Molecular Evolution of Respiratory Enzymes; Functional Conversion from NO Reduction to O2 Reduction

2012 Fiscal Year Final Research Report

• Project/Area Number: 21245041
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Chemistry related to living body
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: SHIRO Yoshitsugu 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)
• Co-Investigator(Renkei-kenkyūsha): SUGIMOTO Hiroshi 独立行政法人理化学研究所, 城生体金属科学研究室, 専任研究員 (90344043) ; KIKUCHI Akihiro 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 (90321752) ; NAGANO Shingo 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 (60286440) ; TOSHA Takehiro 独立行政法人理化学研究所, 城生体金属科学研究室, 専任研究員 (00548993)
• Project Period (FY): 2009 – 2012
• Keywords: 一酸化窒素 / 呼吸酵素 / 脱窒 / 亜酸化窒素 / 温室効果ガス / オゾン層破壊 / 分子進化

Research Abstract

Nitric oxide reductase (NOR) is a key enzyme of anaerobic respiration, which catalyzes decomposition of cyt-toxic NO to N_2O. We determined the crystal structures of the membrane-integrated enzymes, cNOR from P. aeruginosa and qNOR from G. stearothermophillus. On the basis of these structures, we proposed the molecular mechanism of the enzymatic NO reduction and the proton transfer, and discussed the molecular evolution of the respiratory enzymes from anaerobic to aerobic systems.

Research Products

• [Journal Article] Crystal Structures of Nitric Oxide Reductases Provide Key Insights into Functional Conversion of Respiratory Enzymes (2013)
  • Author(s): T. Tosha, Y. Shiro
  • Journal Title: IUBMB (International Union of Biochemistry and Molecular Biology) Volume: Life 65 Pages: 217-226
• [Journal Article] Crystal Structure of Quinol-Dependent Nitric Oxide Reductase from Geobacillus Stearothermophilus (2012)
  • Author(s): Y. Matsumoto, T. Tosha, A. V. Pisliakov, T. Hino, H. Sugimoto, S. Nagano, Y. Sugita, Y. Shiro
  • Journal Title: Nat. Strl. Mol. Biol Volume: 19 Pages: 238-245
  • Peer Reviewed
• [Journal Article] Molecular Dynamic Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase (2012)
  • Author(s): A. V. Pisliakov, T. Hino, Y. Shiro, Y. Sugita
  • Journal Title: POLS Comp. Biol Volume: 8 Pages: e1002674
  • Peer Reviewed
• [Journal Article] Structural Basis for Oxygen Sensing and Signal Transduction of the Heme-Based Sensor Protein Aer2 from Pseudomonas aeruginosa (2012)
  • Author(s): H. Sawai, H. Sugimoto, Y. Shiro, H. Ishikawa, Y. Mizutani, S. Aono
  • Journal Title: Chem. Commun Volume: 48 Pages: 6523-6525
  • DOI: doi: 10.1039/c2cc32549g
  • Peer Reviewed
• [Journal Article] Interactions of Soluble Guanylate Cyclase with a P-Site Inhibitor: Effects of Gaseous Heme Ligands, Azide, and Allosteric Activators on the Binding of 2'-Deoxy-3'-GMP (2012)
  • Author(s): R. Makino, S. Yazawa, H. Hori, Y. Shiro
  • Journal Title: Biochemistry Volume: 51 Pages: 9277-9289
  • Peer Reviewed
• [Journal Article] Coupling Reaction of Indolepyruvic Acid by StaD and Its Product: Implications of Biosynthesis of Indolocarbazole and Violacein (2012)
  • Author(s): S. Asamizu, S. Hirano, H. Onaka, H. Koshino, Y. Shiro, S. Nagano
  • Journal Title: ChemBioChem Volume: 13 Pages: 2495-2500
  • Peer Reviewed
• [Journal Article] Chiral Substrate Analogues Assisted Stereoselective Epoxidation Catalyzed by H_2O_2-Dependent Cytochrome P450SPa (2012)
  • Author(s): T. Fujishiro, O. Shoji, N. Kawakami, T. Watanabe, H. Sugimoto, Y. Shiro, Y. Watanabe
