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Uncovering the catalytic mechanism of nitrile hydratase based on the structure of the novel cyclic reaction intermediate

Research Project

Project/Area Number 15H03832
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Bio-related chemistry
Research InstitutionAkita University

Principal Investigator

ODAKA MASAFUMI  秋田大学, 理工学研究科, 教授 (20224248)

Co-Investigator(Kenkyū-buntansha) 野口 恵一  東京農工大学, 学内共同利用施設等, 准教授 (00251588)
松村 洋寿  秋田大学, 工学(系)研究科(研究院), 講師 (60741824)
Co-Investigator(Renkei-kenkyūsha) KUROKI RYOTA  独立行政法人日本原子力研究開発機構, 量子ビーム応用研究部門, ユニット長 (30391246)
YOHDA MASAFUMI  東京農工大学, 大学院工学研究院, 教授 (50250105)
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2017: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2016: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2015: ¥9,100,000 (Direct Cost: ¥7,000,000、Indirect Cost: ¥2,100,000)
Keywords触媒反応機構 / 反応中間体 / 翻訳後修飾 / 時間分割結晶構造解析 / 顕微分光法 / SFX / XFEL / 時間分割構造解析 / 中性子構造解析 / 質量分析 / FTIR
Outline of Final Research Achievements

In the hydration mechanism of nitrile hydratase (NHase), the substrate nitrile molecule, coordinated to the non-heme iron is attacked nucleophilically by the O-atom of the cysteine-sulfenate ligand, to form a novel cyclic intermediate. To uncover the reaction mechanism followed by the cyclic intermediate by serial femtosecond crystallography, we performed the following researches. βTyr37, which was suggested to be involved in the proton-transfer to the N-atom of the cyclic intermediate based on the hybrid quantum mechanics/molecular mechanics (QM/MM) method, was substituted by Phe, Ile or Ala. All mutant NHases showed significant catalytic activity. And, the crystal structure of the βY37K mutant was basically unchanged except for the substituted residue. We identified the reaction intermediate species of NHase by using time-resolved microspectroscopy. We determined the crystallization condition which is enough small for SFX analyses.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (15 results)

All 2017 2016 2015 Other

All Int'l Joint Research (2 results) Journal Article (3 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 3 results,  Open Access: 2 results) Presentation (10 results) (of which Int'l Joint Research: 4 results,  Invited: 4 results)

  • [Int'l Joint Research] Stanford University(U.S.A.)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Stanford University(米国)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Catalytic Mechanism of Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM Study2016

    • Author(s)
      M. Kayanuma, M. Shoji, M. Yohda, M. Odaka, Y. Shigeta
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 123(13) Issue: 13 Pages: 3259-3266

    • DOI

      10.1021/acs.jpcb.5b11363

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Time-resolved crystal structures of the reaction intermediate of nitrile hydrase reveal a role for the cystein-sulfenic acid ligand as a catalyst nucleophile2015

    • Author(s)
      Yasuaki Yamanaka, Yuki Kato, Koichi Hashimoto, Keisuke Iida, Kazuo Nagasawa, Hiroshi Nakayama, Naoshi Dohmae, Keiichi Noguchi, Takumi Noguchi, Masafumi Yohda, and Masafumi Odaka
    • Journal Title

      Angew. Chem., Int. Ed.

      Volume: 54 Issue: 37 Pages: 10763-10767

    • DOI

      10.1002/anie.201502731

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Spectroscopic and Computational Studies of Nitrile Hydratase: Insights into Geometric and Electronic Structure and the Mechanism of Amide Synthesis2015

    • Author(s)
      Light KM, Yamanaka Y, Odaka M, Solomon EI.
    • Journal Title

      Chem. Sci.

