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Four-dimensional structure analysis of Ndx family enzyme utilizing a new pH-temperature jump trigger

Research Project

Project/Area Number 18370047
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Structural biochemistry
Research InstitutionOsaka City University

Principal Investigator

KAMIYA Nobuo  Osaka City University, Faculty of Science, Professor (60152865)

Co-Investigator(Kenkyū-buntansha) MIYAHARA Ikuko  Osaka City Univ., Faculty of Science, Associate Professor (40271176)
NAKAGAWA Noriko  Osaka University, Faculty of Science, Assistant Professor (50379278)
KURAMITSU Seiki  Osaka University, Faculty of Science, Professor (60153368)
Project Period (FY) 2006 – 2007
Project Status Completed (Fiscal Year 2007)
Budget Amount *help
¥15,790,000 (Direct Cost: ¥14,800,000、Indirect Cost: ¥990,000)
Fiscal Year 2007: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2006: ¥11,500,000 (Direct Cost: ¥11,500,000)
Keywords4-D structure analysis / pH jump / temperature jump / Ndx family / functional genomics
Research Abstract

Before starting our research, we tried to improve crystal quality of ADP-ribose pyro-phosphatase (ADPRase) involved in Ndx family, because we needed high resolution analysis to resolve substrates and products which would co-exist in the reaction cavity of ADPRase in time course of enzyme reaction. Many crystallization conditions were tested, and the observable diffraction limit was expanded to 1.1A resolution from 1.7A, previously reported. In order to start the crystalline state reaction of ADPRase, Zn(II) ions were soaked into the crystals, in which the substrate ADPR was introduced in advance. The reaction was stopped by a temperature jump from 295K to 90K. Crystal structures were determined at 9 points of reaction time, 0, 3, 6, 10, 15, 20, 30, 40, 60min, and the in situ observation of ADPRase reaction was succeeded. Our results showed that the enzyme reaction progressed in crystal after the Zn(II) ion soaking as following. (1) The first Zn(II) ion introduced into reaction cavity changed ADPR conformation to an intermediate state, designated as ADPR^*.
(2) The second Zn(II) ion ligated ADPR^*, gultamate side chain of E82 and E86, and two water molecules making a five-ligands coordination structure. (3) One of two water molecules was activated by the second Zn(II) ion and E82 to hydroxide anion, and (4) the anion attacked nucleophilically the alpha phosphate of ADPR to brake the pyrophosphate bond to produce two products, AMP and ribose-5'-phosphate. The biochemical insight into the in situ observation of ADPRase was discussed.

Report

(3 results)
  • 2007 Annual Research Report   Final Research Report Summary
  • 2006 Annual Research Report
  • Research Products

    (15 results)

All 2009 2008 2007 2006

All Journal Article (12 results) (of which Peer Reviewed: 6 results) Presentation (2 results) Book (1 results)

  • [Journal Article] Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe2009

    • Author(s)
      Goto,M., Yamauchi,T., Miyahara,I., Kamiya,N., Yoshimura,T., Hihara,H., Kurihara,T., Hirotsu,K., Esaki,N.
    • Journal Title

      J.Biol. Chem. 284

      Pages: 25944-25952

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe2009

    • Author(s)
      Goto, M., Yamauchi, T., Miyahara, I., Kamiya, N., Yoshimura, T., Hihara, H., Kurihara, T., Hirotsu, K., Esaki, N.
    • Journal Title

      J.Biol.Chem. 284

      Pages: 25944-25952

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Structural Basis for Different Substrate Specificities of Two A DP-Ribose Pyrophosphatases from Thermus thermophilus HB82008

    • Author(s)
      Wakamatsu,T., Nakagawa,N., Kuramitsu,S., Masui,R.
    • Journal Title

      J.Bacteriol. 190

      Pages: 1108-1117

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Structural Basis for Different Substrate Specificities of Two ADP-Ribose Pyrophosphatases from Thermus thermophilus HB82008

    • Author(s)
      Wakamatsu, T., Nakagawa, N., Kuramitsu, S., Masui, R.
    • Journal Title

      J.Bacteriol. 190

      Pages: 1108-1117

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Structure of Thiocyanate Hydrolasa:A New Nitrile Hydratase Family Protein with a Novel Five-Coordinate Cobalt(III) Center2007

