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Crystallographic Studies on the Short-lived Respiratory Enzyme-Substrate Complex

Research Project

Project/Area Number 19310147
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Living organism molecular science
Research InstitutionThe Institute of Physical and Chemical Research

Principal Investigator

NAGANO Shingo  The Institute of Physical and Chemical Research, 工学研究科, 教授 (60286440)

Co-Investigator(Kenkyū-buntansha) 城 宜嗣  独立行政法人理化学研究所, 城生体金属科学研究室, 主任研究員 (70183051)
松本 悠史  独立行政法人理化学研究所, 城生体金属科学研究室, 協力研究員 (40443030)
平野 聡  独立行政法人理化学研究所, 城生体金属科学研究室, 協力研究員 (10446528)
日野 智也  独立行政法人理化学研究所, 城生体金属科学研究室, 客員研究員 (40373360)
Project Period (FY) 2007 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥19,370,000 (Direct Cost: ¥14,900,000、Indirect Cost: ¥4,470,000)
Fiscal Year 2009: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
Fiscal Year 2008: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2007: ¥14,820,000 (Direct Cost: ¥11,400,000、Indirect Cost: ¥3,420,000)
Keywords呼吸 / 分子進化 / ヘム / 窒素循環 / 呼吸酵素 / 結晶構造
Research Abstract

Nitric oxide reductase (NOR) is an iron-containing enzyme that catalyzes the reduction of nitric oxide (NO) to generate a major greenhouse gas, nitrous oxide (N_2O). In this study, we report the crystal structures of cNOR from Pseudomonas aeruginosa at 2.7 angstrom resolution and qNOR from Geobacillus stearothermophilus at 2.5 angstrom resolution. Although the overall structure of these NORs are closely related to cytochrome oxidase (COX), neither the D- nor K-proton pathway, which connect the COX active center to the intracellular space, was observed. Protons required for the cNOR reaction are probably provided from the extracellular side. On the contrary, qNOR has potential proton channel from the cytoplasmic side to the active center.

Report

(4 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (38 results)

All 2011 2010 2009 2008 2007 Other

All Journal Article (15 results) (of which Peer Reviewed: 14 results) Presentation (18 results) Book (3 results) Remarks (2 results)

  • [Journal Article] Structural Basis of Biological N_20 Generation by Bacterial Nitric Oxide Reductase2011

    • Author(s)
      Hino, T., Matsumoto, Y., Nagano, S., Sugimoto, H., Fukumori, Y., Murata, T., Iwata, S., Shiro, Y.
    • Journal Title

      Science 330

      Pages: 1666-1670

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural Basis of Biological N_2O Generation by Bacterial Nitric Oxide Reductase2011

    • Author(s)
      Tomoya Hino
    • Journal Title

      Science

      Volume: 330 Pages: 1666-1670

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Understanding substrate misrecognition of hydrogen peroxide dependent cytochrome P450 from Bacillus subtilis2010

    • Author(s)
      Shoji, O., Fujishiro, T., Nagano, S., Tanaka, S., Hirose, T., Shiro, Y., Watanabe, Y.
    • Journal Title

      J.Biol.Inorg.Chem. 2010, 15

      Pages: 1331-1339

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Understanding substrate misrecognition of hydrogen peroxide dependent cytochrome P450 from Bacillus subtilis2010

    • Author(s)
      Osami Shoji
    • Journal Title

      J.Biol.Inorg.Chem.

      Volume: 15 Pages: 1331-1339

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical and Experimental Studies of the Conversion of Chromopyrrolic Acid to an Antitumor Derivative by Cytochrome P450 StaP : The Biological Role of Water Molecules2009

    • Author(s)
      Wang, Y., Chen, H., Makino, M., Shiro, Y., Na ang o, S., Asamizu, S., Onaka, H., Sason, S.
    • Journal Title

      J. Am.Chem.Soc 131

      Pages: 6748-6762

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Electron transfer activation of chromopyrrolic acid by cytochrome P450 En route to the formation of an antitumor indolocarbazole derivative : Theory supports experiment2008

    • Author(s)
      Wang, Y., Hirao, H., Chen, H., Onaka, H., Nagano, S., Shaik, S.
    • Journal Title

      J.Am.Chem.Soc. 130

      Pages: 7170-7171

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular design of heteroprotein assemblies providing a bionanocup as a chemical reactor2008

    • Author(s)
      Koshiyama, T., Yokoi, N., Ueno, T., Kanamaru, S., Nagano, S., Shiro, Y., Arisaka, F., Watanabe, Y.
    • Journal Title

      Small 4

      Pages: 50-54

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of VioE, a key player in the construction of the molecular skeleton of violacein2008