  • Journal Title: Chem. Asian J Volume: 7 Pages: 2286-2293
  • Peer Reviewed
• [Journal Article] Molecular Structures and Mechanism of Bacterial Nitric Oxide Reductase (2012)
  • Author(s): T. Hino, S. Nagano, H. Sugimoto, T. Tosha, Y. Shiro
  • Journal Title: Special Issue on Respiratory Oxidases in Biochim Volume: Biophys. Acta - Bioenergetics 1817 Pages: 680-687
• [Journal Article] Proton Transfer in the Quinol-dependent Nitric Oxide Reductase from Geobacillus stearothermophilus during Reduction of Oxygen (2012)
  • Author(s): L. Salomonsson, J. Reimann, T. Tosha, N. Krause, N. Gonska, Y. Shiro, P. Adelroth
  • Journal Title: Special Issue on Respiratory Oxidases in Biochim Volume: Biophys. Acta - Bioenergetics 1817 Pages: 1914-1920
• [Journal Article] "Structural Basis for Nitrous Oxide Generation by Bacterial Nitric Oxide Reductases" the Proceedings of the Royal Society Meeting (2012)
  • Author(s): Y. Shiro, H. Sugimoto, T. Tosha, S. Nagano, T. Hino
  • Journal Title: 'Nitrous oxide, the forgotten greenhouse gas', Philosophical Transactions B, The Royal Society Volume: 367 Pages: 1195-1203
• [Journal Article] "Structure and Function of Bacterial Nitric Oxide Reductases, Anaerobic Enzymes" Special Issue on European BioEnergetic Conference 2012 in Biochim (2012)
  • Author(s): Y. Shiro
  • Journal Title: Biophys. Acta - Bioenergetics Volume: 1817 Pages: 1907-1913
• [Journal Article] 一酸化窒素還元酵素の結晶構造から見えてきた呼吸酵素の機能変換 (2012)
  • Author(s): 日野智也、當舍武彦、城 宜嗣
  • Journal Title: 生物物理 Volume: Vol 52 Pages: 186-189
• [Journal Article] Application of Micro-reactor Chip Technique for Millisecond Quenching of Deuterium Incorporation into 70S Ribosomal Protein Complex (2011)
  • Author(s): T. Yamamoto, Y. Shimizu, T. Ueda, Y. Shiro, M. Suematsu
  • Journal Title: Intl. J. Mass Spectrometry Volume: 302 Pages: 132-138
  • Peer Reviewed
• [Journal Article] Oxygen Binding and Redox Properties of the Heme in Soluble Guanylate Cyclase : Implications for the Mechanism of Ligand Discrimination (2011)
  • Author(s): R. Makino, S.-Y. Park, E. Obayashi, T. Iizuka, H. Hori, Y. Shiro
  • Journal Title: J. Biol. Chem Volume: 286 Pages: 15678-15687
  • Peer Reviewed
• [Journal Article] Crystal Structure of Carbonmonoxide Complex of Human Cytoglobin (2011)
  • Author(s): M. Makino, H. Sawai, Y. Shiro, H. Sugimoto
  • Journal Title: PROTEINS Volume: 79 Pages: 1143-1153
  • Peer Reviewed
• [Journal Article] Characterization and Functional Modification of StaC and RebC, Which are Involved in Pyrrole Oxidation of Indolocarbazole Biosynthesis (2011)
  • Author(s): S. Asamizu, Y. Shiro, Y. Igarashi, S. Nagano, H. Onaka
  • Journal Title: Biosci. Biotechnol. Biochem Volume: 75 Pages: 2184-2193
  • Peer Reviewed
• [Journal Article] Crystal Structure of H_2O_2-dependent Cytochrome P450_<SPa> with Its Bound Fatty Acid Substrate: Insight into the Regioselective Hydroxylation of Fatty Acids at the a Position (2011)
  • Author(s): T. Fujishiro, O. Shoji, S. Nagano, H. Sugimoto, Y. Shiro, Y. Watanabe
  • Journal Title: J. Biol. Chem Volume: 286 Pages: 29941-29950
  • Peer Reviewed
• [Journal Article] Resonance Raman study on the oxygenated and the ferryl-oxo species of indoleamine 2,3-dioxygenase during catalytic turnover (2011)
  • Author(s): S. Yanagisawa, M. Horitani, H. Sugimoto, Y. Shiro, N. Okada, T. Ogura
  • Journal Title: Faraday Discuss Volume: 1814 Pages: 249-256
  • Peer Reviewed
