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Elucidation of enzyme catalytic mechanism regulating transition state by linking conformational change and fluctuations of the active site

Research Project

Project/Area Number 16KT0055
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeMulti-year Fund
Section特設分野
Research Field Transition State Control
Research InstitutionOsaka University

Principal Investigator

Okajima Toshihide  大阪大学, 産業科学研究所, 准教授 (10247968)

Co-Investigator(Kenkyū-buntansha) 中井 忠志  広島工業大学, 生命学部, 准教授 (00333344)
庄司 光男  筑波大学, 計算科学研究センター, 助教 (00593550)
村川 武志  大阪医科大学, 医学部, 助教 (90445990)
Project Period (FY) 2016-07-19 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥18,590,000 (Direct Cost: ¥14,300,000、Indirect Cost: ¥4,290,000)
Fiscal Year 2018: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2017: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2016: ¥9,490,000 (Direct Cost: ¥7,300,000、Indirect Cost: ¥2,190,000)
Keywordsゆらぎ / 酵素 / 反応機構 / 遷移状態 / 中性子構造解析 / 銅アミン酸化酵素 / 補酵素 / 中性子結晶構造 / 銅 / 反応中間体
Outline of Final Research Achievements

Neutron crystallography of copper amine oxidase revealed that the cofactor TPQ has both enolate and keto forms on the basis of its protonation state. It is clear that both forms had a distorted ring structure unlike a planner one that has been believed to be taken. The present study also provide detail information for structural changes of the catalytic intermediates during the catalytic cycle. Structural changes, distortion, and fluctuations of the active-site residues and cofactor can control energy level of transition state so that the rate of enzyme-catalyzed reaction is accelerated.

Academic Significance and Societal Importance of the Research Achievements

本研究で決定されたアミン酸化酵素の中性子構造は、これまでに報告されている中で最大サイズのタンパク質であり、その新規な活性中心構造を含め、国際的にも高く評価された。また、酵素の触媒反応を加速化させる構造基盤の一端を解明に成功しており、酵素活性中心の動き、歪み、およびゆらぎが遷移状態の影響していることが判明した。その知見は有用酵素の改良にも役立つものと考えられる。

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

    (33 results)

All 2020 2019 2018 2017 2016 Other

All Journal Article (4 results) (of which Peer Reviewed: 4 results,  Open Access: 1 results) Presentation (19 results) (of which Int'l Joint Research: 3 results,  Invited: 7 results) Remarks (10 results)

  • [Journal Article] Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing2020

    • Author(s)
      Takeshi Murakawa, Kazuo Kurihara, Mitsuo Shoji, Chie Shibazaki, Tomoko Sunami, Taro Tamada, Naomine Yano, Taro Yamada, Katsuhiro Kusaka, Mamoru Suzuki, Yasuteru Shigeta, Ryota Kuroki, Hideyuki Hayashi, Takato Yano, Katsuyuki Tanizawa, Motoyasu Adachi, Toshihide Okajima
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 印刷中 Issue: 20 Pages: 10818-10824

    • DOI

      10.1073/pnas.1922538117

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] In crystallo thermodynamic analysis of the catalytic reaction in bacterial copper amine oxidase2020

    • Author(s)
      Takeshi Murakawa, Seiki Baba, Toshihide Okajima
    • Journal Title

      SPring-8/SACLA Research Frontiers

      Volume: 印刷中

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] In crystallo thermodynamic analysis of the cofactor conformational change induced during the catalytic reaction of copper amine oxidase2019

    • Author(s)
      村川武志,馬場清喜,岡島俊英
    • Journal Title

      生化学

      Volume: 91 Issue: 4 Pages: 565-571

    • DOI

      10.14952/SEIKAGAKU.2019.910565

    • NAID

      40022022855

    • ISSN
      0037-1017
    • Year and Date
      2019-08-25
    • Related Report
      2019 Annual Research Report 2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] In crystallo thermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase2018

    • Author(s)
      Murakawa Takeshi、Baba Seiki、Kawano Yoshiaki、Hayashi Hideyuki、Yano Takato、Kumasaka Takashi、Yamamoto Masaki、Tanizawa Katsuyuki、Okajima Toshihide
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 116 Issue: 1 Pages: 135-140

