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Relationship between structure, flexibility, and function of an enzyme protein ; a case study using isopropylmalate dehydrogenase

Research Project

Project/Area Number 10044095
Research Category

Grant-in-Aid for international Scientific Research

Allocation TypeSingle-year Grants
SectionJoint Research
Research Field Structural biochemistry
Research InstitutionTokyo University of Pharmacy & Life Science

Principal Investigator

OSHIMA Tairo  School of Life Science, Tokyo University of Pharmacy & Life Science Professor, 生命科学部, 教授 (60167301)

Co-Investigator(Kenkyū-buntansha) TANAKA Nobuo  Tokyo Institute of Technology, Faculty of Bioscience & Biotechnology Professor, 生命理工学部, 教授 (50032024)
YAMAGISHI Akihiko  School of Life Science Associate Professor, 生命科学科, 助教授 (50158086)
ZAVODOSZKY P  ハンガリー科学アカデミー, 酵素研, 教授
PETSKO Greg  ブランダイス大学, 生物化学科, 教授
Project Period (FY) 1998 – 1999
Project Status Completed (Fiscal Year 1999)
Budget Amount *help
¥3,000,000 (Direct Cost: ¥3,000,000)
Fiscal Year 1999: ¥1,500,000 (Direct Cost: ¥1,500,000)
Fiscal Year 1998: ¥1,500,000 (Direct Cost: ¥1,500,000)
Keywordsisopropylmalate dehydrogenase / reversible denaturation / free energy change / temperature jump / denaturation / Laue method / 高度好熱菌 / 進化分子工学 / 実験室内進化 / 熱安定酵素
Research Abstract

The present study has been done using isopropylmalate dehydrogenase as a model enzyme. A variety of mutant enzymes were constructed using the dehydrogenase from an extreme thermophile, Thermus thermophilus, and their structures, stability and flexibility, and catalytic activities were nalyzed. Especially thermodynamics of thermal denaturation reaction of these mutants and the wild type enzyme were investigated in 1999. To find out conditions under which the thermophile enzyme denatures reversibly, has been difficult, but we succeeded to overcome this problem ; we found that the enzyme denatures reversibly in the presence of guanidine chloride and some specific detergents. The enzyme denatures with an intermediate and the intermediate has no catalytic activity. We co-operated with Prof. Tanaka of Tokyo Institute of Technology, and deviced a new method for analyzing 3D structure of the intermediate using Laue method and temperature jump. By using this method, we condluded that the denaturation starts from two loop regions of the enzyme.

Report

(3 results)
  • 1999 Annual Research Report   Final Research Report Summary
  • 1998 Annual Research Report
  • Research Products

    (20 results)

All Other

All Publications (20 results)

  • [Publications] A CHIBA et al.: "Coenzyme Activity of NAD Analogs for 3-Isopropylmalate Dehydrogenase from Thermus thermophilus HB8."Biosci. Biotechnol. Biochem.. 63(9). 1647-1649 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] J.Nathaniel et al.: "of the Isolated Zinc Site in Archaeal Zinc-containing Ferredoxins as Revealed by X-ray Absorption Spectroscopic Analysis and Its Evolutionary Implications."J.Biol. Chem.. 274(33). 23160-23168 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] A.CHIBA et al.: "Synthetic and Mechanistic Studies of(2R,3S)-3-Vinylmalic Acid as a Mechanism-Based Inhibitor of 3-Isopropylmalate Dehydrogenase."J.Org. Chem.. 64(17). 6159-6165 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] S.Akanuma et al.: "Further Improvement of the Thermal Stability of a Partially Stabilized Bacillus subtilis 3-Isopropylmalate Dehydrogenase Variant by Random and Site-Directed Mutagenesis."

