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2001 Fiscal Year Final Research Report Summary

Structural study of [NiFe]hydrogenase

Research Project

Project/Area Number 12680654
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionKYOTO UNIVERSITY

Principal Investigator

HIGUCHI Yoshiki  Kyoto Univ., Graduate School of Sci., Assoc. Prof., 理学研究科, 助教授 (90183574)

Co-Investigator(Kenkyū-buntansha) HIROTA Shun  Nagoya Univ. Graduate School of Sci. Assistant Prof., 大学院・理学研究科, 助手 (90283457)
Project Period (FY) 2000 – 2001
Keywords[Ni-Fe]hydrogenase / CO-bound hydrogenase / Hydrogen metabolism / Cryogenic diffraction study / quasi-dynamic X-ray analysis / High resolution X-ray analysis
Research Abstract

Hydrogenases catalyze the reversible oxidation of molecular hydrogen and play a key role in hydrogen metabolism in various bacteria. Hydrogenases are classified into [non-metal], [Fe], [NiFe], and [NiFeSe] hydrogenases according to the metal composition of their active sites. The [NiFe]hydrogenase from D. vulgaris Miyazaki F is composed of a heterodimer with a total molecular mass of 91 kDa. The active site of the [NiFe] hydrogenases in the oxidized form is composed of Ni and Fe atoms with four cysteinyl sulfur and four non-protein ligands (S/O, CO, CN or SO). Carbon monoxide (CO) was known as a reversible inhibitor of hydrogenases. The carbon monoxide complex of [NiFe]hydrogenase from D. v. Miyazaki has been prepared and characterized by X-ray crystallography, and absorption and Raman spectroscopy. The exogenously added CO was found to be bound to the Ni atom at the Ni-Fe active site. Distinct changes were observed in the electron density distribution of the Ni and sγ(Cys546) atoms between the CO-bound and CO-liberated structures for all the crystals tested. One of the CO-bound structures showed an additional electron density peak between the CO and Sγ(Cys546), suggesting that an intermediate of the catalytic reaction was trapped at the active site. The novel structural features found near the Ni and Sγ(Cys546) atoms suggest that these two atoms at the Ni-Fe active site play a key role during the initial process to bind H_2.

  • Research Products

    (13 results)

All Other

All Publications (13 results)

  • [Publications] K.Suto: "How do the X-ray Structure and the NMR Structure of FMN-binding Protein Differ?"Acta Crystallogr.. D56. 368-371 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Y.Higuchi: "The Presence of SO Molecule in [NiFe] Hydrogenase from Desulfovibrio vulgaris Miyazaki, as Detected by Mass Spectrometry"J. Inorg. Biochem. 80. 205-211 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] N.Mizuno: "Preliminary X-ray Crystallographic Study of DsrD Protein from the Sulfate-reducing Bacterium Desulfovibrio vulgaris"Acta Crystallogr.. D56. 745-755 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] O.Trofanchuk: "Single Crystal EPR Studies of the Oxidized Active Site of [NiFe] Hydrogenase from Desulfovibrio vulgaris Miyazaki F"J. Bio. Inorg. Chem.. 5. 36-44 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] M.Fujihashi: "Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase"Pro. Natl. Acad. Sci.. vol.98. 4337-4342 (2001)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 樋口芳樹: "生体反応・ヒドロゲナーゼ"日本生物物理学会誌. 40(4). 154-182 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 樋口芳樹: "水素の物性・反応の機能性化と応用"生体反応・ヒドロゲナーゼ. 249-253 (2001)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] K. Suto, K. Kawagoe, N. Shibata, Y. Morimoto, Y. Higuchi, M. Kitamura and N. Yasuoka: "HOW do the X-ray Structure and the NMR Structure of FMN-binding Protein Differ?"Acta Crystallogr.. D56. 368-371 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Y. Higuchi, F. Toujou, K. Tsukamoto and T. Yagi: "The Presence of SO Molecule in [NiFe] Hydrogenase from Desulfovibrio vulgaris Miyazaki, as Detected by Mass Spectrometry"J. Inorg. Biochem. 80. 205-211 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] N. Mizuno, D. S. Hittel, K. Miki, G. Voordouw, Y. Higuchi: "Preliminary X-ray Crystallographic Study of DsrD Protein from the Sulfate-reducing Bacterium Desulfovibrio vulgaris"Acta Crystallogr. D56. 754-755 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] O. Trofanchuk, M. Stein, Ch. Gesner, F. Lendzian, Y. Higuchi: "Single Crystal EPR Studies of the Oxidized Active Site of [NiFe] Hydrogenase from Desulfovibrio vulgaris Miyazaki F"J. Bio. Inorg. Chem.. 5. 36-44 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] M. Fujihashi, Y.-W. Zhang, Y. Higuchi, X-Y. Li, T. Koyama and K. Miki: "Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase"Pro. Natl. Acad. Sci.. 98. 4337-4342 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Yoshiki Higuchi: ""[NiFe]hydrogenase" In Hydrogen as a fuel : Learning from Nature"Taylor and Franc publishers (in press). (2002)

    • Description
      「研究成果報告書概要(欧文)」より

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Published: 2003-09-17  

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