Structure and function of bacterial nitric oxide reductases: Nitric oxide reductase, anaerobic enzymes

Biochimica et Biophysica Acta - Bioenergetics

Volumn 1817, Issue 10, 2012, Pages 1907-1913

  Shiro, Yoshitsugu ^a  

^a RIKEN Harima Institute Research   (Japan)

Author keywords

Cytochrome oxidase; Denitrification; Greenhouse gas; NO reductase; Ozone depletion; Respiratory enzyme

Indexed keywords

BACTERIAL ENZYME; CYTOCHROME C OXIDASE; NITRIC OXIDE REDUCTASE;

AMINO ACID SEQUENCE; CATALYSIS; CONFERENCE PAPER; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; GEOBACILLUS STEAROTHERMOPHILUS; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTON TRANSPORT; PSEUDOMONAS AERUGINOSA; REDUCTION;

BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; ELECTRON TRANSPORT COMPLEX IV; GEOBACILLUS STEAROTHERMOPHILUS; NITRIC OXIDE; OXIDOREDUCTASES; OXYGEN; PROTEIN STRUCTURE, TERTIARY; PSEUDOMONAS AERUGINOSA; STRUCTURE-ACTIVITY RELATIONSHIP;

BACTERIA (MICROORGANISMS); GEOBACILLUS STEAROTHERMOPHILUS; PSEUDOMONAS AERUGINOSA;

EID: 84864711477     PISSN: 00052728     EISSN: 18792650     Source Type: Journal    
DOI: 10.1016/j.bbabio.2012.03.001     Document Type: Conference Paper

References (38)