    • Author(s)
      Takatoshi Arakawa, Yoshiaki Kawano, Shingo Kataoka, Yoko Katayama, Nobuo Kamiya, Masafumi Yohda, and Masafumi Odaka.
    • Journal Title

      J.Mol.Biol. 336

      Pages: 1497-1509

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Expression,purification and preliminary X-ray characterization of DL-2-haloacid dehalogenase from Methylobacterium sp.CPA12007

    • Author(s)
      Rie Omi, Keiji Jitsumori, Takahiro Yamauchi, Susumu Ichiyama, Tatsuo Kurihara, Nobuyoshi Esaki, Nobuo Kamiya, Ken Hirotsu and Ikuko Miyahara
    • Journal Title

      Acta Crystallogr. F63

      Pages: 586-589

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Location of PsbY in oxygen-evolving photosystem II revealed by mutagenesis and X-ray crystallography2007

    • Author(s)
      Keisuke Kawakami, Masako Iwai, Masahiko Ikeuchi, Nobuo Kamiya, Jian-Ran Shen.
    • Journal Title

      FEBS Lett. 581

      Pages: 4983-4987

    • NAID

      130006994394

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mutational study on aGln90 of Fe-type nitrile hydratase from Rgidiciccys sp. N7712006

    • Author(s)
      Takarada,H., Kawano,Y., Hashimoto,K., Nakayama,H., Ueda,S., Yohda,M., Kamiya,N., Dohnae,N., Maeda,M., Odaka,M.
    • Journal Title

      Biosci. Biotech. and Biochem. 70

      Pages: 881-889

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Mutational study on aGln90 of Fe-type nitrile hydratase from Rgidiciccys sp.N7712006

    • Author(s)
      Takarada, H., Kawano, Y., Hashimoto, K., Nakayama, H., Ueda, S., Yohda, M., Kamiya, N., Dohnae, N., Maeda, M., Odaka, M.
    • Journal Title

      Biosci.Biotech.and Biochem. 70

      Pages: 881-889

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Mutational study on aGln90 of Fe-type nitrile hydratase from Rgidiciccys so. N7712006

    • Author(s)
      Takarada, H., Kawano, Y., Hashimoto, K., Nakayama, H., Ueda, S., Yohda, M., Kamiya, N., Dohnae, N., Maeda, M., Odaka, M.
    • Journal Title

      Biosci. Biotech. & Biochem. 70

      Pages: 881-889

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Kinetic and Structural Studies on the Catalytic Role of the Aspartic Acid Residue Conserved in Copper Amine Oxidase2006

    • Author(s)
      Chiu, Y-C., Okajima, T., Murakawa, T., Kamiya, N., Kuroda, S., Hayashi, H., Yamamoto, Y., Tanizawa, K.
    • Journal Title

      Biochemistry 45

      Pages: 4105-4120

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Mutational Designing of the Active-Site Architecture of Porcine Kidney D-Amino Acid Oxidase toward Novel Function : Directed Evolution of the "Active-Site Lid" for Substrate Specificity2006

    • Author(s)
      Setoyama, S., Nishina, Y., Mizutani, H., Miyahara, I., Hirotsu, K., Kamiya, N., Shiga, K., Miura, R.
    • Journal Title

      J. Biochem. 139

      Pages: 873-879

    • Related Report
      2006 Annual Research Report
  • [Presentation] Reaction pathway of ADP-ribose pyrophosphatase, revealed by time-resolved X-ray crystallography2008

    • Author(s)
      Kamiya,N., Kai,K., Nakagawa,N., Kuramitsu,S., Miyahara,I
    • Organizer
      XXI Congress of the International Union of Crystallography
    • Place of Presentation
      Osaka, Japan
    • Year and Date
      2008-08-28
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] クライオトラップ法により追跡したMPリボースピロリン酸分解酵素の結晶相反応経路2007

    • Author(s)
      神谷 信夫
    • Organizer
      日本結晶学会
    • Place of Presentation
      東京工業大学
    • Year and Date
      2007-12-01
    • Related Report
      2007 Annual Research Report
  • [Book] 「分子認識と超分子」(早下隆士,築部弘 編著)に「時間分割X線解析」のタイトルで執筆(9ページ)2007

    • Author(s)
      神谷信夫
    • Total Pages
      237
    • Publisher
      三共出版
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary

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Published: 2006-04-01   Modified: 2016-04-21  

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