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Crystal structure analysis for intermediate in enzymatic reaction by using neutron beam

Research Project

Project/Area Number 16KT0063
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeMulti-year Fund
Section特設分野
Research Field Transition State Control
Research InstitutionNational Institutes for Quantum and Radiological Science and Technology

Principal Investigator

Adachi Motoyasu  国立研究開発法人量子科学技術研究開発機構, 量子生命科学領域, グループリーダー(定常) (60293958)

Co-Investigator(Kenkyū-buntansha) 森元 聡  九州大学, 薬学研究院, 教授 (60191045)
老川 典夫  関西大学, 化学生命工学部, 教授 (80233005)
木下 誉富  大阪府立大学, 理学(系)研究科(研究院), 教授 (90405340)
Project Period (FY) 2016-07-19 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥18,460,000 (Direct Cost: ¥14,200,000、Indirect Cost: ¥4,260,000)
Fiscal Year 2019: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2018: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2017: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2016: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Keywords酵素 / 結晶構造解析 / 中性子
Outline of Final Research Achievements

In this study, we aimed to realize neutron structural analysis including orientation of hydrogen atoms and water molecules in reaction intermediates for controlling transition states through three-dimensional structural analysis of enzyme. For the histidine racemase, which is one of the amino acid racemases, we succeeded in X-ray crystallography for the first time in the world. Furthermore, by examining crystallization conditions and continuing optimization, we succeeded in X-ray crystal structure analysis to a high resolution of 1.0 angstrom, and in producing large crystals with a volume of above 1 mm cubed. For CK2, we succeeded in neutron structure analysis for the first time in the world, and showed a hydrogen bond network that traverses the molecule and its functionality.

Academic Significance and Societal Importance of the Research Achievements

反応中間体等の解析は、酵素本来の緻密な反応触媒機構を解明することにつながり、例えばCK2の成果は、間接的に活性を調整するようなアロステリック型の阻害剤の開発に貢献する。またラセマーゼに関しては、得られた知見に基づいて、遷移状態あるいは中間状態を制御した酵素の合理的な改変を行うことで、従来と異なる反応生成物を選択的に得ることができると考えられる。新機能酵素による新たな有機分子合成は、独自の化合物スクリーニングライブラリーの拡充や、複雑な官能基を有する医薬品原料素材の供給を可能にし、国内産業の強みである原料素材産業における国際競争力の強化にも貢献するものと考えられる。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (22 results)

All 2020 2019 2018 2017 Other

All Int'l Joint Research (2 results) Journal Article (6 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 4 results,  Open Access: 1 results) Presentation (13 results) (of which Int'l Joint Research: 4 results,  Invited: 7 results) Book (1 results)

  • [Int'l Joint Research] ミュンヘン工科大学/ユーリッヒ中性子科学センター(ドイツ)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] TUM/JCNS(ドイツ)

    • Related Report
      2018 Research-status Report
  • [Journal Article] Direct Observation of the Protonation States in the Mutant Green Fluorescent Protein2020

    • Author(s)
      Chie Shibazaki, Rumi Shimizu, Yuji Kagotani, Andreas Ostermann, Tobias E. Schrader, Motoyasu Adachi
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 11 Issue: 2 Pages: 492-496

    • DOI

      10.1021/acs.jpclett.9b03252

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] X-Ray diffraction experiments for drug target protein of human casein kinase II2019

    • Author(s)
      Chie Shibazaki, Shigeki Arai, Rumi Shimizu, Motoyasu Adachi
    • Journal Title

      Photon Factory Activity Report 2018

      Volume: 36 Pages: 149-149

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Hydration Structures of the Human Protein Kinase CK2α Clarified by Joint Neutron and X-ray Crystallography2018

    • Author(s)
      Shibazaki Chie、Arai Shigeki、Shimizu Rumi、Saeki Morihisa、Kinoshita Takayoshi、Ostermann Andreas、Schrader Tobias E.、Kurosaki Yuzuru、Sunami Tomoko、Kuroki Ryota、Adachi Motoyasu
    • Journal Title

      Journal of Molecular Biology

      Volume: 430 Issue: 24 Pages: 5094-5104

    • DOI

      10.1016/j.jmb.2018.09.018

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] The first identification and characterization of a histidine-specific amino acid racemase, histidine racemase from a lactic acid bacterium, Leuconostoc mesenteroides subsp. sake NBRC 1024802018

    • Author(s)
      Adachi Motoyasu、Shimizu Rumi、Kato Shiro、Oikawa Tadao
    • Journal Title

      Amino Acids

      Volume: 51 Issue: 2 Pages: 331-343

    • DOI

      10.1007/s00726-018-2671-y

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Deuterated Materials Enhancing Neutron Science for Structure Function Applications2018