    • DOI

      10.1073/pnas.1811837116

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Presentation] 銅アミン酸化酵素のトパキノン補酵素生合成反応における中間体形成の分光学的解析・速度論的解析2020

    • Author(s)
      酒井克輝、佐々木康、村川武志、谷澤克行、岡島俊英
    • Organizer
      日本農芸化学会2020年度大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Structural basis for conformational change of the topaquinone cofactor during the catalytic reaction of bacterial copper amine oxidase2019

    • Author(s)
      Toshihide Okajima, Takeshi Murakawa, Seiki Baba, Satoshi Kanagawa, Hideyuki Hayashi, Takato Yano, Takashi Kumasaka, and Katsuyuki Tanizawa
    • Organizer
      33rd Annual Symposium of The Protein Society
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 銅含有アミン酸化酵素触媒機構の“in crystallo” 熱力学的解析2019

    • Author(s)
      村川武志
    • Organizer
      第42回 SPring-8先端利用技術ワークショップ/大阪大学蛋白質研究所セミナー
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 銅アミン酸化酵素の中性子構造解析と動的構造2019

    • Author(s)
      岡島俊英
    • Organizer
      日本学術振興会回折構造生物第169委員会中性子・放射光連携小委員会合同研究会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] 銅アミン酸化酵素の基質アミン複合体構造に基づく基質認識機構の解析2018

    • Author(s)
      金川哲士,村川武志,谷澤克行,岡島俊英
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] 銅アミン酸化酵素の補酵素生合成における初期反応中間体の解析2018

    • Author(s)
      佐々木康,村川武志,谷澤克行,岡島俊英
    • Organizer
      酵素補酵素研究会2018
    • Related Report
      2018 Research-status Report
  • [Presentation] 銅アミン酸化酵素の基質アミン複合体構造に基づく基質認識機構及び基質特異性の改変2018

    • Author(s)
      金川哲士,村川武志,谷澤克行,岡島俊英
    • Organizer
      第91回日本生化学会大会
    • Related Report
      2018 Research-status Report
  • [Presentation] 銅含有アミン酸化酵素におけるセミキノン ラジカル生成機構についての理論的解明2018

    • Author(s)
      庄司光男, 村川武志, 重田育照, 岡島俊英
    • Organizer
      分子シミュレーション討論会
    • Related Report
      2018 Research-status Report
  • [Presentation] 銅含有アミン酸化酵素の反応中間体構造と触媒機構2018

    • Author(s)
      岡島俊英
    • Organizer
      平成30年度J-PARC MLF産業利用報告会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] In crystallo thermodynamic analysisによる銅アミン酸化酵素の反応機構解析2018

    • Author(s)
      村川武志
    • Organizer
      酵素補酵素研究会2018
    • Related Report
      2018 Research-status Report
  • [Presentation] A quantum chemical study of the glycine formation reactions in interstellar medium2017

    • Author(s)
      M. Shoji,
    • Organizer
      ABC workshop
    • Place of Presentation
      Hiroshima
    • Year and Date
      2017-03-21
    • Related Report
      2016 Research-status Report
  • [Presentation] 銅アミン酸化酵素活性中心の高分解能 X 線および中性子結晶構造2017

    • Author(s)
      岡島 俊英、村川 武志、栗原 和男、安達基泰、柴崎 千枝、 玉田 太郎、林 秀行、谷澤 克行
    • Organizer
      第8回MLFシンポジウム
    • Place of Presentation
      つくば
    • Year and Date
      2017-03-14
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] 非凍結状態結晶の X 線回折測定による酵素触媒反応中間体の解析2017

    • Author(s)
      岡島俊英
    • Organizer
      蛋白研セミナー& SPring-8 先端利用技術ワークショップ「 SPring-8 における蛋白質構造生物学研究の現状と将来」
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 高分解能X 線および中性子構造解析による酸化型銅アミン酸化酵素の活性中心構造2017

