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Molecular Mechanism of Protein Maturation of Hydrogenase

Research Project

Project/Area Number 23247014
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Structural biochemistry
Research InstitutionKyoto University

Principal Investigator

MIKI Kunio  京都大学, 理学(系)研究科(研究院), 教授 (10116105)

Co-Investigator(Renkei-kenkyūsha) ATOMI Haruyuki  京都大学, 大学院工学研究科, 教授 (90243047)
Research Collaborator WATANABE Satoshi  京都大学, 大学院理学研究科, 特定研究員 (50432357)
Project Period (FY) 2011-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥47,060,000 (Direct Cost: ¥36,200,000、Indirect Cost: ¥10,860,000)
Fiscal Year 2013: ¥16,510,000 (Direct Cost: ¥12,700,000、Indirect Cost: ¥3,810,000)
Fiscal Year 2012: ¥16,510,000 (Direct Cost: ¥12,700,000、Indirect Cost: ¥3,810,000)
Fiscal Year 2011: ¥14,040,000 (Direct Cost: ¥10,800,000、Indirect Cost: ¥3,240,000)
Keywords成熟化タンパク質 / X線結晶構造解析 / 金属取り込み / Hypタンパク質 / 複合体構造 / X線結晶構造解析 / 構造生物学
Outline of Final Research Achievements

Six Hyp proteins (HypA, B, C, D, E, and F) are primarily involved in the maturation process of [NiFe] hydrogenases which catalyze reversible hydrogen production and consumption. These Hyp proteins incorporate a complex Ni/Fe cluster into a protein subunit of [NiFe] hydrogenases. On the basis of our previous success in the structure determination of several Hyp proteins, we have investigated structure and function of transient complexes (HypAB, HypCD, and HypCDE complexes, and hydrogenase-large subunit (HyhL) and Hyp protein complexes) and reaction intermediates (carbamoylated and cyanated HypEs) to obtain insights into molecular mechanism of the [NiFe] hydrogenase maturation.

Report

(4 results)
  • 2014 Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (24 results)

All 2014 2013 2012 2011

All Journal Article (6 results) (of which Peer Reviewed: 6 results,  Acknowledgement Compliant: 2 results) Presentation (18 results) (of which Invited: 6 results)

  • [Journal Article] Identification and Structure of a Novel Archaeal HypB for [NiFe] Hydrogenase Maturation2013

    • Author(s)
      D. Sasaki, S. Watanabe, R. Matsumi, T. Shoji, A. Yasukochi, K. Tagashira, W. Fukuda, T. Kanai, H. Atomi, T. Imanaka, and K. Miki
    • Journal Title

      J. Mol. Biol.

      Volume: 425 Issue: 10 Pages: 1627-1640

    • DOI

      10.1016/j.jmb.2013.02.004

    • Related Report
      2013 Annual Research Report 2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Crystal Structures of the Carbamoylated and Cyanated Forms of HypE for [NiFe] Hydrogenase Maturation2013

    • Author(s)
      T. Tominaga, S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, and K. Miki
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: 110 Issue: 51 Pages: 20485-20490

    • DOI

      10.1073/pnas.1313620110

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Structure of the [NiFe] Hydrogenase Maturation Protein HypF from Thermococcus kodakaraensis KOD12012

    • Author(s)
      T. Tominaga, S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, and K. Miki
    • Journal Title

      Acta Crystallogr. Section F

      Volume: F68 Issue: 10 Pages: 1153-1157

    • DOI

      10.1107/s1744309112036421

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural Basis of [NiFe] Hydrogenase Maturation by Hyp Proteins2012

    • Author(s)
      S. Watanabe, D. Sasaki, T. Tominaga, and K. Miki
    • Journal Title

      Biol. Chem.