    • Author(s)
      Hirano, S., Asamizu, S., Onaka, H., Shiro, Y., Nagano, S.
    • Journal Title

      J.Biol.Chem. 283

      Pages: 6459-6466

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Electron Transfer Activation of Chromopyrrolic Acid by Cytochrome P450 En Route to the Formation of an Antitumor Indolocarbazole Derivative : Theory Supports Experiment2008

    • Author(s)
      Wang
    • Journal Title

      J. Am. Chem. Soc. 130

      Pages: 7170-7171

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of VioE,a key player in the construction of the molecular skeleton of violacein2008

    • Author(s)
      Satoshi Hirano
    • Journal Title

      J.Biol.Chem (in press)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 抗がん剤のインドロカルバゾール骨格を作るP450の電子引き抜き反応2008

    • Author(s)
      尾仲 宏康
    • Journal Title

      バイオサイエンスとインダストリー 66

      Pages: 22-24

    • Related Report
      2007 Annual Research Report
  • [Journal Article] Crystal structures and catalytic mechanism of cytochrome P450 StaP that produces the indolocarbazole skeleton2007

    • Author(s)
      Makino, M., Sugimoto, H., Shiro, Y., Asamizu, S., Onaka, H., Nagano, S.
    • Journal Title

      Proc.Natl.Acad.Sci.U.S.A. 104

      Pages: 11591-11596

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Hydrogen peroxide dependent monooxygenations by tricking the substrate recognition of cytochrome P450(BSβ)2007

    • Author(s)
      Shoji, O., Fujishiro, T., Nakajima, H., Kim, M., Nagano, S., Shiro, Y., Watanabe, Y.
    • Journal Title

      Angew.Chem.Int Ed. 46

      Pages: 656-3659

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structures and catalytic mechanism of cytochrome P450 StaP that produces the indolocarbazole skeleton2007

    • Author(s)
      Masatomo Makino
    • Journal Title

      Proc.Natl.Acad.Sci.USA 104

      Pages: 11591-11596

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Hydrogen peroxide dependent monooxygenations by tricking the substrate regognition of cytochrome P450(BS beta)2007

    • Author(s)
      Osami Shoji
    • Journal Title

      Angew.Chem.Int.Ed 46

      Pages: 3656-3659

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] 抗がん剤インドロカルバゾールの基本骨格を構築するP450 StaPの結晶構造解析と反応機構2010

    • Author(s)
      永野真吾
    • Organizer
      BMB2010
    • Place of Presentation
      横浜国際会議場
    • Year and Date
      2010-12-10
    • Related Report
      2009 Annual Research Report
  • [Presentation] 嫌気呼吸系の一酸化窒素還元酵素の構造と分子進化2010

    • Author(s)
      永野真吾
    • Organizer
      第10回日本蛋白質科学会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2010-06-17
    • Related Report
      2009 Annual Research Report
  • [Presentation] BMB2010ワークショップ2010

    • Author(s)
      永野真吾
    • Organizer
      P40および抱合酵素の新たな機能とその応用技術における最近の展開「抗がん剤インドロカルバゾールの基本骨格を構築するP450StaPの結晶構造解析と反応機構」
    • Related Report
      2009 Final Research Report
  • [Presentation] 第10回日本蛋白質科学会ワークショップ2010

    • Author(s)
      永野真吾
    • Organizer
      金属蛋白質の新展開:生体金属のセンシング,輸送と利用「嫌気呼吸系の-酸化窒素還元酵素の構造と分子進化」
    • Related Report
      2009 Final Research Report
  • [Presentation] シトクロムP450の多彩な機能発現の仕組みを構造から理解する2010

    • Author(s)
      永野真吾
    • Organizer
      日本生化学会北海道支部講演会
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] 徳島若手研究者による生体金属分子分光学の新展開「短寿命な気体分子・金属酵素複合体の分子科学の展開を目指して」2010

    • Author(s)
      永野真吾
    • Organizer
      第47回日本生物物理学会
    • Related Report
      2009 Final Research Report
  • [Presentation] 14^<th)International Conference on Biological Inorganic Chemistry (ICBIC14), Nagoya,2010

    • Author(s)
      永野真吾
    • Organizer
      Japan "Structure and Mechanism of Enzymes Involved in Indolocarbazole Biosynthesis".
    • Related Report
      2009 Final Research Report
  • [Presentation] 16^<th>Intemational Conference on Cytochorme P450.2009

