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Studies on the reaction mechanism of peroxidase based on its tertiary structure

Research Project

Project/Area Number 04680055
Research Category

Grant-in-Aid for General Scientific Research (C)

Allocation TypeSingle-year Grants
Research Field 結晶学
Research InstitutionOsaka University

Principal Investigator

FUKUYAMA Keiichi  Osaka University, Department of Biology, Associate Professor, 理学部, 助教授 (80032283)

Project Period (FY) 1992 – 1993
Project Status Completed (Fiscal Year 1993)
Budget Amount *help
¥1,700,000 (Direct Cost: ¥1,700,000)
Fiscal Year 1993: ¥500,000 (Direct Cost: ¥500,000)
Fiscal Year 1992: ¥1,200,000 (Direct Cost: ¥1,200,000)
Keywordsperoxidase / X-ray crystallography / three-dimensional structure
Research Abstract

The reaction mechanism of peroxidase from a fungus Arthromyces ramosus (ARP) has been discussed on the basis of its three-dimensional structure determined by X-ray crystallography.
1. The crystal structure of ARP has been determined by the multiple isomorphous replacement method and refined to R=17.4 % for the 19,191 reflections between 7.0 and 1.9 A resolution. The model includes residues 9 to 344, the heme group, two N-acetylglucosamine residues, two calcium ions and 246 water molecules.
2. The overall tertiary structure of ARP is similar to that of yeast cytochrome c peroxidase (CCP) and that of the lignin peroxidase from Phanerochaete chrysosporium. Although the histidine and arginine residues (His56 and Arg52) at the distal side of the heme are conserved in the amino acid sequences of various heme peroxidases, the orientations of the side chains of these residues relative to the heme in ARP differ significantly from those in CCP and Lip.
In order to explore the role of Arg52 and His56 during the compound I formation, the crystal structure of ARP complexed with a substrate analogue I_3 - has been determined at 2.2 A resolution. Upon I_3" binding the side chain of Arg52 moved little, while that of His56 moved significantly. On the basis of these results the mode of binding of peroxide to the heme has been similated with computer graphics, and the process of the enzyme reaction as well as the role of these residues has been discussed.

Report

(3 results)
  • 1993 Annual Research Report   Final Research Report Summary
  • 1992 Annual Research Report
  • Research Products

    (8 results)

All Other

All Publications (8 results)

  • [Publications] N.Kunishima et al.: "Crystallization and Preliminary X-Ray Diffraction Studies of Peroxidase From a Fungus Arthromyces ramosus" PROTEINS:Structure,Function,and Genetics. 15. 216-220 (1993)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] N.Kunishima et al.: "Crystal Structure of the Fungal Peroxidase from Arthromyces ramosus at 1.9 A Resolution" Journal of Molecular Biology. 235. 331-344 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] N.Kunishima et al.: "Crystal Structure of Arthromyces ramosus Peroxidase Complexed with Triiodide" (発表予定).

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] N.Kunishima, K.Fukuyama, S.Wakabayashi, M.Sumida, M.Takaya, Y.Shibano, T.Amachi, and H.Matsubara: "Crystallization and Preliminary X-Ray Differation Studies of Peroxidase From a Fungus Arthromyces ramosus" PROTEINS : Struct. Func. Genet.15. 216-220 (1993)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] N.Kunishima, K.Fukuyama, H.Matsubara, H.Hatanaka, Y.Shibano, and T.Amachi: "Crystal structure of the Fungal peroxidase from Arthromyces ramosus at 1.9 A Resolution : Structural Comparisons with the Lignin and Cytochrome c Peroxidases" J.Mol. Biol.235. 331-344 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] N.Kunishima, K.Fukuyama, T.Kubota, H.Matsubara, and I.Morishima: "Crystal Structure of Arthromyces ramosus Peroxidase Complexed with Triiodide : Behavior of Arg52 and His56 During the Compound I Formation" (in preparation).

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] Naoki Kunishima: "Crystal Structure of the Fungal Peroxidase from Arthromyces ramosus at 1.9 〓 Resolution" Journal of Molecular Biology. 235. 331-344 (1994)

    • Related Report
      1993 Annual Research Report
  • [Publications] Naoki Kunishima: "Crystallization and Preliminary X-Ray Diffraction Studies of Peroxidase From a Fungus Arthromyces ramosus" PROTEINS:Structure,Function,and Genetics. 15. 216-220 (1993)

    • Related Report
      1992 Annual Research Report

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Published: 1992-04-01   Modified: 2016-04-21  

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