      Volume: 6 Pages: 6280-6294

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Time-resolved crystal structures of the reaction intermediate of nitrile hydratase: revealing a role of cysteine sulfinic acid ligand as a catalytic nucleophile2017

    • Author(s)
      Yamanaka, Y. Kato, K. Hashimoto, K. Iida, K. Nagasawa, H. Nakayama, N. Dohmae, K. Noguchi, T. Noguchi, M. Yohda, and M. Odaka
    • Organizer
      5th Symposium on Advanced Biological Inorganic Chemistry
    • Place of Presentation
      Kolkata, India
    • Year and Date
      2017-01-07
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ニトリルヒドラターゼの触媒反応機構解析-時間分割結晶構造解析に向けた取組2017

    • Author(s)
      林 英輝、高畑祥平、北條晴佳、松村洋寿、當舎武彦、久保 稔、杉本 宏、野口恵一、養王田正文、尾高雅文
    • Organizer
      第12回バイオ関連化学シンポジウム
    • Related Report
      2017 Annual Research Report
  • [Presentation] ニトリルヒドラターゼの触媒反応機構解析-時間分解紫外可視顕微分光スペクトル解析2017

    • Author(s)
      林 英輝、高畑祥平、北條晴佳、松村洋寿、野村高志、當舎武彦、城 宜嗣、野口恵一、養王田正文、尾高雅文
    • Organizer
      酵素工学研究会第78回講演会
    • Related Report
      2017 Annual Research Report
  • [Presentation] βTyr37置換変異体によるニトリルヒドラターゼの触媒機構解析2017

    • Author(s)
      髙畑祥平、北條晴佳、松村洋寿、野口恵一、養王田正文、尾髙雅文
    • Organizer
      酵素工学研究会第78回講演会
    • Related Report
      2017 Annual Research Report
  • [Presentation] ニトリルヒドラターゼの触媒反応機構解析-シリアルフェムト秒結晶構造解析に向けた取組2017

    • Author(s)
      林 英輝、北條晴佳、松村洋寿、小川信明、野村高志、當舎武彦、城 宜嗣、野口恵一、養王田正文、尾高雅文
    • Organizer
      2017年度量子ビームサイエンスフェスタ
    • Related Report
      2017 Annual Research Report
  • [Presentation] Time-resolved crystal structures of the reaction intermediate of nitrile hydratase reveal a role for the cysteine-sulfenic acid ligand as a nucleophile2016

    • Author(s)
      Yasuaki Yamanaka, Yuki Kato, Koichi Hashimoto, Keisuke Iida, Kazuo Nagasawa, Hiroshi Nakayama, Naoshi Dohmae, Keiichi Noguchi, Takumi Noguchi, Masafumi Yohda, and Masafumi Odaka
    • Organizer
      KMB2016 International Symposium and Annual Meeting
    • Place of Presentation
      Daejeon, Korea
    • Year and Date
      2016-06-22
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile2016

    • Author(s)
      Masafumi Odaka
    • Organizer
      8th Japan-Korea Seminars on Biomolecular Science: Experiments and Simulation
    • Place of Presentation
      岡崎
    • Year and Date
      2016-02-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 時間分割構造解析によるニトリルヒドラターゼ反応中体の捕捉と反応機構解析2016

    • Author(s)
      尾高雅文
    • Organizer
      酵素工学研究会第76回講演会
    • Place of Presentation
      東京
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Snapshots of the reaction intermediate of nitrile hydratase reveal a role for the cysteine-sulfenic acid ligand as a catalytic nucleophile2015

    • Author(s)
      Masafumi Odaka, Yasuaki Yamanaka, Yuki Kato, Koichi Hashimoto, Keisuke Iida, Kazuo Nagasawa, Hiroshi Nakayama, Naoshi Dohmae, Keiichi Noguchi, Takumi Noguchi, and Masafumi Yohda
    • Organizer
      The 17th International Conference on Biological Inorganic Chemistry(ICBIC17)
    • Place of Presentation
      Beijing, China
    • Year and Date
      2015-07-20
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ニトリルヒドラターゼの時間分割構造解析-新規環状中間体構造の決定と触媒反応モデルの構築2015

    • Author(s)
      山中 保明、加藤 祐樹、野口 恵一、野口 巧、養王田 正文、尾高 雅文
    • Organizer
      第42回生体分子科学討論会
    • Place of Presentation
      高崎
    • Year and Date
      2015-06-12
    • Related Report
      2015 Annual Research Report

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Published: 2015-04-16   Modified: 2022-08-26  

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