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Following Heme Oxygenase Reaction at Atomic Scale

Research Project

Project/Area Number 14380300
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Functional biochemistry
Research InstitutionTohoku University

Principal Investigator

SAITO Masao  Tohoku University, Institute of Multidisciplinary Research for Advanced Materials, Professor, 多元物質科学研究所, 教授 (70302239)

Co-Investigator(Kenkyū-buntansha) TOMITA Takeshi  Tohoku University, Institute of Multidisciplinary research for Advanced Materials, Research associate, 多元物質科学研究所, 助手 (20302242)
海野 昌喜  東北大学, 多元物質科学研究所, 助手 (10359549)
MATSUI Toshitaka  Tohoku University, Institute of Multidisciplinary Research for Advanced Materials, Research associate, 多元物質科学研究所, 助手 (90323120)
Project Period (FY) 2002 – 2003
Project Status Completed (Fiscal Year 2003)
Budget Amount *help
¥12,100,000 (Direct Cost: ¥12,100,000)
Fiscal Year 2003: ¥4,500,000 (Direct Cost: ¥4,500,000)
Fiscal Year 2002: ¥7,600,000 (Direct Cost: ¥7,600,000)
KeywordsHeme / heme oxygenase / X-ray crystallography / Reaction mechanism / oxygen activation
Research Abstract

Heme oxygenase (HO) oxidatively degrades heme to biliverdin. Specific aim of this research project is to delineate the molecular mechanism of the enzyme action through determination of the high resolution crystal structures of all the catalytically significant reaction intermediates. We have chosen HmuO, a heme oxygenase of Corynebacterium diphtheriae, the spectroscopic and enzymatic properties of which have been extensively studied by our research team.
In the first year, we determined the crystal structures of ferric and ferrous forms of the heme complex of HmuO, the initial and the second steps of the heme degradation at 1.4 and 1.5 Å resolution. We have found that protons required for HO catalysis is channeled from the solvent water to the oxygen activation site through different conduit between mammalian HO and HmuO despite the high similarity in the overall protein fold between these two HO proteins.
In the second year, we have successfully obtained the crystals of the catalytically critical oxy form and determined its structure at 1.85 A resolution. Due to low stability of the oxy form, previous crystallization attempts of oxy HO by other investigators had not been successful, and our publication is the first report of the structure of the catalytically significant oxy form. The structure has resolved long standing important questions on HO, including why oxygen affinity of heme oxygenase is very high, how heme oxygenase prevents product inhibition, and which parts of the active site are relevant to regio-selective hydroxylation of the heme group.
The crystal structures of the HmuO complexes with the final product (biliverdin) and its immediate precursor (iron biliverin) have also been solved. These structures provide clues to understand the mechanism of the substrate release from the HO protein, the rate limiting step of the HO catalysis.

Report

(3 results)
  • 2003 Annual Research Report   Final Research Report Summary
  • 2002 Annual Research Report
  • Research Products

    (37 results)

All Other

All Publications (37 results)

