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Catalytic mechanism of metal-dependent deacetylase and its inhibitor

Research Project

Project/Area Number 15K01815
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Biomolecular chemistry
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

Nakamura Tsutomu  国立研究開発法人産業技術総合研究所, 生命工学領域, 研究グループ長 (10357668)

Co-Investigator(Kenkyū-buntansha) 上垣 浩一  近畿大学, 農学部, 教授 (00356544)
Research Collaborator NAKAYAMA atsuyoshi  
MATSUMURA hiroyoshi  
Project Period (FY) 2015-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2017: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywords脱アセチル化酵素 / 反応中間体 / N-アセチルD-アミノ酸脱アセチル化酵素 / 基質特異性 / 組換えタンパク質発現 / CE-14デアセチラーゼ / D-アミノアシラーゼ / デアセチラーゼ / カドミウム錯体 / CE-14 family
Outline of Final Research Achievements

We solved the tertiary structure of PhDac, which is categorized into CE-14 family, complexed with its substrate analog. This clarified the mechanism of substrate recognition and catalysis of PhDac. The amino acid residues involved in specific interaction with the substrate were spatially conserved in other CE-14 deacetylases, indicating that the substrate recognition mechanism was common in this family proteins.

Academic Significance and Societal Importance of the Research Achievements

グラム陰性菌の細胞壁にはN-アセチルグルコサミン誘導体が含まれており、その脱アセチル化酵素(デアセチラーゼ)の阻害剤は抗菌活性が期待される。また、DAAはD-アミノ酸の工業生産のさいの高額分割に利用可能であり、そのD-アミノ酸は化粧品や食品成分として注目されている。本研究成果は、これらの酵素の利用の基礎となるものである。また、金属依存性デアセチラーゼ一般のメカニズム解明に指針を与えるものである。

Report

(5 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (18 results)

All 2019 2018 2017 2016 2015

All Journal Article (6 results) (of which Peer Reviewed: 6 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (11 results) (of which Int'l Joint Research: 5 results) Patent(Industrial Property Rights) (1 results)

  • [Journal Article] Distinct molecular assembly of homologous peroxiredoxins from Pyrococcus horikoshii and Thermococcus kodakaraensis2019

    • Author(s)
      Himiyama Tomoki、Oshima Maki、Uegaki Koichi、Nakamura Tsutomu
    • Journal Title

      The Journal of Biochemistry

      Volume: 未定 Issue: 1 Pages: 89-95

    • DOI

      10.1093/jb/mvz013

    • NAID

      40021952200

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Application of chromosomal gene insertion into Escherichia coli for expression of recombinant proteins2018

    • Author(s)
      Nakamura Tsutomu、Koma Daisuke、Oshima Maki、Hoshino Hideto、Ohmoto Takashi、Uegaki Koichi
    • Journal Title

      Journal of Bioscience and Bioengineering

      Volume: 126 Issue: 2 Pages: 266-272

    • DOI

      10.1016/j.jbiosc.2018.02.016

    • NAID

      40021645470

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Alteration of molecular assembly of peroxiredoxins from hyperthermophilic archaea2017

    • Author(s)
      Nakamura Tsutomu、Oshima Maki、Yasuda Megumi、Shimamura Akiko、Morita Junji、Uegaki Koichi
    • Journal Title

      The Journal of Biochemistry

      Volume: 162 Issue: 6 Pages: 415-422

    • DOI

      10.1093/jb/mvx045

    • NAID

      40021421315

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Heat-induced native dimerization prevents amyloid formation by variable domain from immunoglobulin light-chain REI2017

    • Author(s)
      Nawata Marina、Tsutsumi Hirotaka、Kobayashi Yuta、Unzai Satoru、Mine Shouhei、Nakamura Tsutomu、Uegaki Koichi、Kamikubo Hironari、Kataoka Mikio、Hamada Daizo
    • Journal Title

      The FEBS Journal

      Volume: 284 Issue: 18 Pages: 3114-3127

    • DOI

      10.1111/febs.14181

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Substrate recognition of N,N′-diacetylchitobiose deacetylase from Pyrococcus horikoshii2016

