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2013 Fiscal Year Final Research Report

Reaction Mechansim of [NiFe]-hydrogenase by Neutron Structural Chmeistry

Research Project

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Project/Area Number 24657077
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeSingle-year Grants
Research Field Structural biochemistry
Research InstitutionUniversity of Hyogo

Principal Investigator

HIGUCHI Yoshiki  兵庫県立大学, 生命理学研究科, 教授 (90183574)

Project Period (FY) 2012-04-01 – 2014-03-31
Keywordsヒドロゲナーゼ / X線結晶解析 / 反応機構 / Ni酵素 / 燃料電池
Research Abstract

The goal of this study is to elucidate the reaction mechansim of at the active site of [NiFe]-hydrogenase by neutron diffraction study. For this purpose, we have tried to prepare large crystals of hydrogenase in high quality in D2O.
We have improved the crystallization condition by using 2-methyl-2,4-pentanediol(MPD) as a precipitant in D2O. We found that MPD is oxidized to be 4-hydroxy-4-methyl-2-pentanone(HMPO) which causes a serious damage to the quality of the crystals. We have successfully determined the more suitable crystallization condition under anaerobic condition. As a result, we have succeeded in prearation of a crystal with a volume of 11 mm3. In addition, we have found the condition to freeze the large crystals without damage. Unfortunately, the reactor (neutron source) of JAEA in Tokai is still in preparatory period due to a serious disaster in the area of East Japan in 2011, we will try to do neutron diffraction study in the near future.

  • Research Products

    (26 results)

All 2014 2013 2012

All Journal Article (10 results) (of which Peer Reviewed: 5 results) Presentation (14 results) Book (2 results)

  • [Journal Article] Studies on Hydrogenase2013

    • Author(s)
      T. Yagi and Y. Higuchi
    • Journal Title

      Proc. Jpn. Acad.

      Volume: Ser. B 89 Pages: 16-33

    • DOI

      10.2183/pjab.89.16

    • Peer Reviewed
  • [Journal Article] Structural aspects of [NiFe]-hydrogenases2013

    • Author(s)
      Y. Shomura, Y. Higuchi
    • Journal Title

      Reviews in Inorganic Chemistry

      Volume: 33 Pages: 173-192

    • DOI

      10.1515/revic-2013-0005

    • Peer Reviewed
  • [Journal Article] 膜結合型ヒドロゲナーゼの酸素耐性機構の解明2013

    • Author(s)
      庄村康人,樋口芳樹
    • Journal Title

      生物物理

      Volume: 53-2 Pages: 82-85

  • [Journal Article] Structural Basis for the Reaction Mechanism of S-carbamoylation of HypE by HypF in the Maturation of [NiFe]-hydrogenases2012

    • Author(s)
      Y. Shomura, Y. Higuchi
    • Journal Title

      J. Biol. Chem.

      Volume: 287

    • DOI

      10.1074/jbc.M112.387134

    • Peer Reviewed
  • [Journal Article] Crystal Structure Analysis of the Translation Factor RF3 (release factor 3)2012

    • Author(s)
      K. Kihira, Y. Shimizu, Y. Shomura, N. Shibata, M. Kitamura, A. Nakagawa, T. Ueda, K. Ochi, Y. Higuchi
    • Journal Title

      FEBS Letters

      Volume: 586 Pages: 3705- 3709

    • DOI

      10.1016/j.febslet.2012.08.029

    • Peer Reviewed
  • [Journal Article] Photosensitivity of the Ni-A State of [NiFe] Hydrogenase from Desulfovibrio vulgaris Miyazaki F with Visible Light, Biochem2012

    • Author(s)
      H. Osuka, Y. Shomura, H. Komori, N. Shibata, S. Nagao, Y. Higuchi, S. Hirota
    • Journal Title

      Byophys. Res. Commun.

      Volume: 430 Pages: 284-288

    • DOI

      10.1016/j.bbrc.2012.10.136

    • Peer Reviewed
  • [Journal Article] Crystal structure of O_2-tolerant [NiFe] hydrogenase reveals the mechanism of O_2-tolerance attributable to a redox-dependent conformational change of [4Fe-3S] cluster2012

    • Author(s)
      Y. Shomura and Y. Higuchi
    • Journal Title

      SPring-8 Research Frontier

      Volume: 2011 Pages: 5-6

    • URL

      http://www.spring8.or.jp/ja/news_publications/publications/research_frontiers/html/rf11

  • [Journal Article] [4Fe-3S]クラスターによる[NiFe]ヒドロゲナーゼの酸素耐性機構の構造基盤2012

    • Author(s)
      樋口芳樹,庄村康人
    • Journal Title

      SPring-8利用者情報誌

      Volume: Vol.17 No.2 Pages: 105-110

    • URL

      http://user.spring8.or.jp/sp8info/

  • [Journal Article] 酸素耐性ヒドロゲナーゼの構造化学的研究-酵素分子に見出された活性保護機構-2012

    • Author(s)
      庄村康人,樋口芳樹
    • Journal Title

      燃料電池

      Volume: VOL.11 No.4 Pages: 67-72

  • [Journal Article] ヒドロゲナーゼの新規酸素耐性機構-膜結合型[NiFe]ヒドロゲナーゼ2012

    • Author(s)
      庄村康人,樋口芳樹
    • Journal Title

      化学

      Volume: Vol. 67 Pages: 70-71

  • [Presentation] Purification and Crystallization of NAD+-reducing [NiFe]-hydrogenase2014

