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

2009 Fiscal Year Final Research Report

• Project/Area Number: 19310147
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Living organism molecular science
• Research Institution: The 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)
• Project Period (FY): 2007 – 2009
• Keywords: 呼吸 / 分子進化 / ヘム / 窒素循環

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.

Research Products

• [Journal Article] Structural Basis of Biological N_20 Generation by Bacterial Nitric Oxide Reductase (2011)
  • 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
  • Peer Reviewed
• [Journal Article] Understanding substrate misrecognition of hydrogen peroxide dependent cytochrome P450 from Bacillus subtilis (2010)
  • 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
  • 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 Molecules (2009)
  • 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
  • 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 experiment (2008)
  • Author(s): Wang, Y., Hirao, H., Chen, H., Onaka, H., Nagano, S., Shaik, S.
  • Journal Title: J.Am.Chem.Soc. 130 Pages: 7170-7171
  • Peer Reviewed
• [Journal Article] Molecular design of heteroprotein assemblies providing a bionanocup as a chemical reactor (2008)
  • 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
  • Peer Reviewed
• [Journal Article] Crystal structure of VioE, a key player in the construction of the molecular skeleton of violacein (2008)
  • Author(s): Hirano, S., Asamizu, S., Onaka, H., Shiro, Y., Nagano, S.
  • Journal Title: J.Biol.Chem. 283 Pages: 6459-6466
  • Peer Reviewed
• [Journal Article] Crystal structures and catalytic mechanism of cytochrome P450 StaP that produces the indolocarbazole skeleton (2007)
  • 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
  • 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
  • Peer Reviewed
• [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」
  • Year and Date: 20101200
• [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
  • Year and Date: 20101000
• [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".
  • Year and Date: 20100700
• [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」
  • Year and Date: 20100600
• [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
  • Year and Date: 20100600
• [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"
  • Year and Date: 20090700
• [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
  • Year and Date: 20090300
• [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
  • Year and Date: 20080700
• [Book] HandbookofPorphyrinScience, Kadish,K.,Smith,K.,Guilard,R.Eds. Vol.V,Chapter25. World Scientific.(著書) (2010)
  • Author(s): Shiro,y., Nagano,s.
  • Total Pages: 123-163
  • Publisher: No Chemistry by Heme Enzymes
• [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
  • Total Pages: 35-45, 281-283
  • Publisher: 講談社サイエンティフィク
• [Remarks] ホームページ等
  • URL: http://www.bio.tottori-u.ac.jp/~bioeng/