    • Author(s)
      Tsutomu Nakamura, Yasushige Yonezawa, Yuko Tsuchiya, Mayumi Niiyama, Kurumi Ida, Maki Oshima, Junji Morita, Koichi Uegaki
    • Journal Title

      Journal of Structural Biology

      Volume: 3 Issue: 3 Pages: 286-293

    • DOI

      10.1016/j.jsb.2016.07.015

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Multiple crystal forms of N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus2015

    • Author(s)
      Tsutomu Nakamura, Mayumi Niiyama, Wakana Hashimoto, Kurumi Ida, Manabu Abe, Junji Morita, and Koichi Uegaki
    • Journal Title

      Acta Crystallographica Section F Structural Biology Communications

      Volume: 71 Issue: 6 Pages: 657-662

    • DOI

      10.1107/s2053230x15005695

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Caldanaerobacter subterraneus 由来CE-4 酵素のドメインマッピング2019

    • Author(s)
      佐々本 康平、森芳 邦彦、大本 貴士、上垣 浩一、西矢 芳昭、中村 努
    • Organizer
      日本農芸化学会2019年度大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] リンゴ酸デヒドロゲナーゼの構造変化と基質認識メカニズムの関係2019

    • Author(s)
      下澤 勇弥、西矢 芳昭、佐々本 康平、氷見山 幹基、中村 努
    • Organizer
      日本農芸化学会2019年度大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 大腸菌染色体挿入による組換えタンパク質発現2018

    • Author(s)
      中村 努、駒 大輔、大嶋 真紀、星野 英人、大本 貴士、上垣 浩一
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Decameric and dodecameric structures of archaeal peroxiredoxins2018

    • Author(s)
      Nakamura, T., Himiyama, T., Oshima, M., and Uegaki, K.
    • Organizer
      AsCA2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Conversion of molecular assembly of peroxiredoxin2017

    • Author(s)
      Nakamura, T., Oshima, M., and Uegaki, K.
    • Organizer
      24th Congress and General Assembly of the International Union of Crystallography
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Molecular assembly of peroxiredoxin2017

    • Author(s)
      Nakamura, T., Oshima, M., and Uegaki, K.
    • Organizer
      42nd FEBS Congress
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] ペルオキシレドキシンの会合状態の変換2017

    • Author(s)
      中村 努、大嶋 真紀、上垣 浩一
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Substrate recognition of CE-14 family enzymes2016

    • Author(s)
      Tsutomu Nakamura, Yasushige Yonezawa, Yuko Tsuchiya, Mayumi Niiyama, Maki Oshima, Koichi Uegaki
    • Organizer
      AsCA2016 (Asian Crystallographic Association)
    • Place of Presentation
      ハノイ(ベトナム)
    • Year and Date
      2016-12-05
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] ペルオキシレドキシンの分子集合2016

    • Author(s)
      中村 努、大嶋 真紀、上垣 浩一
    • Organizer
      日本結晶学会平成28年度年会
    • Place of Presentation
      水戸
    • Year and Date
      2016-11-17
    • Related Report
      2016 Research-status Report
  • [Presentation] CE-14ファミリー酵素の基質結合2016

    • Author(s)
      中村 努、米澤 康滋、土屋 裕子、新山 真由美、大嶋 真紀、上垣 浩一
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡
    • Year and Date
      2016-06-07
    • Related Report
      2016 Research-status Report
  • [Presentation] Crystal structure and multiple crystal forms of archaeal N,N′-diacetylchitobiose deacetylase2015

    • Author(s)
      Tsutomu Nakamura, Mayumi Niiyama, and Koichi Uegaki
    • Organizer
      The 13th Conference of the Asian Crystallographic Association
    • Place of Presentation
      Kolkata, India
    • Year and Date
      2015-12-05
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Patent(Industrial Property Rights)] N,N’-ジアセチルキトビオースデアセチラーゼ阻害剤及び新規化合物2015

    • Inventor(s)
      中村努、上垣浩一
    • Industrial Property Rights Holder
      産業技術総合研究所
    • Industrial Property Rights Type
      特許
    • Filing Date
      2015
    • Acquisition Date
      2018
    • Related Report
      2018 Annual Research Report

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Published: 2015-04-16   Modified: 2020-03-30  

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