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Structural basis and reaction mechanism of [FeFe] hydrogenases

Research Project

Project/Area Number 20H03215
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43040:Biophysics-related
Research InstitutionUniversity of Hyogo (2022)
Nara Institute of Science and Technology (2021)
Hokkaido University (2020)

Principal Investigator

Ogata Hideaki  兵庫県立大学, 理学研究科, 教授 (30795935)

Project Period (FY) 2020-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥18,070,000 (Direct Cost: ¥13,900,000、Indirect Cost: ¥4,170,000)
Fiscal Year 2022: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2021: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2020: ¥10,270,000 (Direct Cost: ¥7,900,000、Indirect Cost: ¥2,370,000)
Keywords金属酵素 / ヒドロゲナーゼ / 水素 / クライオ電子顕微鏡 / 構造解析 / 赤外分光法 / 酸化還元電位 / 立体構造 / 反応機構 / クライオ電顕 / 電子伝達分岐 / 鉄硫黄クラスター / 酵素 / 赤外分光 / 電気化学 / 酵素反応 / 生物無機化学 / 分光学
Outline of Research at the Start

ヒドロゲナーゼは多くの微生物が持つ金属酵素で、水素分子の分解や合成を可逆的に触媒する。その水素触媒能力は高価なプラチナなどを用いた化学触媒と同等以上の効率とされる。本研究は、超好熱菌Thermotoga maritima由来の「電子伝達分岐型[FeFe]ヒドロゲナーゼ」の特異な電子伝達分岐反応機構や、「水素センサー型[FeFe]ヒドロゲナーゼ」のシグナル応答の仕組みを構造解析・分光学的分析手法を駆使して分子レベルで解明する。

Outline of Final Research Achievements

[FeFe] hydrogenases (an electron-bifurcating and a sensory types) from thermophilic bacteria have successfully been maturated with the chemically synthesized di-iron complexes. We mutated the amino acid residues in vicinity of the active site of the sensory [FeFe] hydrogenase. One of the variants showed significantly less activity compared to the wild type hydrogenase enzyme. It suggested that the electronic structure of the active site [4Fe-4S] sub-cluster could be changed. The cryo-electron microscpic structure of the electron-bifurcating [FeFe] hydrogenase showed the tetramer of the promoters which consists of three subunits.

Academic Significance and Societal Importance of the Research Achievements

電子伝達分岐型[FeFe]ヒドロゲナーゼのクライオ電子顕微鏡法による構造解析から3つのサブユニットで構成される4量体を構成していることが明らかとなった。複雑な電子伝達経路を持っており、FMNが結合している領域で電子伝達分岐が分岐する可能性が示された。また、センサー型[FeFe]ヒドロゲナーゼでは、第2配位圏の違いにより活性中心の鉄硫黄クラスターの酸化還元電位の変化が顕著に見られた。これらの結果から、金属中心近傍の構造が機能に重要であることが示唆された。本研究で明らかとなった知見は水素発生系ヒドロゲナーゼを模した錯体の設計に重要な指針を与える。

Report

(4 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • Research Products

    (26 results)

All 2023 2022 2021 2020 Other

All Int'l Joint Research (6 results) Journal Article (4 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 4 results,  Open Access: 2 results) Presentation (13 results) (of which Int'l Joint Research: 3 results,  Invited: 4 results) Book (3 results)

  • [Int'l Joint Research] マックスプランク研究所(ドイツ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] ヨーク大学/オックスフォード大学/エセックス大学(英国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] CSIR海洋学国立研究所(インド)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] マックスプランク研究所(ドイツ)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] ヨーク大学(英国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] マックスプランク研究所(ドイツ)

    • Related Report
      2020 Annual Research Report
  • [Journal Article] Redox tuning of the H-cluster by second coordination sphere amino acids in the sensory [FeFe] hydrogenase from Thermotoga maritima2023

    • Author(s)
      Chongdar Nipa、Rodriguez-Macia Patricia、Reijerse Edward J.、Lubitz Wolfgang、Ogata Hideaki、Birrell James A.
    • Journal Title

      Chemical Science

      Volume: 14 Issue: 13 Pages: 3682-3692

    • DOI

      10.1039/d2sc06432d

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase2022

    • Author(s)
      Furlan Chris、Chongdar Nipa、Gupta Pooja、Lubitz Wolfgang、Ogata Hideaki、Blaza James N、Birrell James A
    • Journal Title

      eLife

      Volume: 11

    • DOI

      10.7554/elife.79361

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase2022

    • Author(s)
      Stripp Sven T.、Duffus Benjamin R.、Fourmond Vincent、Leger Christophe、Leimkuhler Silke、Hirota Shun、Hu Yilin、Jasniewski Andrew、Ogata Hideaki、Ribbe Markus W.
    • Journal Title

      Chemical Reviews

      Volume: 122 Issue: 14 Pages: 11900-11973

    • DOI

      10.1021/acs.chemrev.1c00914

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Structural and spectroscopic characterization of CO inhibition of [NiFe]-hydrogenase from Citrobacter sp. S-772022

