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

• Project/Area Number: 22770096
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Structural biochemistry
• Research Institution: Ibaraki 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: ¥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.

Research Products

• [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
  • Peer Reviewed
• [Journal Article] S100 and S100 fused-type protein families in epidermal maturation with special focus on S100A3 in mammalian hair cuticles (2011)
  • Author(s): Kizawa, K., et al.
  • Journal Title: Biochimie Volume: 93 Issue: 12 Pages: 2038-2047
  • DOI: 10.1016/j.biochi.2011.05.028
  • Peer Reviewed
• [Journal Article] Binding and selectivity of the marine toxins neodysiherbaine A, and its synthetic analogues, to GluK1 and GIuK2 kainate receptors (2011)
  • 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
  • Peer Reviewed
• [Journal Article] Refined Crystal Structures of Human Ca^<2+>/Zn^<2+>-Binding S100 A3 Protein Characterized by Two Disulfide Bridges (2011)
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Dioxygen Activation for the Self-Degradation of Heme : Reaction Mechanism and Regulation of Heme Oxygenase (2010)
  • 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
  • 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
• [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
  • Peer Reviewed
• [Journal Article] Precise Structural and Functional Analyses of Cytochrome c' Revealed by Quantum Beams and Other Multiple Methods (2010)
  • Author(s): Unno, M., et al.
  • Journal Title: Photon Factory Activity Report 2009, PART B Volume: 27 Pages: 242-242
• [Journal Article] Structure-based Drug Design for Kainate-type Ionotropic Glutamate Receptors, GluK1 and GluK2, from Human Brain (2010)
  • Author(s): Unno, M., et al.
  • Journal Title: Photon Factory Activity Report 2009, PART B Volume: 27 Pages: 241-241
• [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
  • Peer Reviewed
• [Journal Article] Dioxygen Activation for the Self-Degradation of Heme : Reaction Mechanism and Regulation of Heme Oxygenase (2010)
  • Author(s): Matsui, T., et al.
  • Journal Title: Inorg.Chem. Volume: 49 Pages: 3602-3609
  • 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
• [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
• [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
• [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
• [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
• [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
• [Presentation] Precise X-ray Crystallographic Analysis of a Cytochrome c' from Alcalygenes xylosoxidans NCIMB 11015 (2010)
  • 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
• [Presentation] X-ray crystal analyses of a blue copper protein, pseudoazurin from Achoromobacter cycloclastes IAM1013 and its mutant proteins (2010)
  • 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
• [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
• [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
• [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
• [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
• [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
• [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
• [Presentation] Ring Opening Mechanism of Verdoheme Catalyzed by Heme Oxygenase (2010)
  • 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
• [Presentation] Crystal Growth of Pcy A, a Ferredoxin-Dependent Billin Reductase, for Neutron Crystallographic Analysis (2010)
  • 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
• [Presentation] Crystal Growth of PcyA, a Ferredoxin-Dependent Billin Reductase, for Neutron Crystallographic Analysis (2010)
  • 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
• [Presentation] X-ray crystal structure analysis of a blue copper protein, pseudazurin at 1.35 A resolution (2010)
  • 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
• [Presentation] Understanding of Nitric Oxide-Binding Mechanism of Cytochrome c' Based on Atomic Resolution Structure (2010)
  • 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
• [Presentation] Atomic Resolution X-ray Crystallographic Analyses and Spectroscopic Studies of a Cytochrome c' from Alicaligenes Xylosoxidans (2010)
  • 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
• [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
• [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
• [Remarks]
  • URL: http://www.fas.ibaraki.ac.jp/?page_id=827
• [Remarks]
  • URL: http://www.fas.ibaraki.ac.jp/?page_id=827