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Investigation of the structural change of orotidine 5'-monophosphate decarboxylase during the reaction and its catalytic mechanism

Research Project

Project/Area Number 20770081
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Structural biochemistry
Research InstitutionKyoto University

Principal Investigator

FUJIHASHI Masahiro  Kyoto University, 理学研究科, 助教 (10397581)

Project Period (FY) 2008 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2009: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2008: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Keywords酵素 / 触媒反応機構 / X線結晶構造解析 / 基質構造の歪み / ODCase / OMPDC / OMPDCase / 反応中間体構造 / 反応機構 / 酵素基質複合体 / ピリミジン新規合成
Research Abstract

Crystal structures of substrate-product complexes of orotidine 5'-monophosphate decarboxylase (ODCase), obtained at various steps in its catalysis of the unusual transformation of 6-cyano-uridine 5'-monophosphate into barbituric acid ribosyl monophosphate, show that the cyano substituent of the substrate, when bound to the active site, is first bent significantly from the plane of the pyrimidine ring and then replaced by an oxygen atom. The structure together with other observation showed that ODCase distorts the C6 substituent on its substrate during the reaction.

Report

(3 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • Research Products

    (13 results)

All 2009 2008

All Journal Article (2 results) (of which Peer Reviewed: 2 results) Presentation (11 results)

  • [Journal Article] Structural Characterization of the Molecular Events during a Slow Substrate-Product Transition in Orotidine 5'-Monophosphate Decarboxylase2009

    • Author(s)
      Masahiro Fujihashi, Lianhu Wei, Lakshmi P. Kotra, Emil F. Pai
    • Journal Title

      J. Mol. Biol 387

      Pages: 1199-1210

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural Characterization of the Molecular Events during a Slow Substrate-Product Transition in Orotidine2009

    • Author(s)
      Masahiro Fujihashi, Lianhu Lakshmi P. Kotra. Emil F. Pai
    • Journal Title

      J. Mol. Biol 387

      Pages: 1199-1210

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] Distortion in Substrate-Product Transition in Orotidine 5'-Monophosphate Decarboxylase.2009

    • Author(s)
      Masahiro Fujihashi, Lianhu Wei, Lakshmi P. Kotra, Emil F. Pai
    • Organizer
      2009 American Crystallographic Assosiation Meeting
    • Place of Presentation
      Sheraton City Centre Hotel, Toronto
    • Year and Date
      2009-07-30
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] 触媒反応進行中のオロチジン一リン酸脱炭酸酵素の構造2009

    • Author(s)
      藤橋雅宏, Angelica M. Bello, Lakshmi P. Kotra, Emil F. Pai
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ
    • Year and Date
      2009-05-22
    • Related Report
      2009 Final Research Report
  • [Presentation] 触媒反応進行中のオロチジンーリン酸脱炭酸酵素の構造2009

    • Author(s)
      藤橋雅宏, Angelica M.Bello, Lakshmi P.Kotra, Emil F.Pai
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ
    • Year and Date
      2009-05-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] Molecular events of a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase2009

    • Author(s)
      Masahiro Fujihashi, Angelica M. Bello, Lakshmi P. Kotra, Emil F. Pai
    • Organizer
      237th American Chemical Society National Meeting & Exposition
    • Place of Presentation
      Salt Lake City, UT, USA
    • Year and Date
      2009-03-23
    • Related Report
      2009 Final Research Report
  • [Presentation] Molecular events of a slow substrate-product transition in ototidine 5'-mononhosnhate decarboxylase2009

    • Author(s)
      Masahiro Fujihashi, Angelica M. Bello, Lakshmi P. Kotra. Emil F
    • Organizer
      237th American Chemical Society National Meeting & Exposition
    • Place of Presentation
      Salt Lake City, UT, USA
    • Year and Date
      2009-03-23
    • Related Report
      2008 Annual Research Report
  • [Presentation] Structural investigation of orotidine monophosphate decarboxylase: the role of the catalytic lysine2008

    • Author(s)
      Shingo Kuroda, Masahiro Fujihashi, Lakshmi, P. Kotra, Emil F. Pai, Kunio Miki
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡国際会議場・福岡
    • Year and Date
      2008-12-03
    • Related Report
      2009 Final Research Report
  • [Presentation] Structural investigation of orotidine monophosphate decarboxylase : the role of the catalytic lysine2008

    • Author(s)
      Shingo Kuroda, Masahiro Fujihashi, Lakshmi, P. Kotra
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡国際会議場, 福岡
    • Year and Date
      2008-12-03
    • Related Report
      2008 Annual Research Report
  • [Presentation] Catalytic promiscuity and mechanistic determinants of ODCase - a high-resolution investigation -2008

    • Author(s)
      Masahiro Fujihashi, Shingo Kuroda, Lakshmi P. Kotra, Kunio Miki
    • Organizer
      XXI Congress and General Assembly of the Interational Union of Crystallography
    • Place of Presentation
      Osaka, Japan
    • Year and Date
      2008-08-29
    • Related Report
      2009 Final Research Report
  • [Presentation] Catalytic promiscuity and mechanistic determinants of ODCase-a high-resolution investigation-2008

    • Author(s)
      Masahiro Fujihashi, Shingo Kuroda, Lakshmi P. Kotra, Kunio
    • Organizer
      XXI Congress and General Assembly of the Interational : Union of Crystallography
    • Place of Presentation
      Osaka, Japan
    • Year and Date
      2008-08-29
    • Related Report
      2008 Annual Research Report
  • [Presentation] 求電子反応・求核反応をともに触媒する、オロチジン一リン酸脱炭酸酵素の反応機構の研究2008

    • Author(s)
      藤橋雅宏, 黒田新悟, Angelica M. Bello, Ewa Poduch, Wanda Gillon, Lakshmi P. Kotra, Emil F. Pai, 三木邦夫
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      タワーホール船堀・東京
    • Year and Date
      2008-06-10
    • Related Report
      2009 Final Research Report
  • [Presentation] 求電子反応・求核反応をともに触媒する、オロチジンーリン酸脱炭酸酵素の反応機構の研究2008

    • Author(s)
      藤橋雅宏, 黒田新悟, Angelica M. Bello, Ewa Poduch, Wanda Gillon, Lakshmi P. Kotra, Emil F. Pai 三木邦夫
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      タワーホール船堀・東京
    • Year and Date
      2008-06-10
    • Related Report
      2008 Annual Research Report

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Published: 2008-04-01   Modified: 2016-04-21  

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