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Studies on archaeal antioxidation system involving thioredoxin proteins

Research Project

Project/Area Number 21510237
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Living organism molecular science
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

NAKAMURA Tsutomu  独立行政法人産業技術総合研究所, 健康工学研究部門, 主任研究員 (10357668)

Co-Investigator(Renkei-kenkyūsha) INOUE Tsuyoshi  大阪大学, 大学院・工学研究科, 教授 (20263204)
MATSUMURA Hiroyoshi  大阪大学, 大学院・工学研究科, 准教授 (30324809)
TAMADA Taro  日本原子力研究開発機構, 量子ビーム応用研究部門, 研究主幹 (50391248)
Project Period (FY) 2009 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2011: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2010: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2009: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords活性発現の分子機構 / 活性酸素 / 抗酸化システム / 反応中間体 / ペルオキシレドキシン / スーパーオキシドディスムターゼ / 反応機構 / 大型結晶 / 過酸化水素 / 基質結合 / X線結晶構造解析
Research Abstract

In order to elucidate the evolution process of antioxidation system in life from the viewpoint of protein science, we structurally characterized archaeal peroxiredoxin(Prx) and related antioxidant proteins. Especially, structure determination of the complex of Prx and its substrate, hydrogen peroxide, enabled discussion on the very early stage and the transition state of the Prx reaction. Furthermore, we determined the 3D structure of an archaeal cambialistic superoxide dismutase, which revealed the relationship between metal selectivity and the local 3D structure of the enzyme. Elucidation of protein reaction mechanism involving hydrogen atoms needs collection of neutron diffraction data of the protein. We developed methods for obtaining large protein crystals for the purpose of the neutron diffraction study.

Report

(4 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (26 results)

All 2012 2011 2010 2009 Other

All Journal Article (12 results) (of which Peer Reviewed: 8 results) Presentation (14 results)

  • [Journal Article] Characterization and Crystal Structure of the Thermophilic ROK Hexokinase from Thermus thermophilus2012

    • Author(s)
      Tsutomu Nakamura, Yasuhiro Kashima, Shouhei Mine, Takashi
    • Journal Title

      J.Biosci.Bioeng.

      Volume: (印刷中) Issue: 2 Pages: 150-154

    • DOI

      10.1016/j.jbiosc.2012.03.018

    • NAID

      110009495420

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Growth of protein crystals by syringe-type top-seeded solution growth2011

    • Author(s)
      Hiroyoshi Matsumura, Keisuke Kakiniuchi, Tsutomu Nakamura, Shigeru Sugiyama, Mihoko Maruyama, Hiroaki Adachi, Kazufumi Takano, Satoshi Murakami, Tsuyoshi Inoue, and Yusuke Mori
    • Journal Title

      Cryst. Growth Des

      Volume: 11 Issue: 5 Pages: 1486-1492

    • DOI

      10.1021/cg101361n

    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Journal Article] Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1 : insights into enzyme mechanism and stability2011

    • Author(s)
      Tsutomu Nakamura, Kasumi Torikai, Koichi Uegaki, Junji Morita, Kodai Machida, Atsushi Suzuki, Yasushi Kawata
    • Journal Title

      FEBS J

      Volume: 278 Issue: 4 Pages: 598-609

    • DOI

      10.1111/j.1742-4658.2010.07977.x

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization and preliminary crystallographic analysis of a putative glucokinase/hexokinase from Thermus thermophilus2011

    • Author(s)
      Tsutomu Nakamura, Yasuhiro Kashima, Shouhei Mine, Takashi
    • Journal Title

      Acta Crystallogr.Sect.F

      Volume: 67 Issue: 12 Pages: 1559-1562

    • DOI

      10.1107/s1744309111041145

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1-insights into the enzyme mechanism and stability2011

    • Author(s)
      T.Nakamura, K.Torikai, K.Uegaki, J.Morita, K.Machida, A.Suzuki, Y.Kawata
    • Journal Title

      The FEBS Journal

      Volume: 278 Pages: 598-609

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Growth of large protein crystals by a large-scale hanging-drop method2010

