• 1
    Ravishankara, A. R., Daniel, J. S., and Portmann R. W. ( 2009) Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century. Science 326, 123125.
  • 2
    Stevanin, T. M., Laver, J. R., Poole, R. K., Moir, J. W., and Read, R. C. ( 2007) Metabolism of nitric oxide by Neisseria meningitidis modifies release of NO-regulated cytokines and chemokines by human macrophages. Microbes Infect. 9, 981987.
  • 3
    Falsetta, M. L., Steichen, C. T., McEwan, A. G., Cho, C. M., Ketterer, M., et al. ( 2011) The composition and metabolic phenotype of Neisseria gonorrhoeae biofilms. Front. Microbiol. 2, 75.
  • 4
    Saraste, M. and Castresana, J. ( 1994) Cytochrome oxidase evolved by tinkering with denitrification enzymes. FEBS Lett. 341, 14.
  • 5
    Zumft, W. G. ( 2005) Nitric oxide reductases of prokaryotes with emphasis on the respiratory, heme-copper oxidase type. J. Inorg. Biochem. 99, 194215.
  • 6
    Ducluzeau, A. L., van Lis, R., Duval, S., Schoepp-Cothenet, B., Russell, M. J. et al. ( 2009) Was nitric oxide the first deep electron sink? Trends. Biochem. Sci. 34, 915.
  • 7
    Pereira, M. M., Santana, M., and Teixeira, M. ( 2001) A novel scenario for the evolution of haem-copper oxygen reductases. Biochim. Biophys. Acta 1505, 185208.
  • 8
    Fujiwara, T. and Fukumori Y. ( 1996) Cytochrome cb-type nitric oxide reductase with cytochrome c oxidase activity from Paracoccus denitrificans ATCC 35512. J. Bacteriol. 178, 18661871.
  • 9
    Giuffre, A., Stubauer, G., Sarti, P., Brunori, M., Zumft, W. G., et al. ( 1999) The heme-copper oxidases of Thermus thermophilus catalyze the reduction of nitric oxide: evolutionary implications. Proc. Natl. Acad. Sci. USA 96, 1471814723.
  • 10
    Hayashi, T., Lin, M. T., Ganesan, K., Chen, Y., Fee, J. A., et al. ( 2009) Accommodation of two diatomic molecules in cytochrome bo: insights into NO reductase activity in terminal oxidases. Biochemistry 48, 883890.
  • 11
    Hendriks, J. H., Jasaitis, A., Saraste, M., and Verkhovsky, M. I. ( 2002) Proton and electron pathways in the bacterial nitric oxide reductase. Biochemistry 41, 23312340.
  • 12
    Reimann, J., Flock, U., Lepp, H., Honigmann, A., and Adelroth, P. ( 2007) A pathway for protons in nitric oxide reductase from Paracoccus denitrificans. Biochim. Biophys. Acta 1767, 362373.
  • 13
    Hino, T., Matsumoto, Y., Nagano, S., Sugimoto, H., Fukumori, Y., etal. ( 2010) Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330, 16661670.
  • 14
    Matsumoto, Y., Tosha, T., Pisliakov, A. V., Hino, T., Sugimoto, H., et al. ( 2012) Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus Stearothermophilus. Nat. Struct. Mol. Biol. 19, 238245.
  • 15
    Hendriks, J., Oubrie, A., Castresana, J., Urbani, A., Gemeinhardt, S., et al. ( 2000) Nitric oxide reductases in bacteria. Biochim. Biophys. Acta 1459, 266273.
  • 16
    Buschmann, S., Warkentin, E., Xie, H., Langer, J. D., Ermler, U., et al. ( 2010) The structure of cbb 3 cytochrome oxidase provides insights into proton pumping. Science 329, 327330.
  • 17
    Ouyang, H., Han, H., Roh, J. H., Hemp, J., Hosler, J. P., et al. ( 2012) Functional importance of a pair of conserved glutamic acid residues and of Ca2+ binding in the cbb 3-type oxygen reductases from Rhodobacter sphaeroides and Vibrio cholerae. Biochemistry 51, 72907296.