      Volume: 393 Issue: 10 Pages: 1089-1100

    • DOI

      10.1515/hsz-2012-0197

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal Structures of the HypCD Complex and the HypCDE Ternary Complex: Transient Intermediate Complexes during [NiFe] Hydrogenase Maturation2012

    • Author(s)
      S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, and K. Miki
    • Journal Title

      Structure

      Volume: 20 Issue: 12 Pages: 2124-2137

    • DOI

      10.1016/j.str.2012.09.018

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterization and in vitro Interaction Study of a [NiFe] Hydrogenase Large Subunit from the Hyperthermophilic Archaeon Thermococcus kodakarensis KOD12012

    • Author(s)
      D. Sasaki, S. Watanabe, T. Kanai, H. Atomi, T. Imanaka, and K. Miki
    • Journal Title

      Biochem. Biophys. Res. Commun.

      Volume: 417 Issue: 1 Pages: 192-196

    • DOI

      10.1016/j.bbrc.2011.11.083

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] [NiFe]ヒドロゲナーゼ成熟化に関与するHypAB複合体のX線結晶構造解析2014

    • Author(s)
      河島拓未,渡部 聡,西谷優一,金井 保,跡見晴幸,今中忠行,三木邦夫
    • Organizer
      日本結晶学会2014年度年会
    • Place of Presentation
      東京都,東京大学農学部
    • Year and Date
      2014-11-01 – 2014-11-03
    • Related Report
      2013 Annual Research Report
  • [Presentation] Studies on intermediate HypAB complexes for Ni insertion during [NiFe] hydrogenase maturation2014

    • Author(s)
      T. Kawashima, S. Watanabe, Y. Nishitani, T. Kanai, H. Atomi, T. Imanaka, and K. Miki
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌市,札幌コンベンションセンター
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2013 Annual Research Report
  • [Presentation] Structural basis for the biosynthesis of the CN ligand of [NiFe] hydrogenase2014

    • Author(s)
      S. Watanabe, T. Tominaga, R. Matsumi, H. Atomi, T. Imanaka, and K. Miki
    • Organizer
      XXIII Congress and General Assembly, International Union of Crystallography
    • Place of Presentation
      Montréal, Canada
    • Year and Date
      2014-08-05 – 2014-08-12
    • Related Report
      2013 Annual Research Report
  • [Presentation] タンパク質結晶学の歴史 - はじめに2014

    • Author(s)
      三木邦夫
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      横浜市,ワークピア横浜/横浜産貿ホールマリネリア
    • Year and Date
      2014-06-25 – 2014-06-27
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] [NiFe]ヒドロゲナーゼ成熟化におけるシアノ基生合成中間体の構造解析2014

    • Author(s)
      渡部 聡,富永大河,松見理恵,跡見晴幸,今中忠行,三木邦夫
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      横浜市,ワークピア横浜/横浜産貿ホールマリネリア
    • Year and Date
      2014-06-25 – 2014-06-27
    • Related Report
      2013 Annual Research Report
  • [Presentation] 放射光と中性子の連携利用による構造生物学2014

    • Author(s)
      三木邦夫
    • Organizer
      物構研サイエンスフェスタ,第5回MLFシンポジウム,第31回PFシンポジウム
    • Place of Presentation
      つくば市,つくば国際会議場エポカル
    • Year and Date
      2014-03-18 – 2014-03-19
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 放射光と中性子線の相補利用による新しいタンパク質結晶学2013

    • Author(s)
      三木邦夫
    • Organizer
      第13回日本蛋白質科学会年会
    • Place of Presentation
      鳥取市,とりぎん文化会館
    • Year and Date
      2013-06-12 – 2013-06-14
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] [NiFe]ヒドロゲナーゼ成熟化タンパク質HypFの結晶構造2012

    • Author(s)
      富永大河,渡部 聡,松見理恵,跡見晴幸,今中忠行,三木邦夫
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋市,名古屋国際会議場
    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
  • [Presentation] [NiFe]ヒドロゲナーゼ成熟化を担う新規なHypBの同定と構造2012