    • Author(s)
      永野真吾
    • Organizer
      Okinawa, Japan. "Structure and Chemistry of Enzymes Involved in Indolocarbazole Biosynthesis"
    • Related Report
      2009 Final Research Report
  • [Presentation] 若手研究者が語る次世代生物無機化学「インドロカルバゾール生合成酵素群の構造と化学」9^<th>International Symposium on Cytochrome P450 Biodiversity and Biotechnology. Nice, France "Structure and Catalytic Mechanism of P450StaP, a Key Enzyme in Indolocarbazole Biosynthesis" Nagano, S.2009

    • Author(s)
      永野真
    • Organizer
      日本化学会第89春季年会
    • Related Report
      2009 Final Research Report
  • [Presentation] インドロカルバゾール系天然物の骨格構造を構築する酵素の構造と機能2008

    • Author(s)
      永野真吾
    • Organizer
      第81回日本生化学会大会第31回日本分子生物学会年会合同大会
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2008-12-10
    • Related Report
      2008 Annual Research Report
  • [Presentation] インドロカルバゾール系生理活性物質の分子骨格を構築するシトクロムP450StaPの構造と反応メカニズム2008

    • Author(s)
      永野真吾
    • Organizer
      第58回錯体化学討論会
    • Place of Presentation
      金沢大学
    • Year and Date
      2008-09-21
    • Related Report
      2008 Annual Research Report
  • [Presentation] インドール含有生理活性物質生合成酵素群の結晶構造解析2008

    • Author(s)
      永野真吾
    • Organizer
      第22回内藤コンファレンス
    • Place of Presentation
      シャトレーゼガトーキングダム札幌
    • Year and Date
      2008-09-11
    • Related Report
      2008 Annual Research Report
  • [Presentation] Structure and mechanism of P450 StaP, a key enzyme in indolocarbazole biosynthesis2008

    • Author(s)
      永野真吾
    • Organizer
      9th international symposium on cytochrome P450 biodiversity and biotechnology
    • Place of Presentation
      Nice, France
    • Year and Date
      2008-06-09
    • Related Report
      2008 Annual Research Report
  • [Presentation] 冨山インドロカルバゾールの骨格構造を作るシトクロムP450StaPの結晶構造と反応機構:抗がん剤とペルオキシダーゼの意外な接点2008

    • Author(s)
      永野真吾
    • Organizer
      第10回P450研究会
    • Related Report
      2009 Final Research Report
  • [Presentation] 膜貫通型-酸化窒素還元酵素の発現と結晶化2007

    • Author(s)
      松本 悠史
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      横浜
    • Year and Date
      2007-12-23
    • Related Report
      2007 Annual Research Report
  • [Presentation] 抗がん剤の骨格を形成するチトクロムP450 StaPのX線結晶構造はP450の珍しい触媒機構を示唆する2007

    • Author(s)
      牧野 正知
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      横浜
    • Year and Date
      2007-12-23
    • Related Report
      2007 Annual Research Report
  • [Presentation] Identification of an active site of VioE,which constructs a violacein skeleton,by crystallographic and mutagenesis analyses2007

    • Author(s)
      平野 聡
    • Organizer
      第30回日本分子生物学会年会・第80回日本生化学会大会合同大会
    • Place of Presentation
      横浜
    • Year and Date
      2007-12-11
    • Related Report
      2007 Annual Research Report
  • [Presentation] Crystal Structure of Cytochrome P450 StaP-Chromopyrrolic Acid Complex:Implications for Indolocarbazole Core Biosynthesis2007

    • Author(s)
      Masatomo Makino
    • Organizer
      15^<th>International Conference on Cytochrome P450
    • Place of Presentation
      Bled,Slovenia
    • Year and Date
      2007-06-18
    • Related Report
      2007 Annual Research Report
  • [Book] HandbookofPorphyrinScience, Kadish,K.,Smith,K.,Guilard,R.Eds. Vol.V,Chapter25. World Scientific.(著書)2010

    • Author(s)
      Shiro,y., Nagano,s.
    • Publisher
      No Chemistry by Heme Enzymes
    • Related Report
      2009 Final Research Report
  • [Book] Handbook of Porphyrin Science2010

    • Author(s)
      Yoshitsugu Shiro
    • Publisher
      World Scientific
    • Related Report
      2009 Annual Research Report
  • [Book] P450の分子構造:X線結晶構造解析を中心に(著書P450の分子生物学第二版)2009

    • Author(s)
      永野真吾、杉本宏、城宜嗣
    • Publisher
      講談社サイエンティフィク
    • Related Report
      2009 Final Research Report
  • [Remarks] ホームページ等

    • URL

      http://www.bio.tottori-u.ac.jp/~bioeng/

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://www.bio.tottori-u.ac.jp/~bioeng/

    • Related Report
      2009 Annual Research Report

URL: 

Published: 2007-04-01   Modified: 2016-04-21  

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