  • [Publications] Davydov et al.: "Catalytic mechanism of heme oxygenase through EPR and ENDOR of cryoreduced oxy-heme oxygenase and its Asp 140 mutants"J.Am.Chem.Soc.. 124(8). 1798-1808 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Denisov et al.: "Cryogenic absorption spectra of hydroperoxo-ferric heme oxygenase, the active intermediate of enzymatic heme oxygenation"FEBS Lett.. 532(1-2). 203-206 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Gonzalez et al.: "Nature of the displaceable heme-axial residue in the EcDos protein, a heme-based sensor from Escherichia coli"Biochemistry. 41(26). 8414-8421 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Tomita et al.: "A comparative resonance Raman analysis of heme-binding PAS domains : heme iron coordination structures of the BjFixL, AxPDEA1, EcDos, and MtDos proteins"Biochemistry. 41(15). 4819-4826 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Bulteau et al.: "Redox-dependent modulation of aconitase activity in intact mitochondria"Biochemistry. 42(50). 14846-14855 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Coyle et al.: "FeNO structure in distal pocket mutants of myoglobin based on resonance Raman spectroscopy"Biochemistry. 42(17). 4896-4903 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Davydov et al.: "Kinetic isotope effects on the rate-limiting step of heme oxygenase catalysis indicate concerted proton transfer/heme hydroxylation"J.Am.Chem.Soc.. 125(52). 16208-16209 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Li et al.: "Solution 1H NMR investigation of the active site molecular and electronic structures of substrate-bound, cyanide-inhibited HmuO, a bacterial heme oxygenase from Corynebacterium diphtheriae"J.Biol.Chem.. 278(9). 6651-6663 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] 富田毅ら: "最近のヘムタンパク質研究"生化学. 75(7). 577-587 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Zhang et al.: "Stereoselectivity of each of the three steps of the heme oxygenase reaction : hemin to meso-hydroxyhemin, meso-hydroxyhemin to verdoheme, and verdoheme to biliverdin"Biochemistry. 42(24). 7418-7426 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Hirotsu et al.: "The crystal structures of the ferric and ferrous forms of the heme complex of HmuO, a heme oxygenase of Corynebacterium diphtheriae"J.Biol.Chem.. 279(12). 11937-11947 (2004)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Unno et al.: "Crystal Structure of the Dioxygen-bound Heme Oxygenase from Corynebacterium diphtheriae : IMPLICATIONS FOR HEME OXYGENASE FUNCTION"J.Biol.Chem.. 279(20). 21055-21061 (2004)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Davydov, et al.: "Catalytic mechanism of heme oxygenase through ERP and ENDOR of cryoreduced oxy-heme oxygenase and its Asp 140 mutants"J.Am.Chem.Soc.. 124(8). 1798-1808 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Denisov, et al.: "Cryogenic absorption spectra of hydroperoxo-ferric heme oxygenase, the active intermediate of enzymatic heme oxygenation"FEBS Lett.. 532(1-2). 203-206 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Gonzalez, et al.: "Nature of the displaceable heme-axial residue in the EcDos protein, a heme-based sensor from Escherichia coli"Biochemistry. 41(26). 8414-8421 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Tomita, et al.: "A comparative resonance Raman analysis of heme-binding PAS domains : heme iron coordination structures of the BjFixL, AxPDEA1, EcDos, and MtDos proteins"Biochemistry. 41(15). 4819-4826 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Bulteau, et al.: "Redox-dependent modulation of aconitase activity in intact mitochondria"Biochemistry. 42(50). 14846-14855 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Coyle, et al.: "FeNO structure in distal pocket mutants of myoglobin from resonance Raman spectroscopy"Biochemistry. 42(17). 4896-4903 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Davydov, et al.: "Kinetic isotope effects on the rate-limiting step of heme oxygenase catalysis indicate concerted proton transfer/heme hydroxylation"J.Am.Chem.Soc.. 125(52). 16208-16209 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Li, et al.: "Solution 1H NMR Investigation of the Active Site Molecular and Electronic Structures of Substrate-bound, Cyanide-inhibited HmuO, a Bacterial Heme Oxygenase from Corynebacterium diphtheriae"J.Biol.chem.. 278(9). 6651-6663 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Tomita, et al.: "Recent progress in biochemical studies of hemoprotein"Seikagaku. 75(7). 577-587 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Zhang, et al.: "Stereoselectivity of each of the three steps of the heme oxygenase reaction : hemin to meso-hydroxyhemin, meso-hydroxyhemin to verdoheme, and verdoheme to biliverdin"Biochemistry. 42(24). 7418-7426 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Hirotsu, et al.: "The crystal structures of the ferric and ferrous forms of the heme complex of HmuO, a heme oxygenase of Corynebacterium diphtheriae"J.Biol.Chem.. 279(12). 11937-11947 (2004)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Unno, et al.: "Crystal structure of the dioxygen-bound heme oxygenase from Corynebacterium diphtheriae: implications for heme oxygenase function"J.Biol.chem.. 279(20). 21055-21061 (2004)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Davydov et al.: "Kinetic isotope effects on the rate-limiting step of heme oxygenase catalysis indicate concerted proton transfer/heme hydroxylation"J.Am.Chem.Soc.. 125(52). 16208-16209 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Unno et al.: "Crystal structure of the dioxygen-bound heme oxygenase from Corynebacterium diphtheriae : Implications for heme oxygenase function"J.Biol.Chem.. (In press). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Hirotsu et al.: "The crystal structures of the ferric and ferrous forms of the heme complex of Hmu O, a heme oxygenase of Corynebacterium diphtheriae"J.Biol.Chem.. 279(12). 11937-11947 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Voegtle et al.: "Spectroscopic characterization of five- and six-coordinate ferrous-NO heme complexes. Evidence for heme Fe-proximal cysteinate bond cleavage in the ferrous-No adducts of the Trp-409Tyr/Phe proximal"Biochemistry. 42(8). 2475-2484 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Li et al.: "Solution 1H NMR investigation of the active site molecular and electronic structures of substrate-bound, cyanide-inhibited HmuO, a bacterial heme oxygenase from Corynebacterium"J.Biol.Chem.. 278(9). 6651-6663 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Zhang et al.: "Stereoselectivity of each of the three steps of the heme oxygenase reaction : hemin to meso-hydroxyhemin, meso-hydroxyhemin to verdoheme, and verdoheme to biliverdin"Biochemistry. 42(24). 7418-7426 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Davydov, R., Ikeda-Saito, M., 他4名: "Catalytic mechanism of heme oxygenase through EPR and ENDOR of cryoreduced oxy-heme oxygenase and its Asp 140 mutants"J.Am.Chem.Soc.. 124. 1798-1808 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Li, Y., Ikeda-Saito, M., 他3名: "Cryogenic absorption spectra of hydroperoxo-ferric heme oxygenase, the active intermediate of enzymatic hemeoxygenation"J.Biol.Chem.. 532. 203-206 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Tomita, T., Ikeda-Saito, M., 他3名: "A comparative resonance Raman analysis of heme-binding PAS domains : heme iron coordination structures of the BjFixL, AxPDEA1, EcDos, and MtDos proteins"Biochemistry. 41. 4819-4826 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Gonzalez, G., Tomita, T., Ikeda-Saito, M., 他5名: "Nature of the displaceable heme-axial residue in the EcDos protein, a heme-based sensor from Escherichia coli"Biochemistry. 41. 8414-8421 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Watanabe, M., Matsui, T., 他3名: "Unusual cyanide bindings to a heme-regulated phosphodiesterase from Echerichia coli : effect of Met95 mutations"Biochem.Biophys.Res.Commun.. 299. 169-172 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Sasakura, Y., Matsui, T., 他7名: "Characterization of a direct oxygen sensor heme protein from Echerichia coli. Effects of the heme redox states and mutations at the heme-binding site on catalysis and structure"J.Biol.Chem.. 277. 23821-23827 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 海野昌喜, 月原富武: "細胞工学2002年9月号"秀潤社. 160 (2002)

    • Related Report
      2002 Annual Research Report

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Published: 2002-04-01   Modified: 2016-04-21  

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