    • Author(s)
      岡島俊英
    • Organizer
      平成29年度第1回構造生物学研究会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 銅含有アミン酸化酵素における触媒反応中のプロトン化状態についての理論的解明2017

    • Author(s)
      庄司光男, 村川武志, 重田育照, 岡島俊英
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] スレオニン合成酵素における生成物支援機構の理論的解明2016

    • Author(s)
      氏家謙、庄司光男、原田隆平、村川武志、重田育照、林秀行
    • Organizer
      第54回生物物理会年会
    • Place of Presentation
      つくば
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] X-ray crystallographic structure of semiquinone radical intermediate formed in bacterial copper amine oxidase2016

    • Author(s)
      T. Okajima, T. Nakai, K. Tanizawa, T. Murakawa, and H. Hayashi
    • Organizer
      Fifth International Conference on Cofactors (ICC-05) & Active Enzyme Molecule 2016
    • Place of Presentation
      黒部
    • Year and Date
      2016-09-04
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Analysis of the Catalytic Mechanism of Copper Amine Oxidase from Arthrobacter globiformis.2016

    • Author(s)
      H. Yamaguchi, T. Murakawa, M. Kataoka, Y. Kawano, H. Hayashi, K. Tanizawa and T. Okajima
    • Organizer
      International Symposium on Diffraction Structural Biology 2016
    • Place of Presentation
      Knoxville, Tennessee, U.S.A
    • Year and Date
      2016-08-07
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] 銅アミン酸化酵素の反応中間体構造と中性子構造解析の現状2016

    • Author(s)
      岡島俊英
    • Organizer
      2016年度第1回水和ナノ構造研究会
    • Place of Presentation
      東京
    • Related Report
      2016 Research-status Report
    • Invited
  • [Remarks] 宙に浮く水素イオン?! 大型タンパク質の中性子結晶構造解析で見えた特異な世界

    • URL

      https://resou.osaka-u.ac.jp/ja/research/2020/20200428_1

    • Related Report
      2019 Annual Research Report
  • [Remarks] 宙に浮く水素イオン?! ―大型タンパク質の中性子結晶構造解析で見えた特異な世界―

    • URL

      https://www.sanken.osaka-u.ac.jp/hot_topics/topics_20200428/

    • Related Report
      2019 Annual Research Report
  • [Remarks] 宙に浮く水素イオン?! ―大型タンパク質の中性子結晶構造解析で見えた特異な世界―

    • URL

      https://www.osaka-med.ac.jp/news/research/f2pjgc000000fjnt.html

    • Related Report
      2019 Annual Research Report
  • [Remarks] 宙に浮く水素イオン?!―大型タンパク質の中性子結晶構造解析で見えた特異な世界―

    • URL

      https://www.qst.go.jp/site/press/40567.html

    • Related Report
      2019 Annual Research Report
  • [Remarks] 宙に浮く水素イオン?!―大型タンパク質の中性子結晶構造解析で見えた特異な世界―

    • URL

      http://www.tsukuba.ac.jp/attention-research/p202004280400.html

    • Related Report
      2019 Annual Research Report
  • [Remarks] 結晶の中でタンパク質の“生きた状態”の観察に成功

    • URL

      https://www.sanken.osaka-u.ac.jp/toppage/hot_topics/topics_20181220/

    • Related Report
      2018 Research-status Report
  • [Remarks] 結晶の中でタンパク質の“生きた状態”の観察に成功

    • URL

      https://resou.osaka-u.ac.jp/ja/research/2018/20181220_1

    • Related Report
      2018 Research-status Report
  • [Remarks] 結晶の中でタンパク質の“生きた状態”の観察に成功

    • URL

      https://www.osaka-med.ac.jp/news/research/v9oak00000006j6e.html

    • Related Report
      2018 Research-status Report
  • [Remarks] AGAO

    • URL

      https://www.sanken.osaka-u.ac.jp/labs/smb/agao.html

    • Related Report
      2018 Research-status Report
  • [Remarks] AGAO (Anthrobacter globiformis amine oxidase)

    • URL

      http://www.sanken.osaka-u.ac.jp/labs/smb/AGAO.html

    • Related Report
      2016 Research-status Report

URL: 

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

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