    • Author(s)
      Keisuke Kakinouchi, Tsutomu Nakamura, Taro Tamada, Hiroaki Adachi, Shigeru Sugiyama, Mihoko Maruyama, Yoshinori Takahashi, KazufumiTakano, Satoshi Murakami, Tsuyoshi Inoue, Ryota Kuroki, Yusuke Mori and Hiroyoshi Matsumura
    • Journal Title

      J. Appl. Cryst

      Volume: 43 Issue: 4 Pages: 937-939

    • DOI

      10.1107/s0021889810015967

    • Related Report
      2011 Final Research Report
  • [Journal Article] Crystal structure of peroxiredoxin from Aeropyrum pernix K1 complexed with its substrate, hydrogen peroxide2010

    • Author(s)
      Tsutomu Nakamura, Yuji Kado, Takafumi Yamaguchi, Hiroyoshi Matsumura, Kazuhiko Ishikawa and Tsuyoshi Inoue
    • Journal Title

      J. Biochem

      Volume: 147 Issue: 1 Pages: 109-115

    • DOI

      10.1093/jb/mvp154

    • NAID

      10027873408

    • Related Report
      2011 Final Research Report
  • [Journal Article] Growth of large protein crystals by a large-scale hanging drop method2010

    • Author(s)
      K.Kakinouchi, T.Nakamura, T.Tamada, H.Adachi, S.Sugiyama, M.Maruyama, Y.Takahashi, K.Takano, S.Murakami, T.Inoue, R.Kuroki, Y.Mori, H.Matsumura
    • Journal Title

      Journal of Applied Crystallography

      Volume: 43 Pages: 937-939

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Kinetic and crystallographic analyses of the catalytic domain of chitinase from Pyrococcus furiosus-the role of conserved residues in the active site2010

    • Author(s)
      H.Tsuji, S.Nishimura, T.Inui, Y.Kado, K.Ishikawa, T.Nakamura, K.Uegaki
    • Journal Title

      The FEBS Journal

      Volume: 277 Pages: 2683-2695

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of peroxiredoxin from Aeropyrum pernix K1 complexed with its substrate, hydrogen peroxide2010

    • Author(s)
      中村努、門祐示、山口隆文、松村浩由、石川一彦、井上豪
    • Journal Title

      Journal of Biochemistry Vol147

      Pages: 109-115

    • NAID

      10027873408

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Hypervalent intermediate in the oxidation of archaeal peroxiredoxin2009

    • Author(s)
      中村努
    • Journal Title

      SPring-8 Research Frontiers 2008

      Pages: 26-27

    • Related Report
      2009 Annual Research Report
  • [Journal Article] Growth of protein crystals by syringe-type top-seeded solution growth

    • Author(s)
      H.Matsumura, K.Kakinouchi, T.Nakamura, S.Sugiyama, M.Maruyama, H.Adachi, K.Takano, S.Murakami, T.Inoue, Y.Mori
    • Journal Title

      Crystal Growth & Design

      Volume: (掲載確定)

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] Crystal Structure of Archaeal Cambialistic Superoxide Dismutase2011

    • Author(s)
      Tsutomu Nakamura, Kasumi Torikai, Junji Morita, Yasushi Kawata, and Koichi Uegaki
    • Organizer
      XXII Congress and General Assembly of the International Union of Crystallography
    • Place of Presentation
      Madrid
    • Year and Date
      2011-08-27
    • Related Report
      2011 Final Research Report
  • [Presentation] Crystal Structure of Archaeal Cambialistic Superoxide Dismutase2011

    • Author(s)
      Tsutomu Nakamura, Kasumi Torikai, Junji Morita, Yasushi
    • Organizer
      XXII Congress and General Assembly of the International Union of Crystallograph
    • Place of Presentation
      Palacio Municipal de Congresos, Madrid, Spain
    • Year and Date
      2011-08-27
    • Related Report
      2011 Annual Research Report
  • [Presentation] 不溶性セルロース分解を目指した耐熱性人工セルラーゼ創製に関する研究2011

    • Author(s)
      上垣浩一、中村努、峯昇平、佐藤孝
    • Organizer
      第11回日本蛋白質科学会年会
    • Place of Presentation
      大阪府、ホテル阪急エキスポ
    • Year and Date
      2011-06-07
    • Related Report
      2011 Annual Research Report
  • [Presentation] 耐熱性cambialistic SODの立体構造と金属イオン選択性2011