    • Author(s)
      H. Nakagawa, M. Taketa, M. Habukawa, K. Kihira, N. Shibata, H. Nishihara, K.-S. Yoon, S. Ogo, Ma. Ishii, Y. Igarashi, Y. Shomura and Y. Higuchi
    • Organizer
      第1回ピコバイロジー研究所国際シンポジウム
    • Place of Presentation
      兵庫
    • Year and Date
      20140107-08
  • [Presentation] Crystallization of [NiFe]-hydrogenase maturation protein complex HypA-HypB2014

    • Author(s)
      Y. Okawa, Y. Higuchi, and Y. Shomura
    • Organizer
      第1回ピコバイロジー研究所国際シンポジウム
    • Place of Presentation
      兵庫
    • Year and Date
      20140107-08
  • [Presentation] NAD^+還元型ヒドロゲナーゼの結晶学的研究2013

    • Author(s)
      中川英恵,竹田翠,土生川真央,木平清人,柴田直樹,樋口芳樹
    • Organizer
      平成25年度日本結晶学会年会
    • Place of Presentation
      熊本
    • Year and Date
      20131012-13
  • [Presentation] [NiFe]-ヒドロゲナーゼ成熟化タンパク質HypAの結晶化2013

    • Author(s)
      大川雄嗣,樋口芳樹,庄村康人
    • Organizer
      平成25年度日本結晶学会
    • Place of Presentation
      熊本
    • Year and Date
      20131012-13
  • [Presentation] X-ray Structural Study of O_2-tolerant [NiFe] hydrogenase2013

    • Author(s)
      Y. Higuchi, K.-S. Yoon, H. Nishihara and Y. Shomura
    • Organizer
      International Conference on Bio/Mimetic Solar Energy Conversion (iSEC) 2013
    • Place of Presentation
      大阪
    • Year and Date
      2013-11-23
  • [Presentation] 水素分解酵素の成熟化機構の解明2013

    • Author(s)
      大川雄嗣,樋口芳樹,庄村康人
    • Organizer
      兵庫県立大学シンポジウム
    • Year and Date
      2013-09-24
  • [Presentation] 水素-化学エネルギー変換・ヒドロゲナーゼの構造化学2013

    • Author(s)
      神戸中川英恵,竹田翠,庄村康人,樋口芳樹
    • Organizer
      兵庫県立大学シンポジウム
    • Place of Presentation
      神戸
    • Year and Date
      2013-09-24
  • [Presentation] Reaction Mechanism of S-Carbamoylation of HypE by HypF in the Maturation of [NiFe]-hydrogenase2013

    • Author(s)
      Y. Higuchi and Y. Shomura
    • Organizer
      10th International Hydrogenase Conference・Szeged
    • Place of Presentation
      ハンガリー
    • Year and Date
      2013-07-09
  • [Presentation] H. thermoluteolus TH-1由来NAD^+還元ヒドロゲナーゼの分光学研究2013

    • Author(s)
      太虎林,竹田翠,庄村康人,西川幸志,鈴木雅之,樋口芳樹,廣田俊
    • Organizer
      日本化学会第94春季年会
    • Place of Presentation
      名古屋
    • Year and Date
      2013-03-29
  • [Presentation] Catalytic cycle of cytochrome-c3 hydrogenase, a [NiFe]-hydrogenase2012

    • Author(s)
      八木達彦,樋口芳樹
    • Organizer
      第85回日本生化学会大会
    • Place of Presentation
      福岡
    • Year and Date
      2012-12-14
  • [Presentation] Structural Study of O_2-Tolerant [NiFe] Hydrogenase2012

    • Author(s)
      Y. Higuchi
    • Organizer
      The 2nd International Conference on MEXT Project of Integrated Research on Chemical Synthesis
    • Place of Presentation
      愛知
    • Year and Date
      2012-12-11
  • [Presentation] [NiFe]ヒドロゲナーゼの酸素耐性機構の解明-放射光X線利用による精密構造化学-2012

    • Author(s)
      樋口芳樹
    • Organizer
      日本農芸化学会関西支部第477回講演会
    • Place of Presentation
      兵庫
    • Year and Date
      2012-12-01
  • [Presentation] [NiFe]ヒドロゲナーゼ成熟化因子HypE,HypFのX線結晶構造解析2012

    • Author(s)
      庄村康人,尹基石,西原宏史,樋口芳樹
    • Organizer
      第49回日本生物物理学会年会
    • Place of Presentation
      愛知
    • Year and Date
      2012-09-24
  • [Presentation] 酸素耐性[NiFe]ヒドロゲナーゼの結晶構造解析2012

    • Author(s)
      庄村康人,尹基石,西原宏史,樋口芳樹
    • Organizer
      酸素耐性[NiFe]ヒドロゲナーゼの結晶構造解析
    • Place of Presentation
      愛知
    • Year and Date
      2012-06-22
  • [Book] CSJカレントレビュー15,次世代のバイオ水素エネルギー開発2014

    • Author(s)
      庄村康人,樋口芳樹
    • Total Pages
      174(80-85)
    • Publisher
      化学同人
  • [Book] 光合成のエネルギー利用と環境応用(三宅淳,佐々健監修)2014

    • Author(s)
      樋口芳樹,ヒドロゲナーゼ
    • Total Pages
      33-42
    • Publisher
      CMC出版

URL: 

Published: 2015-06-25  

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