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] T.IWASAKI et al.: "Respiratory Complex II from the Thermophilic Archaeon, Sulfolobus sp.Strain 7 : Genes and Protein."in "Flavins and Flavoproteins 1999" (eds. by S.Ghisla et al.) Rudolf Weber, Berlin. 779-786

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] A.CHIBA et al.: "Coenzyme Activity of NAD Analogs for 3-Isopropylmalate Dehydrogenase from Thermus thermophilus HB8."Biosci.Biotechnol.Biochem.. 63(9). 1647-1649 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] J.Nathaniel et al.: "Structural Conservation of the Isolated Zinc Site in Archaeal Zinc-containing Ferredoxins as Revealed by X-ray Absorption Spectroscopic Analysis and Its Evolutionary Implications."J.Biol.Chem.. 274(33). 23160-23168 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] S.AKANUMA et al.: "Further Improvement of the Thermal Stability of a Partially Stabilized Bacillus subtilis 3-Isopropylmalate Dehydrogenase Variant by Random and Site-Directed Mutagenesis."Eur.J.Biochem.. 260. 499-504 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] C.MOTONO et al.: "Urea-Induced Unfolding and Conformational Stability of 3N-Isopropylmalate Dehydrogenase from the Thermophile Thermus thermophilus and Its Mesophilic counterpart from escherichia coli."Biochemistry. 38{4}. 1332-1337 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] M.NISHIHARA et al.: "sn-Glyceol-1-Phosphate-Forming Activities in Archaea : Separation of Archaeal Phospholipid Biosynthesis and Glycerol Catabolism by Glycerophosphate Enantiomers."J.Bacteriol.. 181[4]. 1330-1333 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] A.CHIBA et al.: "Synthetic and Mechanistic Studies of (2R, 3S)-3-Vinylmalic Acid as a Mechanism-Based Inhibitor of 3-Isopropylmalate Dehydrogenase."J.Org.Chem.. 64(17). 6159-6165 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] A.CHIBA et al.: "Coenzyme Activity of NAD Analogs for 3-Isopropylmalate Dehydrogenase from Thermus thermophilus HB8"Biosci.Biotechnol. Biochem.. 63(9). 1647-1649 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] J.Nathaniel et al.: "of the Isolated Zinc Site in Archaeal Zinc-containing Ferredoxins as Revealed by X-ray Absorption Spectroscopic Analysis and Its Evolutionary Im;lications"J.Biol.Chem. 274(33). 23160-23168 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] A.CHIBA et al.: "Synthetic and Mechanistic Studies of (2R,3S)-3-Vinylmalic Acid as a Mechanism-Based Inhibitor of 3-Isopropylmalate Dehydrogenase"J.Org.Chem. 64(17). 6159-6165 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] S.AKANUMA et al.: "Further Improvement of the Thermal Stability of a Partially Stabilized Bacillus subtilis 3-Isopropylmalate Dehydrogenase Variant by Random and Site-Directed Mutagenesis"

    • Related Report
      1999 Annual Research Report
  • [Publications] Fujii,T.: "The crystal structure of zinc-containing ferredoxin from the thermoacidophilic a rchaeon Sulfolobus sp.Strain 7." Biochemistry. 36. 1505-1513 (1997)

    • Related Report
      1998 Annual Research Report
  • [Publications] Qu,C.: "A mutation at the interface between domains causes rearrangement of domains in 3-isopropylmalate dehydrogenase." Protein Eng.10. 45-52 (1997)

    • Related Report
      1998 Annual Research Report
  • [Publications] Wallon,G.: "Crystal structure of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus." J.Mol.Biol.266. 1016-1031 (1997)

    • Related Report
      1998 Annual Research Report
  • [Publications] Wallon,G.: "Purification,catalytic properties and thermostability of 3-isopropylmalate dehydrogenase from Escherichia coli." Biochem.Biophys.Acta. 1337. 105-112 (1997)

    • Related Report
      1998 Annual Research Report
  • [Publications] Tamakoshi,M.: "The organization of the leuC,leuD and leuB genes of the extreme thermophile The rmus thermophilus." Gene. 222. 125-132 (1998)

    • Related Report
      1998 Annual Research Report

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Published: 1998-04-01   Modified: 2019-02-15  

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