    • Author(s)
      阿久津 和宏 , 安達 基泰 , 川北 至信
    • Journal Title

      JAEA-Review

      Volume: J-PARC 17-06

    • Related Report
      2017 Research-status Report
  • [Journal Article] Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type2017

    • Author(s)
      Hiromoto Takeshi、Meilleur Flora、Shimizu Rumi、Shibazaki Chie、Adachi Motoyasu、Tamada Taro、Kuroki Ryota
    • Journal Title

      Protein Science

      Volume: 26 Issue: 10 Pages: 1953-1963

    • DOI

      10.1002/pro.3230

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 中性子による最近の構造解析研究Ⅱ2020

    • Author(s)
      安達 基泰
    • Organizer
      重水素化薬剤研究会2020横浜
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Neutron crystal structure analysis of human casein kinase II (CK2)2019

    • Author(s)
      Motoyasu Adachi
    • Organizer
      27th International Society of Heterocyclic Chemistry (ISHC) Congress
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A NOVEL PYRIDOXAL 5′-PHOSPHATE-DEPENDENT HISTIDINE RACEMASE FROM LEUCONOSTOC MESENTEROIDES SUBSP. SAKE NBRC 102480: DISCOVERY AND STRUCTURAL CHARACTERIZATION2019

    • Author(s)
      Motoyasu Adachi, Rumi Shimizu, Shiro Kato, Tadao Oikawa
    • Organizer
      The 4th International Conference of D-Amino Acid Research (IDAR2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] タンパク質の中性子結晶構造解析とその未来への展望:ヒト由来プロテインキナーゼCK2の解析から2019

    • Author(s)
      安達 基泰
    • Organizer
      バイオサイエンスセミナー
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 量子効果と量子ダイナミクス解析によるタンパク質研究の パラダイムシフト2019

    • Author(s)
      安達 基泰
    • Organizer
      次世代放射光超高分解能RIXS ワークショップ
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Conformation analysis of hydrogen atoms around ligand-binding pocket based on quantum chemical calculation2019

    • Author(s)
      Chiduru Watanabe, Kaori Fukuzawa, Yoshio Okiyama, Motoyasu Adachi, Shigenori Tanaka, Teruki Honma
    • Organizer
      CBI学会2019年大会, 情報計算化学生物学会(CBI学会)
    • Related Report
      2019 Annual Research Report
  • [Presentation] ヒト由来プロテインキナーゼCK2の中性子結晶構造解析2019

    • Author(s)
      安達 基泰
    • Organizer
      CBI学会2019年大会 (第20回FMO研究会 生命現象を量子構造生物学で解き明かす), 情報計算化学生物学会(CBI学会)
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] First neutron stuructural analaysis of human casein kinase II2018

    • Author(s)
      Motoyasu Adachi, Chie Shibazaki, Rumi Shimizu, Shigeki Arai, Andreas Ostermann, Tobias E. Schrader
    • Organizer
      The 31st European Crystallographic Meeting (ECM31)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Long hydrogen bonding network responsible for catalytic activity of human casein kinase II2018

    • Author(s)
      Chie Shibazaki, Rumi Shimizu, Shigeki Arai, Motoyasu Adachi
    • Organizer
      3rd International Symposium of Quantum Beam Science
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] ヒトカゼインキナーゼIIの触媒活性に係わる新たな水素結合ネットワークの発見2018

    • Author(s)
      柴崎千枝、清水瑠美、新井栄揮、安達基泰、黒木良太
    • Organizer
      2017年度量子ビームサイエンスフェスタ (第9回MLFシンポジウム・第35回PFシンポジウム)
    • Related Report
      2017 Research-status Report
  • [Presentation] 非凍結結晶を用いたβ-アミラーゼ(E380A)と基質との複合体のpH変化の解析2018

    • Author(s)
      三上文三、安達基泰、姜有那、水谷公彦
    • Organizer
      日本農芸化学会2018年度大会
    • Related Report
      2017 Research-status Report
  • [Presentation] HIV-1 プロテーゼの中性子構造解析2017

    • Author(s)
      安達基泰
    • Organizer
      第8回東海地区中性子生命科学検討会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Perdeuteration and protein neutron crystallography (for beginners)2017

    • Author(s)
      Motoyasu Adachi
    • Organizer
      J-PARC WORKSHOP Deuterated Materials Enhancing Neutron Science for Structure Function Applications
    • Related Report
      2017 Research-status Report
  • [Book] Structural Biology in Drug Discovery: Methods, Techniques, and Practices2020

    • Author(s)
      Motoyasu Adachi, Ryota Kuroki
    • Total Pages
      17
    • Publisher
      WILEY
    • ISBN
      9781118681015
    • Related Report
      2019 Annual Research Report

URL: 

Published: 2016-07-20   Modified: 2023-03-08  

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