• [Journal Article] 一酸化窒素還元酵素NOR ―呼吸酵素の分子進化と温室効果ガスの産生メカニズム― (2011)
  • Author(s): 日野智也、城 宜嗣
  • Journal Title: 化学 Volume: Vol 66 Pages: 30-35
• [Journal Article] Unique Properties and reactivity of High-Valent Manganese-Oxo versus Manganese-Hydroxo in the Salen Platform (2010)
  • Author(s): T. Kurahashi, A. Kikuchi, Y. Shiro, M. Hada, H. Fujii
  • Journal Title: Inorg. Chem Volume: 49 Pages: 6664-6672
  • Peer Reviewed
• [Journal Article] Three-step Hydroxylations of Vitamin D_3 by a Genetically Engineered CYP105A1 (2010)
  • Author(s): K. Hayashi, K. Yasuda, H. Sugimoto, S. Ikushiro, M. Kamakura, A. Kittaka, R. Horst, T. Chen, M. Ohta, Y. Shiro, T. Sakaki
  • Journal Title: FEBS Lett Volume: 277 Pages: 3999-4009
  • Peer Reviewed
• [Journal Article] Design of Novel Hypoxia-targeting IDO Hybrid Inhibitors Conjugated with an Unsubstituted L-TRP as an IDO Affinity Moiety (2010)
  • Author(s): H. Nakashima, K. Ikkyu, K. Nakashima, K. Sano, Y. Uto, E. Nakata, H. Nagasawa, H. Sugimoto, Y. Shiro, Y. Nakagawa, H. Hori
  • Journal Title: Adv. Exp. Med. Biol Volume: 662 Pages: 415-421
  • Peer Reviewed
• [Journal Article] Bioconversion of Vitamin D to Its Active Form by Bacterial or Mammalian Cytochromes P450 (2010)
  • Author(s): T. Sakaki, H. Sugimoto, K. Hayashi, K. Yasuda, E. Munetsna, M. Kamakura, S. Ikushiro, Y. Shiro
  • Journal Title: Biochim. Biophys. Acta Volume: 1814 Pages: 249-256
  • Peer Reviewed
• [Journal Article] A novel Glycerophosphodiester Phosphodiesterase GDE5 Controls Skeletal Muscle Development via a Non-enzymatic Mechanism (2010)
  • Author(s): Y. Okazaki, N. Ohshima, I. Yoshizawa, Y. Kamei, S. Mariggio, K. Okamoto, M. Maeda, Y. Nogusa, Y. Fujioka, T. Izumi, Y. Ogawa, Y. Shiro, M. Wada, N. Kato, D. Corda, N. Yanaka
  • Journal Title: J. Biol. Chem Volume: 285 Pages: 27652-27663
  • Peer Reviewed
• [Journal Article] ONIOM Study on a Missing Piece in Our Understanding of Heme Chemistry: Bacterial Tryptophan 2,3-Dioxygenase with Dual Oxidants (2010)
  • Author(s): L. W. Chung, X. Li, H. Sugimoto, Y. Shiro, K. Morokuma
  • Journal Title: J. Am. Chem. Soc Volume: 132 Pages: 11993-12005
  • Peer Reviewed
• [Journal Article] Understanding Substrate Misrecognition of Hydrogen Peroxide-Dependent Cytochrome P450 from Bacillus subtilis (2010)
  • Author(s): O. Shoji, T. Fujishiro, S. Nagano, S. Tanaka, T. Hirose, Y. Shiro, Y. Watanabe
  • Journal Title: J. Bio. Inorg. Chem Volume: 15 Pages: 1331-1339
  • Peer Reviewed
• [Journal Article] A Specific Interaction of L-Tryptophan with CO of CO-Bound Indoleamine 2,3-Dioxygenase Identified by Resonance Raman Spectroscopy (2010)
  • Author(s): S. Yanagisawa, H. Sugimoto, Y. Shiro, T. Ogura
  • Journal Title: Biochemistry Volume: 49 Pages: 10081-10088
  • Peer Reviewed
• [Journal Article] Structural Basis of Biological N2O Generation by Bacterial Nitric Oxide Reductase (2010)
  • Author(s): T. Hino, Y. Matsumoto, S. Nagano, H. Sugimoto, Y. Fukumori, T. Murata, S. Iwata, Y. Shiro
  • Journal Title: Science Volume: 330 Pages: 1666-1670
  • Peer Reviewed
• [Journal Article] Mg^<2+> Dependence of 70S Ribosomal Protein Flexibility Revealed by Hydrogen/Deuterium Exchange and Mass Spectrometry (2010)
  • Author(s): T. Yamamoto, Y. Shimizu, T. Ueda, Y. Shiro
  • Journal Title: J. Biol. Chem Volume: 285 Pages: 5646-5652
  • Peer Reviewed
• [Journal Article] Excited States of Fluorescent Proteins, mKO and DsRed: Chromophore-protein Electrostatic Interaction Behind the Color Variations (2010)
