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Elucidation of the protonation mechanisms of ferredoxin-dependent bilin reductase by neutron crystallography

Research Project

Project/Area Number 22770096
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Structural biochemistry
Research InstitutionIbaraki University

Principal Investigator

UNNO Masaki  茨城大学, フロンティア応用原子科学研究センター, 准教授 (10359549)

Research Collaborator FUKUYAMA Keiichi  大阪大学, 理学研究科, 教授 (80032283)
Project Period (FY) 2010 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2011: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2010: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywords酵素 / フィコシアノビリン / PcyA / 中性子結晶解析 / 水素原子 / 反応機構 / 大型結晶 / 宇宙実験 / 高分解能 / 中性子結晶構造解析 / ビリン還元酵素 / シアノバクテリア / 結晶成長
Research Abstract

We succeeded obtaining a big crystal of PcyA, a ferredoxin-dependent bilin reductase, which biosynthesizes an important pigment pytochromobilin. The crystal diffracted neutron up to 2.6 A resolution. If we can obtain bigger crystal than this one, we will able to structural analysis beyond 2 A resolution, and determine the position of hydrogen atoms in the structure. The reaction mechanism will be elucidated, soon.

Report

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

    (37 results)

All 2011 2010 Other

All Journal Article (13 results) (of which Peer Reviewed: 10 results) Presentation (22 results) Remarks (2 results)

  • [Journal Article] 金属タンパク質のX線結晶構造解析:ヘム分解酵素の反応中間体2011

    • Author(s)
      海野昌喜、松井敏高、齋藤正男
    • Journal Title

      日本結晶学会誌

      Volume: 53 Pages: 213-218

    • NAID

      10029371570

    • Related Report
      2011 Annual Research Report 2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] S100 and S100 fused-type protein families in epidermal maturation with special focus on S100A3 in mammalian hair cuticles2011

    • Author(s)
      Kizawa, K., et al.
    • Journal Title

      Biochimie

      Volume: 93 Issue: 12 Pages: 2038-2047

    • DOI

      10.1016/j.biochi.2011.05.028

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Binding and selectivity of the marine toxins neodysiherbaine A, and its synthetic analogues, to GluK1 and GIuK2 kainate receptors2011

    • Author(s)
      M.Unno, M.Shinohara, K.Takayama, H.Tanaka, K.Teruya, K.Doh-ura, R.Sakai, M.Sasaki, M.Ikeda-Saito
    • Journal Title

      Journal of Molecular Biology

      Volume: 413 Issue: 3 Pages: 667-683

    • DOI

      10.1016/j.jmb.2011.08.043

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Refined Crystal Structures of Human Ca^<2+>/Zn^<2+>-Binding S100 A3 Protein Characterized by Two Disulfide Bridges2011

    • Author(s)
      Unno, M., et al.
    • Journal Title

      J.Mol.Biol.

      Volume: 408 Issue: 3 Pages: 477-490

    • DOI

      10.1016/j.jmb.2011.02.055

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enzymatic Ring-Opening Mechanism of Verdoheme by the Heme Oxygenase : A Combined X-ray Crystallography and QM/MM Study.2010

    • Author(s)
      Lai, W., Chen, H., Matsui, T., Omori, K., Unno, M., Ikeda-Saito, M., Shaik, S.
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 132 Pages: 12960-12970

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Solution 1H NMR characterization of substrate-free C. diphtheriae heme oxygenase : Pertinence for determining magnetic axes in paramagnetic substrate complexes.2010

    • Author(s)
      Du, Z., Unno, M., Matsui, T., Ikeda-Saito, M., La Mar, G., N.
    • Journal Title

      J. Inorg. Biochem

      Volume: 104 Pages: 1063-1070

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Dioxygen Activation for the Self-Degradation of Heme : Reaction Mechanism and Regulation of Heme Oxygenase2010

    • Author(s)
      Matsui, T., Iwasaki, M., Sugiyama, R., Unno, M., Ikeda-Saito, M.
    • Journal Title

      Inorg. Chem

      Volume: 49 Issue: 8 Pages: 3602-3609

    • DOI

      10.1021/ic901869t

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] 量子ビームを活用したシトクロムc'の多元的精密構造・機能解析2010

    • Author(s)
      海野昌喜, 他
    • Journal Title

      平成21年度黎明研究成果報告書JAEA-Review 2010-071

      Volume: 132 Pages: 9-13

    • Related Report
      2010 Annual Research Report
  • [Journal Article] Enzymatic Ring-Opening Mechanism of Verdoheme by the Heme Oxygenase : A Combined X-ray Crystallography and QM/MM Study.2010

    • Author(s)
      Lai, W., et al.
    • Journal Title

      J.Am.Chem.Soc.