1. W.G. Zumft Cell biology and molecular basis of denitrification Microbiol. Mol. Biol. Rev. 61 1997 533 616
2. W.G. Zumft Nitric oxide reductases of prokaryotes with emphasis on the respiratory, heme-copper oxidase type J. Inorg. Biochem. 99 2005 194 215
3. N.J. Watmough, S.J. Field, R.J. Hughes, and D.J. Richardson The bacterial respiratory nitric oxide reductase Biochem. Soc. Trans. 37 2009 392 399
4. J. Hendriks, A. Oubrie, J. Castresana, A. Urbani, S. Gemeinhardt, and M. Saraste Nitric oxide reductases in bacteria Biochim. Biophys. Acta 1459 2000 266 273
5. T.M. Stevanin, J.W. Moir, and R.C. Read Nitric oxide detoxification systems enhance survival of Neisseria meningitidis in human macrophages and in nasopharyngeal mucosa Infect. Immun. 73 2005 3322 3329
6. L. Philippot Denitrification in pathogenic bacteria: for better or worst? Trends Microbiol. 13 2005 191 192
7. A.R. Ravishankara, J.S. Daniel, and R.W. Portmann Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century Science 326 2009 123 125
8. D.E. Canfield, A.N. Glazer, and P.G. Falkowski The evolution and future of earth's nitrogen cycle Science 330 2010 192 196
9. M.J. Prather, and J. Hsu Coupling of nitrous oxide and methane by global atmospheric chemistry Science 330 2010 952 954
10. D.J. Wuebbles Atmosphere. Nitrous oxide: no laughing matter Science 326 2009 56 57
11. M. Saraste, and J. Castresana Cytochrome oxidase evolved by tinkering with denitrification enzymes FEBS Lett. 341 1994 1 4
12. J. van der Oost, A.P. de Boer, J.W. de Gier, W.G. Zumft, A.H. Stouthamer, and R.J. van Spanning The heme-copper oxidase family consists of three distinct types of terminal oxidases and is related to nitric oxide reductase FEMS Microbiol. Lett. 121 1994 1 9
13. T. Fujiwara, and Y. Fukumori Cytochrome cb-type nitric oxide reductase with cytochrome c oxidase activity from Paracoccus denitrificans ATCC 35512 J. Bacteriol. 178 1996 1866 1871
14. A. Giuffre, G. Stubauer, P. Sarti, M. Brunori, W.G. Zumft, G. Buse, and T. Soulimane The heme-copper oxidases of Thermus thermophilus catalyze the reduction of nitric oxide: evolutionary implications Proc. Natl. Acad. Sci. U. S. A. 96 1999 14718 14723
15. T. Hayashi, M.T. Lin, K. Ganesan, Y. Chen, J.A. Fee, R.B. Gennis, and P. Moenne-Loccoz Accommodation of two diatomic molecules in cytochrome bo: insights into NO reductase activity in terminal oxidases Biochemistry 48 2009 883 890
16. T. Hino, Y. Matsumoto, S. Nagano, H. Sugimoto, Y. Fukumori, T. Murata, S. Iwata, and Y. Shiro Structural basis of biological N2O generation by bacterial nitric oxide reductase Science 330 2010 1666 1670
17. Y. Matsumoto, T. Tosha, A.V. Pisliakov, T. Hino, H. Sugimoto, S. Nagano, Y. Sugita, and Y. Shiro Crystal Structure of Quinol-dependent Nitric Oxide Reductase from Geobacillus Stearothermophilus Nat. Struct. Mol. Biol. 19 2012 238 245
18. U. Flock, F.H. Thorndycroft, A.D. Matorin, D.J. Richardson, N.J. Watmough, and P. Adelroth Defining the proton entry point in the bacterial respiratory nitric-oxide reductase J. Biol. Chem. 283 2008 3839 3845
19. G. Butland, S. Spiro, N.J. Watmough, and D.J. Richardson Two conserved glutamates in the bacterial nitric oxide reductase are essential for activity but not assembly of the enzyme J. Bacteriol. 183 2001 189 199
20. F.H. Thorndycroft, G. Butland, D.J. Richardson, and N.J. Watmough A new assay for nitric oxide reductase reveals two conserved glutamate residues form the entrance to a proton-conducting channel in the bacterial enzyme Biochem. J. 401 2007 111 119
21. U. Flock, P. Lachmann, J. Reimann, N.J. Watmough, and P. Adelroth Exploring the terminal region of the proton pathway in the bacterial nitric oxide reductase J. Inorg. Biochem. 103 2009 845 850
22. S. Buschmann, E. Warkentin, H. Xie, J.D. Langer, U. Ermler, and H. Michel The structure of cbb3 cytochrome oxidase provides insights into proton pumping Science 329 2010 327 330
23. S. Iwata, C. Ostermeier, B. Ludwig, and H. Michel Structure at 2.8 A resolution of cytochrome c oxidase from Paracoccus denitrificans Nature 376 1995 660 669
24. T. Tsukihara, H. Aoyama, E. Yamashita, T. Tomizaki, H. Yamaguchi, K. Shinzawa-Itoh, R. Nakashima, R. Yaono, and S. Yoshikawa The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A Science 272 1996 1136 1144
25. T. Soulimane, G. Buse, G.P. Bourenkov, H.D. Bartunik, R. Huber, and M.E. Than Structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from Thermus thermophilus EMBO J. 19 2000 1766 1776
26. P. Moenne-Loccoz Spectroscopic characterization of heme iron-nitrosyl species and their role in NO reductase mechanisms in diiron proteins Nat. Prod. Rep. 24 2007 610 620
27. R.A. Steiner, I.M. Kooter, and B.W. Dijkstra Functional analysis of the copper-dependent quercetin 2,3-dioxygenase. 1. Ligand-induced coordination changes probed by X-ray crystallography: inhibition, ordering effect, and mechanistic insights Biochemistry 41 2002 7955 7962
28. F. Fusetti, K.H. Schroter, R.A. Steiner, P.I. van Noort, T. Pijning, H.J. Rozeboom, K.H. Kalk, M.R. Egmond, and B.W. Dijkstra Crystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus Structure 10 2002 259 268
29. P. Moenne-Loccoz, O.-M.H. Richter, H.W. Huang, I.M. Wasser, R.A. Ghiladi, K.D. Karlin, and S. de Vries Nitric oxide reductase from Paracoccus denitrificans contains an oxo-bridged heme/non-heme diiron center J. Am. Chem. Soc. 122 2000 9344 9345
30. P. Moenne-Loccoz, and S. de Vries Structural characterization of the catalytic high-spin heme b of nitric oxide reductase: a resonance Raman study J. Am. Chem. Soc. 120 1998 5147 5152
31. E. Pinakoulaki, S. Gemeinhardt, M. Saraste, and C. Varotsis Nitric-oxide reductase. Structure and properties of the catalytic site from resonance Raman scattering J. Biol. Chem. 277 2002 23407 23413
32. H. Kumita, K. Matsuura, T. Hino, S. Takahashi, H. Hori, Y. Fukumori, I. Morishima, and Y. Shiro NO reduction by nitric-oxide reductase from denitrifying bacterium Pseudomonas aeruginosa: characterization of reaction intermediates that appear in the single turnover cycle J. Biol. Chem. 279 2004 55247 55254
33. J.P. Shapleigh, and W.J. Payne Nitric oxide-dependent proton translocation in various denitrifiers J. Bacteriol. 163 1985 837 840
34. L.C. Bell, D.J. Richardson, and S.J. Ferguson Identification of nitric oxide reductase activity in Rhodobacter capsulatus: the electron transport pathway can either use or bypass both cytochrome c2 and the cytochrome bc1 complex J. Gen. Microbiol. 138 1992 437 443
35. J. Reimann, U. Flock, H. Lepp, A. Honigmann, and P. Adelroth A pathway for protons in nitric oxide reductase from Paracoccus denitrificans Biochim. Biophys. Acta 1767 2007 362 373
36. J.H. Hendriks, A. Jasaitis, M. Saraste, and M.I. Verkhovsky Proton and electron pathways in the bacterial nitric oxide reductase Biochemistry 41 2002 2331 2340
37. J. Hemp, H. Han, J.H. Roh, S. Kaplan, T.J. Martinez, and R.B. Gennis Comparative genomics and site-directed mutagenesis support the existence of only one input channel for protons in the C-family (cbb3 oxidase) of heme-copper oxygen reductases Biochemistry 46 2007 9963 9972
38. T. Tsukihara, K. Shimokata, Y. Katayama, H. Shimada, K. Muramoto, H. Aoyama, M. Mochizuki, K. Shinzawa-Itoh, E. Yamashita, M. Yao, Y. Ishimura, and S. Yoshikawa The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process Proc. Natl. Acad. Sci. U. S. A. 100 2003 15304 15309