  • Author(s): J. Hasegawa, Y. Ise, K. Fujimoto, A. Kikuchi, E. Fukumura, A. Miyawaki, Y. Shiro
  • Journal Title: J. Phys. Chem Volume: B 114 Pages: 2971-2979
  • Peer Reviewed
• [Journal Article] Cooperative Binding of L-Trp to Human Tryptophan 2,3-Dioxygenase: Resonance Raman Spectroscopic Analysis (2009)
  • Author(s): E. Fukumura, H. Sugimoto, Y. Misumi, T. Ogura, Y. Shiro
  • Journal Title: J. Biochem Volume: 145 Pages: 505-515
  • Peer Reviewed
• [Journal Article] Ligand Energy Controls the Heme-Fe Valence in Aqueous Myoglobins (2009)
  • Author(s): Y. Harada, M. Taguchi, Y. Miyajima, T. Tokushima, Y. Horikawa, A. Chainani, Y. Shiro, Y. Senba, H. Ohashi, H. Fukuyama, S. Shin
  • Journal Title: J. Phys. Soc. Jpn Volume: 78 Pages: 044802-1 - 5
  • Peer Reviewed
• [Journal Article] Crystal Structure of a New Cyan Fluorescent Protein and Its Blue-shifted Variants (2009)
  • Author(s): A. Kikuchi, E. Fukumura, S. Karasawa, Y. Shiro, A. Miyawaki
  • Journal Title: Biochemistry Volume: 48 Pages: 5276-5283
  • 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): Y. Wang, H. Chen, M. Makino, Y. Shiro, S. Nagano, S. Asamizu, H. Onaka, S. Sason
  • Journal Title: J. Am. Chem. Soc Volume: 131 Pages: 6748-6762
  • Peer Reviewed
• [Journal Article] Heme-dependent Autophosphorylation of a Heme Sensor Kinase, ChrS from Corynebacterium diphtheriae Reconstituted in Proteoliposomes (2009)
  • Author(s): Y. Ito, S. Nakagawa, A. Komagata, M. Ikeda-Saito, Y. Shiro, H. Nakamura
  • Journal Title: FEBS Lett Volume: 583 Pages: 2244-2248
  • Peer Reviewed
• [Journal Article] Structure of PAS-linked Histidine Kinase and the Response Regulator Complex (2009)
  • Author(s): S. Yamada, H. Sugimoto, M. Kobayashi, A. Ohno, H. Nakamura, Y. Shiro
  • Journal Title: Structure Volume: 17 Pages: 1333-1344
  • Peer Reviewed
• [Journal Article] X-ray Crystal Structure of the Michaelis Complex of Aldoxime Dehydratase (2009)
  • Author(s): H. Sawai, H. Sugimoto, Y. Kato, Y. Asano, Y. Shiro, S. Aono
  • Journal Title: J. Biol. Chem Volume: 284 Pages: 32089-32096
  • Peer Reviewed
• [Journal Article] Identification of the Fe-O_2 and the Fe=O Heme Species for Indoleamine 2,3-Dioxygenase during Catalytic Turnover (2009)
  • Author(s): S. Yanagisawa, K. Yotsuya, Y. Hashiwaki, M. Horitani, H. Sugimoto, Y. Shiro, E. H. Appelman, T. Ogura
  • Journal Title: Chem. Lett Volume: 39 Pages: 36-37
  • Peer Reviewed
• [Presentation] Functional Characterization of Some Hemoproteins Based on Their Molecular Structures (2012)
  • Author(s): Shiro, Y
  • Organizer: The First International Symposium on Biofunctional Chemistry (ISBC2012)
  • Place of Presentation: Tokyo
  • Year and Date: 20121128-30
• [Presentation] Functional Characterization of Some Hemoproteins Based on Their Molecular Structures (2012)
  • Author(s): Shiro, Y
  • Organizer: The 6^<th> Asian Biological Inorganic Chemistry Conference (AsBIC6)
  • Place of Presentation: Hong Kong, Plenary Lecture
  • Year and Date: 20121105-08
• [Presentation] Structural Basis for NO Reduction by Bacterial Nitric Oxide Reductases (2012)
  • Author(s): Shiro, Y
  • Organizer: 17^<th> European Bioenergetics Conference 2012 (EBEC 2012)
  • Place of Presentation: Freiburg, Germany
  • Year and Date: 20120915-20
• [Presentation] Molecular Structures and Mechanism of Bacterial Nitric Oxide Reductase (2012)