      Volume: 132 Pages: 12960-12970

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Precise Structural and Functional Analyses of Cytochrome c' Revealed by Quantum Beams and Other Multiple Methods2010

    • Author(s)
      Unno, M., et al.
    • Journal Title

      Photon Factory Activity Report 2009, PART B

      Volume: 27 Pages: 242-242

    • Related Report
      2010 Annual Research Report
  • [Journal Article] Structure-based Drug Design for Kainate-type Ionotropic Glutamate Receptors, GluK1 and GluK2, from Human Brain2010

    • Author(s)
      Unno, M., et al.
    • Journal Title

      Photon Factory Activity Report 2009, PART B

      Volume: 27 Pages: 241-241

    • Related Report
      2010 Annual Research Report
  • [Journal Article] Solution (1)H NMR characterization of substrate-free C.diphtheriae heme oxygenase : Pertinence for determining magneticaxes in paramagnetic substrate complexes.2010

    • Author(s)
      Du, Z., et al.
    • Journal Title

      J.Inorg.Biochem.

      Volume: 104 Pages: 1063-1070

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dioxygen Activation for the Self-Degradation of Heme : Reaction Mechanism and Regulation of Heme Oxygenase2010

    • Author(s)
      Matsui, T., et al.
    • Journal Title

      Inorg.Chem.

      Volume: 49 Pages: 3602-3609

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] フェレドキシン依存性ビリン還元酵素PcyAの大型結晶作製の試みと高分解能結晶構造解析2011

    • Author(s)
      石川久美子,伊中浩治,萩原義徳,和田啓,黒木良太,玉田太郎,福山恵一,海野昌喜
    • Organizer
      日本化学会関東支部、茨城地区交流会
    • Place of Presentation
      東海村
    • Year and Date
      2011-11-04
    • Related Report
      2011 Final Research Report
  • [Presentation] フェレドキシン依存性ビリン還元酵素PcyAの大型結晶作製の試みと高分解能結晶構造解析2011

    • Author(s)
      石川久美子, 他
    • Organizer
      日本化学会関東支部 茨城地区研究交流会
    • Place of Presentation
      東海村
    • Year and Date
      2011-11-04
    • Related Report
      2011 Annual Research Report
  • [Presentation] ブルー銅タンパク質シュウドアズリンにおける銅イオンのダイナミクス2011

    • Author(s)
      浅村紗矢香, 他
    • Organizer
      日本化学会第91春季年会
    • Place of Presentation
      横浜
    • Year and Date
      2011-03-26
    • Related Report
      2010 Annual Research Report
  • [Presentation] 原子レベル分解能でのAlcaligenes Xylosoxidans由来シトクロムc'の分子構造と分光学的性質2011

    • Author(s)
      高階明子, 他
    • Organizer
      日本化学会第91春季年会
    • Place of Presentation
      横浜
    • Year and Date
      2011-03-26
    • Related Report
      2010 Annual Research Report
  • [Presentation] ブルー銅タンパク質シュウドアズリンThr36Lys変異体の構造と性質2011

    • Author(s)
      松儀可奈子, 他
    • Organizer
      日本化学会第91春季年会
    • Place of Presentation
      横浜
    • Year and Date
      2011-03-26
    • Related Report
      2010 Annual Research Report
  • [Presentation] DNA損傷修復タンパク質の構造解析に向けて2011

    • Author(s)
      海野昌喜
    • Organizer
      茨城大学理学部 公開シンポジウム(第4回Quantum Medicine研究会)茨城大学研究推進プロジェクト「がん放射線治療に関する生命基礎研究」講演会
    • Place of Presentation
      水戸
    • Year and Date
      2011-02-05
    • Related Report
      2010 Annual Research Report
  • [Presentation] Precise X-ray Crystallographic Analysis of a Cytochrome c' from Alcalygenes xylosoxidans NCIMB 110152010

    • Author(s)
      Akiko Takashina, et al.
    • Organizer
      2010環太平洋国際化学会議~PACIFICHEM2010~
    • Place of Presentation
      Hawaii
    • Year and Date
      2010-12-17
    • Related Report
      2010 Annual Research Report
  • [Presentation] X-ray crystal analyses of a blue copper protein, pseudoazurin from Achoromobacter cycloclastes IAM1013 and its mutant proteins2010

    • Author(s)
      Sayaka Asamura, et al.
    • Organizer
      2010環太平洋国際化学会議~PACIFICHEM2010~
    • Place of Presentation
      Hawaii
    • Year and Date
      2010-12-17
    • Related Report
      2010 Annual Research Report
  • [Presentation] 中性子結晶構造解析を目指したフェレドキシン依存性ビリン還元酵素PcyAの結晶成長2010

    • Author(s)
      石川久美子,萩原義徳,和田啓,小原裕二,黒木良太,玉田太郎,福山恵一,海野昌喜
    • Organizer
      日本結晶学会2010,創立60周年記念大会
    • Place of Presentation
      大阪
    • Year and Date
      2010-12-05
    • Related Report
      2011 Final Research Report
  • [Presentation] 中性子結晶構造解析を目指したフェレドキシン依存性ビリン還元酵素PcyAの結晶成長2010

