X-ray structural study of the membrane-bound[NiFe]-hydrogenase

• Project/Area Number: 22770111
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Structural biochemistry
• Research Institution: University of Hyogo
• Principal Investigator: SHOMURA Yasuhito 兵庫県立大学, 大学院・生命理学研究科, 助教 (50423900)
• Project Period (FY): 2010 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2011: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2010: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
• Keywords: 水素代謝 / 金属タンパク質 / ヒドロゲナーゼ / X線結晶構造解析 / 膜タンパク質

Research Abstract

Hydrogenases play key roles in hydrogen metabolism by catalyzing synthesis and decomposition of molecular hydrogen. While most of the hydrogenases exhibit no activity in the presence of O2, the membrane-bound[NiFe]-hydrogenase is known to be O2-tolerant, of which mechanism had been poorly understood. In this study, X-ray crystal structures of the membrane-bound[NiFe]-hydrogenase have been determined for three different redox states at resolutions of 1.2-1.4 A. One of the Fe-S clusters showed an unprecedented structure and its redox dependent conformational changes, to which the O2-tolerant property of this hydrogenase should be ascribable.

Research Products

• [Journal Article] Structural and Enzymatic Characterization of BacD, An L-amino Acid Dipeptide Ligase from Bacillus subtilis (2012)
  • Author(s): Shomura, Y., Hinokuchi, E., Ikeda, H., Senoo, A., Takahashi, Y., Saito, J., Komori, H., Shibata, N., Yonetani, Y., Higuchi, Y.
  • Journal Title: Protein Sci. Volume: 21(5) Pages: 707-716
• [Journal Article] Structural basis for[4Fe-3S] cluster in the O2-tolerant membrane-bound[NiFe] hydrogenase (2011)
  • Author(s): Shomura, Y., Yoon, K-S., Nishihara, H. and Higuchi, Y.
  • Journal Title: Nature Volume: 479(7372) Pages: 253-256
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of membrane-bound respiratory[NiFe] hydrogenase from Hydrogenovibrio marinus (2011)
  • Author(s): Shomura, Y., Hagiya, K., Yoon, K. S., Nishihara, H., Higuchi, Y.
  • Journal Title: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun Volume: 67(7) Pages: 827-829
• [Journal Article] Structural Basis for a[4Fe-3S] Cluster in the Oxygen-tolerant Membrane-bound[Ni-Fe]-hydrogenase (2011)
  • Author(s): Y. Shomura, K. Yoon, H. Nishihara, Y. Higuchi
  • Journal Title: Nature Volume: 479 Issue: 7372 Pages: 253-257
  • DOI: 10.1038/nature10504
  • Peer Reviewed
• [Journal Article] Crystallization and Preliminary X-ray Diffraction Analysis of Membrane-bound Respiratory [NiFe] Hydrogenase from Hydrogenovibrio marinus (2011)
  • Author(s): Y.Shomura, et al
  • Journal Title: Acta Crystallgor Volume: 67 Issue: 7 Pages: 827-829
  • DOI: 10.1107/s1744309111019804
  • Peer Reviewed
• [Journal Article] Crystallographic Characterization of the DIX Domain of the Wnt Signalling Positive Regulator Ccd1 (2011)
  • Author(s): S.Terawaki, et al
  • Journal Title: Acta Crystallgor Volume: F67 Issue: 7 Pages: 758-761
  • DOI: 10.1107/s1744309111016526
  • Peer Reviewed
• [Presentation] 酸素耐性[NiFe]ヒドロゲナーゼのX線結晶構造解析 (2012)
  • Author(s): 庄村康人
  • Organizer: 大阪大学蛋白質研究所セミナー「結晶学でみるタンパク質の化学と物理」
  • Place of Presentation: 大阪大学
  • Year and Date: 2012-03-07
• [Presentation] 平成23年度生物構造学研究会「蛋白質中の水素・水分子の役割～中性子構造生物学の展望～」(口頭) (2011)
  • Author(s): 庄村康人・尹基石・西原宏史・樋口芳樹
  • Organizer: 平成23年度生物構造学研究会
  • Place of Presentation: 東海村
  • Year and Date: 2011-12-20
• [Presentation] 酸素耐性[NiFe]ヒドロゲナーゼの構造化学的研究(Structural study of the O2-tolerant[NiFe] hydrogenase) (2011)
  • Author(s): Yasuhito Shomura, Ki-Seok Yoon, Hirofumi Nishihara, Yoshiki Higuchi
  • Organizer: 日本生物物理学会年会
  • Place of Presentation: 兵庫県立大学
  • Year and Date: 2011-09-17
• [Presentation] Structural study of the O2-tolerant [NiFe] hydrogenase (2011)
  • Author(s): Yasuhito Shomura, Yoshiki Higuchi
  • Organizer: 生物物理学会
  • Place of Presentation: 兵庫県立大学姫路書写キャンパス(兵庫県)
  • Year and Date: 2011-09-17
• [Presentation] Structural studies on dissimilatory sulfite reductase (2011)
  • Author(s): 庄村康人
  • Organizer: International symposium on chemistry of reductases IV
  • Place of Presentation: 名古屋大学
  • Year and Date: 2011-01-21
• [Presentation] Structural Basis for the Reaction Mechanism of Dissimilatory Sulfite Reductase学術創成シンポジウム (2011)
  • Author(s): Yasuhito Shomura and Yoshiki Higuchi
  • Organizer: International symposium on chemistry of reductases
  • Place of Presentation: 名古屋大学
  • Year and Date: 2011-01-20
• [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
  • Organizer: 日本結晶学会
  • Place of Presentation: 大阪大学
  • Year and Date: 2010-12-05