  • Author(s): Shiro, Y
  • Organizer: Seventh International Conference on Porphyrins and Phtalocyanines
  • Place of Presentation: Jeju, Korea
  • Year and Date: 20120701-06
• [Presentation] Iron in Biology (2011)
  • Author(s): Shiro, Y
  • Organizer: RIKEN - University of Liverpool Joint Symposium
  • Place of Presentation: Liverpool, UK
  • Year and Date: 20110913-15
• [Presentation] Molecular Structures and Mechanism of Bacterial Nitric Oxide Reductase (2011)
  • Author(s): Shiro, Y
  • Organizer: 15th International Conference of Biological Inorganic Chemistry
  • Place of Presentation: Vancouver, Canada, Keynote Lecture
  • Year and Date: 20110807-12
• [Presentation] Structural Basis for Nitrous Oxide Generation by Bacterial Nitric Oxide Reductases (2011)
  • Author(s): Shiro, Y
  • Organizer: Royal Society Theo Murphy Meetin
  • Place of Presentation: Buckinghamshire, UK
  • Year and Date: 20110523-24
• [Presentation] Molecular Structures and Mechanism of Bacterial Nitric Oxide Reductase (2011)
  • Author(s): Shiro, Y
  • Organizer: Mini-symposium on "Proton Transport across Biological Membranes" of the Royal Swedish Academy of Sciences
  • Place of Presentation: Stockholm, Sweden
  • Year and Date: 2011-06-14
• [Presentation] Molecular Structures and Mechanism of Bacterial Nitric Oxide Reductase (2011)
  • Author(s): Hino, T., Matsumoto, Y., Pisliakov, A., Nagano, S., Sugimoto, H., Sugita, Y., Shiro, Y
  • Organizer: Third Korea-Japan Seminars on Biomolecular Sciences - Experiments and Simulations
  • Place of Presentation: Jeju, Korea
  • Year and Date: 2011-02-28
• [Presentation] Two-Component Regulatory System: Cellular Signal Transduction Systems Sensing Exogenous Stimuli (2010)
  • Author(s): Shiro, Y., Nakamura, H., Ito, Y., Sugimoto, H
  • Organizer: 2010 International Chemical Congress of Paci.c Basin Societies
  • Place of Presentation: Honolulu, USA
  • Year and Date: 20101200
• [Presentation] Nitric Oxide Reductases: Chemistry of N-O bond Cleavage and N-N Bond Formation (2010)
  • Author(s): Shiro, Y., Hino, T., Matsumoto, Y., Nagano, S., Sugimoto, H., Tosha, T
  • Organizer: Sixth International Conference on Porphyrins and Phtalocyanines
  • Place of Presentation: New Mexico, USA
  • Year and Date: 20100704-09
• [Presentation] Structure and Function of Nitric Oxide Reductases; Chemistry of NO Reduction and N_2O Formation (2009)
  • Author(s): Shiro, Y
  • Organizer: 14th International Conference of Biological Inorganic Chemistry
  • Place of Presentation: Nagoya, Japan
  • Year and Date: 20090700
• [Presentation] Structure and Function of Nitric Oxide Reductases; Chemistry of NO Reduction and N_2O formation (2009)
  • Author(s): Shiro, Y
  • Organizer: 1st Korea-Japan Seminars on Biomolecular Sciences - Experiments and Simulations
  • Place of Presentation: Seoul, Korea
  • Year and Date: 20090200-0300
• [Book] in Handbook of Porphyrin Science (K. M. Kadish, K. M. Smith, R. Guilard, Eds.) Vol. 5, Chapter 24 (2011)
  • Author(s): H. Sugimoto, O. Takikawa, Y. Shiro
  • Total Pages: 71-122
  • Publisher: Tryptophan Catabolism by Heme Dioxygenases
• [Book] in Handbook of Porphyrin Science (K. M. Kadish, K. M. Smith, R. Guilard, Eds.) Vol. 5, Chapter 25 (2010)
  • Author(s): Y. Shiro, S. Nagano
  • Total Pages: 123-163
  • Publisher: NO Chemistry by Heme-Enzyme
• [Remarks]
  • URL: http://www.riken.jp/biometal/index.htm