    • Author(s)
      佐々木大輔,渡部 聡,松見理恵,東海林寿久,安河内綾子,田頭健太,福田青郎,金井 保,跡見晴幸,今中忠行,三木邦夫
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋市,名古屋国際会議場
    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
  • [Presentation] Crystal Structures of the HypCD and HypCDE Transient Complexes for [NiFe] Hydrogenase Maturation2012

    • Author(s)
      S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, and K. Miki
    • Organizer
      Annual Meeting of American Crystallographic Association
    • Place of Presentation
      Boston, USA
    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
  • [Presentation] Identification and Structure of a Novel Archaeal HypB for [NiFe] Hydrogenase Maturation2012

    • Author(s)
      D. Sasaki, S. Watanabe, R. Matsumi, T. Shoji, A. Yasukochi, K. Tagashira, W. Fukuda, T. Kanai, H. Atomi, T. Imanaka, and K. Miki
    • Organizer
      27th European Crystallographic Meeting
    • Place of Presentation
      Bergen, Norway
    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
  • [Presentation] Structural Basis of [NiFe] Hydrogenase Maturation Process by Hyp Proteins2012

    • Author(s)
      K. Miki
    • Organizer
      Alumni Symposium: Protein Crystallography in Martinsried, its Beginnings, Maturation, Dissemination, and no End
    • Place of Presentation
      Martinsried, Germany
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] [NiFe]ヒドロゲナーゼ成熟化に関与する新規HypBの同定と構造解析2012

    • Author(s)
      佐々木大輔,渡部 聡,松見理恵,東海林寿久,安河内綾子,田頭健太,福田青郎,金井 保,跡見晴幸,今中忠行,三木邦夫
    • Organizer
      第29回PFシンポジウム
    • Place of Presentation
      つくば市,つくば国際会議場エポカル
    • Related Report
      2011 Annual Research Report
  • [Presentation] [NiFe] ヒドロゲナーゼ成熟化因子 Hypタンパク質の過渡的相互作用の構造基盤2011

    • Author(s)
      渡部 聡,松見理恵,跡見晴幸,今中忠行,三木邦夫
    • Organizer
      第11回日本蛋白質科学会年会
    • Place of Presentation
      吹田市,ホテル阪急エキスポパーク
    • Related Report
      2011 Annual Research Report
  • [Presentation] [NiFe]ヒドロゲナーゼ成熟化因子HypBの結晶構造解析2011

    • Author(s)
      佐々木大輔,渡部 聡,松見理恵,跡見晴幸,今中忠行,三木邦夫
    • Organizer
      第28回PFシンポジウム
    • Place of Presentation
      つくば市,つくば国際会議場エポカル
    • Related Report
      2011 Annual Research Report
  • [Presentation] [NiFe]ヒドロゲナーゼ成熟化因子Hyp タンパク質複合体の結晶構造2011

    • Author(s)
      渡部 聡,松見理恵,跡見晴幸,今中忠行,三木邦夫
    • Organizer
      第28回PFシンポジウム
    • Place of Presentation
      つくば市,つくば国際会議場エポカル
    • Related Report
      2011 Annual Research Report
  • [Presentation] Crystal Structure of Hyp Protein Complexes for [NiFe] Hyodrogenase Maturation2011

    • Author(s)
      S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, and K. Miki
    • Organizer
      15th International Conference of Biological Inorganic Chemistry, ICBIC15
    • Place of Presentation
      Vancouver, Canada
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] Crystal structures of [NiFe] hydrogenase maturase complexes2011

    • Author(s)
      S. Watanabe,R. Matsumi,H. Atomi,T. Imanaka,K. Miki
    • Organizer
      XXII Congress and General Assembly, International Union of Crystallography
    • Place of Presentation
      Madrid, Spain
    • Related Report
      2011 Annual Research Report
    • Invited

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Published: 2011-04-06   Modified: 2019-07-29  

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