    • Author(s)
      石川久美子, 他
    • Organizer
      日本結晶学会年会2010創立60周年記念大会
    • Place of Presentation
      大阪
    • Year and Date
      2010-12-05
    • Related Report
      2010 Annual Research Report
  • [Presentation] 精密構造解析からみえるブルー銅タンパク質における弱い相互作用の効果2010

    • Author(s)
      浅村紗矢香, 他
    • Organizer
      第21回 日本化学会関東支部 茨城地区研究交流会
    • Place of Presentation
      日立
    • Year and Date
      2010-11-05
    • Related Report
      2010 Annual Research Report
  • [Presentation] 超高分解能X線結晶構造解析によるヘムタンパク質シトクロームc'の特異的構造変化2010

    • Author(s)
      高階明子, 他
    • Organizer
      第21回 日本化学会関東支部 茨城地区研究交流会
    • Place of Presentation
      日立
    • Year and Date
      2010-11-05
    • Related Report
      2010 Annual Research Report
  • [Presentation] 中性子結晶解析で見るビリン還元酵素のプロトンを使った反応機構2010

    • Author(s)
      海野昌喜
    • Organizer
      茨城県中性子利用促進研究会(生命物質構造研究会)合同研究会
    • Place of Presentation
      東京
    • Year and Date
      2010-10-01
    • Related Report
      2011 Final Research Report
  • [Presentation] 中性子結晶解析で見るビリン還元酵素のプロトンを使った反応機構2010

    • Author(s)
      海野昌喜
    • Organizer
      茨城県中性子利用促進研究会 生命物質構造解析研究会 合同研究会
    • Place of Presentation
      東京
    • Year and Date
      2010-10-01
    • Related Report
      2010 Annual Research Report
  • [Presentation] Ring Opening Mechanism of Verdoheme Catalyzed by Heme Oxygenase2010

    • Author(s)
      Toshitaka Matsui, Masaki Unno, Masao Ikeda-Saito
    • Organizer
      2010年日本生物物理学会第48回年会
    • Place of Presentation
      仙台
    • Year and Date
      2010-09-22
    • Related Report
      2011 Final Research Report 2010 Annual Research Report
  • [Presentation] Crystal Growth of Pcy A, a Ferredoxin-Dependent Billin Reductase, for Neutron Crystallographic Analysis2010

    • Author(s)
      Kumiko Ishikawa, Yoshinori Hagiwara, Kei Wada, Yuji Obara, Ryota Kuroki, Taro Tamada, Keiichi Fukuyama, Masaki Unno
    • Organizer
      2010年日本生物物理学会第48回年会
    • Place of Presentation
      仙台
    • Year and Date
      2010-09-22
    • Related Report
      2011 Final Research Report
  • [Presentation] Crystal Growth of PcyA, a Ferredoxin-Dependent Billin Reductase, for Neutron Crystallographic Analysis2010

    • Author(s)
      Kumiko Ishikawa, et al.
    • Organizer
      2010年日本生物物理学会第48回年会
    • Place of Presentation
      仙台
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] X-ray crystal structure analysis of a blue copper protein, pseudazurin at 1.35 A resolution2010

    • Author(s)
      Sayaka Asamura, et al.
    • Organizer
      2010年日本生物物理学会第48回年会
    • Place of Presentation
      仙台
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] Understanding of Nitric Oxide-Binding Mechanism of Cytochrome c' Based on Atomic Resolution Structure2010

    • Author(s)
      Masaki Unno
    • Organizer
      2010年日本生物物理学会第48回年会
    • Place of Presentation
      仙台
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] Atomic Resolution X-ray Crystallographic Analyses and Spectroscopic Studies of a Cytochrome c' from Alicaligenes Xylosoxidans2010

    • Author(s)
      Akiko Takashiha, et al.
    • Organizer
      2010年日本生物物理学会第48回年会
    • Place of Presentation
      仙台
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] カイニン酸受容体を制御する化合物~複合体結晶構造から見えたもの~2010

    • Author(s)
      海野昌喜
    • Organizer
      日本化学会 第4回関東支部会(2010)
    • Place of Presentation
      つくば
    • Year and Date
      2010-08-30
    • Related Report
      2010 Annual Research Report
  • [Presentation] 金属タンパク質の構造の信頼性について2010

    • Author(s)
      海野昌喜
    • Organizer
      第23回生物無機化学夏季セミナー
    • Place of Presentation
      河口湖
    • Year and Date
      2010-08-28
    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://www.fas.ibaraki.ac.jp/?page_id=827

    • Related Report
      2011 Final Research Report
  • [Remarks]

    • URL

      http://www.fas.ibaraki.ac.jp/?page_id=827

    • Related Report
      2011 Annual Research Report

URL: 

Published: 2010-08-23   Modified: 2016-04-21  

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