    • Author(s)
      Imanishi Takahiro、Nishikawa Koji、Taketa Midori、Higuchi Katsuhiro、Tai Hulin、Hirota Shun、Hojo Hironobu、Kawakami Toru、Hataguchi Kiriko、Matsumoto Kayoko、Ogata Hideaki、Higuchi Yoshiki
    • Journal Title

      Acta Crystallographica Section F Structural Biology Communications

      Volume: 78 Issue: 2 Pages: 66-74

    • DOI

      10.1107/s2053230x22000188

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Structure of an electron-bifurcating [FeFe] hydrogenase2022

    • Author(s)
      C. Furian, N. Chongdar, P. Gupta, W. Lubitz, H. Ogata, J. N. Blaza, J. A. Birrell
    • Organizer
      10th Asian Biological Inorganic Chemistry Conference
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase from Thermotoga maritima2022

    • Author(s)
      C. Furian, N. Chongdar, P. Grupta, W. Lubitz, H. Ogata, J. N. Blaza, J. A. Birrell
    • Organizer
      EBEC2022, the 21st European Bioenergetics Conference
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] New Assay System for the Enzymatic Reaction with Gaseous Substrates by Using Raman Spectroscopy2022

    • Author(s)
      K. Nishikawa, Y. Nakagawa, S. Inoue, T. Chuji, H. Ogata, S. Nakashima, Y. Shigeta, K. Fukutani, Y. Higuchi
    • Organizer
      10th Asian Biological Inorganic Chemistry Conference
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Raman分光法を用いたガス状分子を基質とする酵素反応の新規活性測定法2022

    • Author(s)
      西川幸志, 中川由佳, 井上翔太, 中地隆文, 中島聡, 緒方英明, 重田育照, 福谷克之, 樋口芳樹
    • Organizer
      第16回バイオ関連化学シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] 水素酸化還元酵素の反応機構の解明2022

    • Author(s)
      緒方英明
    • Organizer
      第42回STクラブ
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] タンパク質によって水素分子が分解される様子を構造解析で捉える2022

    • Author(s)
      緒方英明
    • Organizer
      兵庫県立大学バイオダイナミクスセンターセミナー
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 水素センサータンパク質の異種発現と精製法2022

    • Author(s)
      田中宏幸, 緒方英明
    • Organizer
      兵庫県立大学播磨理学キャンパス 技術・人材マッチング交流会2022
    • Related Report
      2022 Annual Research Report
  • [Presentation] [FeFe]ヒドロゲナーゼの電子伝達経路の構造学的研究2022

    • Author(s)
      緒方英明, C. Furlan, N. Chongdar, P. Gupta, W. Lubitz, J. Blaza, J. Birrell
    • Organizer
      日本化学会第102春季年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Construction and structural characterization of a unique dimer of ferredoxin from Thermotoga maritima2022

    • Author(s)
      N. A. Binti Azmi, T. Mashima, H. Ogata, H. Komori, T. Ando, M. Yamanaka, S. Hirota
    • Organizer
      日本化学会第102春季年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] αヘリックスで連結した3ユニット環状ヘムタンパク質の設計と構築2022

    • Author(s)
      大西遥喜, 藤原綱大, 真島剛史, 小林直也, 山中優, 緒方英明, 廣田俊
    • Organizer
      日本化学会第102春季年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] センサー型[FeFe]ヒドロゲナーゼの変異体による水素酸化還元反応2021

    • Author(s)
      N. Chongdar, J. A. Birrell, E. Reijerse, W. Lubitz, H. Ogata
    • Organizer
      第21回日本蛋白質科学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 金属酵素の結晶構造化学的研究2020

    • Author(s)
      緒方英明
    • Organizer
      日本結晶学会令和 2 年(2020 年)度年会および会員総会 70 周年記念大会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Spectroelectrochemical FTIR studies of an electron-bifurcating [FeFe] hydrogenase2020

    • Author(s)
      N. Chongdar, K. Pawlak, O. Rudiger, E. J. Reijerse, P. Rodriguez-Marcia, W. Lubitz, J. A. Birrell, H. Ogata
    • Organizer
      第 58 回日本生物物理学会年会
    • Related Report
      2020 Annual Research Report
  • [Book] Encyclopedia of Biological Chemistry 3rd Edition2021

    • Author(s)
      Hideaki Ogata, Wolfgang Lubitz
    • Total Pages
      8
    • Publisher
      Elsevier
    • ISBN
      9780128194607
    • Related Report
      2021 Annual Research Report
  • [Book] 生命金属ダイナミクス2021

    • Author(s)
      緒方英明、樋口芳樹(城宜嗣, 津本浩平編)
    • Total Pages
      7
    • Publisher
      株式会社エヌ・ティー・エス
    • Related Report
      2020 Annual Research Report
  • [Book] Encyclopedia of Biological Chemistry 3rd edition2021

    • Author(s)
      Hideaki Ogata and Wolfgang Lubitz
    • Total Pages
      8
    • Publisher
      Elsevier
    • Related Report
      2020 Annual Research Report

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Published: 2020-04-28   Modified: 2024-01-30  

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