, et al.
    • Journal Title

      Protein Science

      Volume: 19 Pages: 2279-2290

    • Peer Reviewed
  • [Presentation] Structural Basis for the Reaction Mechanism of Dissimilatory Sulfite Reductase2011

    • Author(s)
      Y.Shomura, et al.
    • Organizer
      International Symposium on Chemistry of Reductases IV
    • Place of Presentation
      名古屋
    • Year and Date
      20110120-20110121
  • [Presentation] Crystallization and X-ray Analysis of ATP-sulfurylase from Sulfate-reducing Bacteria2011

    • Author(s)
      M.Taketa, et al.
    • Organizer
      International Symposium on Chemistry of Reductases IV
    • Place of Presentation
      名古屋
    • Year and Date
      20110120-20110121
  • [Presentation] 中性子構造化学でヒドロゲナーゼの水素分子活性化機構は理解できるか?2011

    • Author(s)
      樋口芳樹
    • Organizer
      中性子構造生物学およびタンパク質水和構造に関するシンポジウム
    • Place of Presentation
      水戸
    • Year and Date
      2011-03-04
  • [Presentation] 枯草菌由来フェレドキシン-NADPH還元酵素のX線結晶構造解析2010

    • Author(s)
      小森博文, et al.
    • Organizer
      2010年度日本結晶学会年会
    • Place of Presentation
      吹田
    • Year and Date
      20101203-20101205
  • [Presentation] 膜結合型[NiFe]ヒドロゲナーゼのX線結晶構造解析2010

    • Author(s)
      庄村康人, et al.
    • Organizer
      2010年度日本結晶学会年会
    • Place of Presentation
      吹田
    • Year and Date
      20101203-20101205
  • [Presentation] B12-補酵素関与エタノールアミアンモニアリアーゼの立体構造に基づく立体化学経路の解明2010

    • Author(s)
      柴田直樹, et al.
    • Organizer
      2010年度日本結晶学会年会
    • Place of Presentation
      吹田
    • Year and Date
      20101203-20101205
  • [Presentation] Basis for the Lack of Stereospecificity in Coenzyme B_<12>-dependent Ethanolamine ammonia-lyase2010

    • Author(s)
      N.Shibata, et al.
    • Organizer
      The 10th Conference of the Asian Crystallographic Association
    • Place of Presentation
      Pusan
    • Year and Date
      20101101-20101103
  • [Presentation] The Role of the π-electron System in Regulation of Reduction Potentials of Tetraheme Cytochrome C_<3>2010

    • Author(s)
      H.Akutsu, et al.
    • Organizer
      The 10th Conference of the Asian Crystallographic Association
    • Place of Presentation
      Pusan
    • Year and Date
      20101101-20101103
  • [Presentation] Improved Technologies for High-resolution X-ray Crystallography2010

    • Author(s)
      H.Tanaka, et al.
    • Organizer
      The 10th Conference of the Asian Crystallographic Association
    • Place of Presentation
      Pusan
    • Year and Date
      20101101-20101103
  • [Presentation] Enzymatic Degradation and Synthesis of Nylon-6 Related Compounds.2010

    • Author(s)
      S.Negoro, et al.
    • Organizer
      International Symposium on BioPolymers 2010
    • Place of Presentation
      Stuttgart
    • Year and Date
      2010-10-04
  • [Presentation] Cytochrome c Polymerization by Successive Domain Swapping at the C-terminal Helix2010

    • Author(s)
      S.Hirota, et al.
    • Organizer
      日本生物物理学会第48回年会
    • Place of Presentation
      仙台
    • Year and Date
      2010-09-22
  • [Presentation] ナイロンオリゴマ-分解酵素の精密構造解析2010

    • Author(s)
      樋口芳樹
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌
    • Year and Date
      2010-06-18
  • [Book] 構造生物学-原子構造からみた生命現象の営み2010

    • Author(s)
      樋口芳樹, 中川敦史
    • Total Pages
      253
    • Publisher
      共立出版株式会社

URL: 

Published: 2012-07-19  

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