    • Author(s)
      中村努、鳥養香澄、上垣浩一、森田潤司
    • Organizer
      LS-BT合同研究発表会
    • Place of Presentation
      産総研つくばセンター
    • Year and Date
      2011-02-01
    • Related Report
      2010 Annual Research Report
  • [Presentation] Aeropyrum pernix K1由来SODの金属イオン配位構造2010

    • Author(s)
      中村努、鳥養香澄、上垣浩一、森田潤司
    • Organizer
      日本結晶学会2010年度年会
    • Place of Presentation
      大阪大学コンベンションセンター
    • Year and Date
      2010-12-05
    • Related Report
      2010 Annual Research Report
  • [Presentation] 中性子線構造解析に向けたタンパク質大型結晶の高効率育成新技術の開発2010

    • Author(s)
      垣之内啓介、杉山成、丸山美帆子、村井良多、中村努、安達基泰、玉田太郎、黒木良太、安達宏昭、高野和文、村上聡、井上豪、森勇介、松村浩由
    • Organizer
      日本結晶学会2010年度年会
    • Place of Presentation
      大阪大学コンベンションセンター
    • Year and Date
      2010-12-03
    • Related Report
      2010 Annual Research Report
  • [Presentation] Aeropyrum pernix K1由来cambialistic SODの立体構造と金属選択性2010

    • Author(s)
      中村努、鳥養香澄、上垣浩一、森田潤司
    • Organizer
      第5回産業用酵素シンポジウム
    • Place of Presentation
      長浜バイオ大学
    • Year and Date
      2010-11-06
    • Related Report
      2010 Annual Research Report
  • [Presentation] 超好熱菌Pyrococcus furiosus由来キチナーゼが有するキチン結合ドメインChBD1の構造解析2010

    • Author(s)
      峯昇平、中村努、石川一彦、池上貴久、上垣浩一
    • Organizer
      第5回産業用酵素シンポジウム
    • Place of Presentation
      長浜バイオ大学
    • Year and Date
      2010-11-06
    • Related Report
      2010 Annual Research Report
  • [Presentation] 耐熱性アーケア(Pyrococcus furiosus)由来のキチン分解酵素の構造機能とその利用2010

    • Author(s)
      上垣浩一、中村努、峯昇平、石川一彦、川崎一則、林田稔、池上貴久、辻裕明、西村重徳、乾隆
    • Organizer
      食品酵素化学研究会第10回学術講演会
    • Place of Presentation
      大阪府立大学
    • Year and Date
      2010-09-04
    • Related Report
      2010 Annual Research Report
  • [Presentation] Aeropyrum pernix K1由来スーパーオキシドディスムターゼの立体構造解析2010

    • Author(s)
      中村努、鳥養香澄、上垣浩一、森田潤司
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌
    • Year and Date
      2010-06-17
    • Related Report
      2011 Final Research Report
  • [Presentation] Aeropyrum pernix K1由来スーパーオキシドディスムターゼの立体構造解析2010

    • Author(s)
      中村努、鳥養香澄、上垣浩一、森田潤司
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションホール
    • Year and Date
      2010-06-17
    • Related Report
      2010 Annual Research Report
  • [Presentation] 古細菌ペルオキシレドキシンと過酸化水素の結合2010

    • Author(s)
      中村努、門祐示、石川一彦、松村浩由、井上豪
    • Organizer
      平成21年度 産総研・産技連LS-BT合同研究発表会
    • Place of Presentation
      つくば
    • Year and Date
      2010-02-04
    • Related Report
      2009 Annual Research Report
  • [Presentation] ペルオキシレドキシンの酸化反応における超原子価中間体の結晶解析2010

    • Author(s)
      中村努
    • Organizer
      生命物質構造解析研究会
    • Place of Presentation
      東京
    • Year and Date
      2010-01-15
    • Related Report
      2009 Annual Research Report
  • [Presentation] 古細菌ペルオキシレドキシンと過酸化水素複合体の立体構造2009

    • Author(s)
      中村努、門祐示、松村浩由、井上豪
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本
    • Year and Date
      2009-05-20
    • Related Report
      2011 Final Research Report 2009 Annual Research Report

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Published: 2009-04-01   Modified: 2016-04-21  

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