  • 18
    Iwata, S., Ostermeier, C., Ludwig, B., and Michel, H. ( 1995) Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 376, 660669.
  • 19
    Tsukihara, T., Aoyama, H., Yamashita, E., Tomizaki, T., Yamaguchi, H., et al. ( 1996) The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å. Science 272, 11361144.
  • 20
    Soulimane, T., Buse, G., Bourenkov, G. P., Bartunik, H. D., Huber, R., et al. ( 2000) Structure and mechanism of the aberrant ba 3-cytochrome c oxidase from Thermus thermophilus. EMBO J. 19, 17661776.
  • 21
    Abramson, J., Riistama, S., Larsson, G., Jasaitis, A., Svensson-Ek, M., et al. ( 2000) The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site. Nat. Struct. Biol. 7, 910917.
  • 22
    Sousa, F. L., Alves, R. J., Ribeiro, M. A., Pereira-Leal, J. B., Teixeira, M., et al. ( 2012) The superfamily of heme-copper oxygen reductases: types and evolutionary considerations. Biochim. Biophys. Acta 1817, 629637.
  • 23
    Castresana, J., Lubben, M., Saraste, M., and Higgins, D. G. ( 1994) Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen. EMBO J. 13, 25162525.
  • 24
    Lin, Y. W., Yeung, N., Gao, Y. G., Miner, K. D., Tian, S., et al. ( 2010) Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin. Proc. Natl. Acad. Sci. USA 107, 85818586.
  • 25
    Hayashi, T., Miner, K. D., Yeung, N., Lin, Y. W., Lu, Y., et al. ( 2011) Spectroscopic characterization of mononitrosyl complexes in heme–nonheme diiron centers within the myoglobin scaffold (Fe(B)Mbs): relevance to denitrifying NO reductase. Biochemistry 50, 59395947.
  • 26
    Kumita, H., Matsuura, K., Hino, T., Takahashi, S., Hori, H., et al. ( 2004) 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, 5524755254.
  • 27
    Moenne-Loccoz, P. ( 2007) Spectroscopic characterization of heme iron-nitrosyl species and their role in NO reductase mechanisms in diiron proteins. Nat. Prod. Rep. 24, 610620.
  • 28
    Blomberg, M. R. and Siegbahn, P. E. ( 2012) Mechanism for N2O generation in bacterial nitric oxide reductase: a quantum chemical study. Biochemistry 51, 51735186.
  • 29
    Timoteo, C. G., Pereira, A. S., Martins, C. E., Naik, S. G., Duarte, A. G., et al. ( 2011) Low-spin heme b 3 in the catalytic center of nitric oxide reductase from Pseudomonas nautica. Biochemistry 50, 42514262.
  • 30
    Collman, J. P., Dey, A., Yang, Y., Decreau, R. A., Ohta, T., et al. ( 2008) Intermediates involved in the two electron reduction of NO to N2O by a functional synthetic model of heme containing bacterial NO reductase. J. Am. Chem. Soc. 130, 1649816499.
  • 31
    Shiro, Y. ( 2012) Structure and function of bacterial nitric oxide reductases: nitric oxide reductase, anaerobic enzymes. Biochim. Biophys. Acta 1817, 19071913.
  • 32
    Shiro, Y., Sugimoto, H., Tosha, T., Nagano, S., and Hino, T. ( 2012) Structural basis for nitrous oxide generation by bacterial nitric oxide reductases. Philos. Trans. R. Soc. Lond. B Biol. Sci. 367, 11951203.
  • 33
    Hunsicker-Wang, L. M., Pacoma, R. L., Chen, Y., Fee, J. A., and Stout, C. D. ( 2005) A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba3 oxidase from Thermus thermophilus. Acta Crystallogr. D Biol. Crystallogr. 61, 340343.
  • 34
    Liu, B., Chen, Y., Doukov, T., Soltis, S. M., Stout, C. D., et al. ( 2009) Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba 3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme. Biochemistry 48, 820826.
  • 35
    Lyons, J. A., Aragao, D., Slattery, O., Pisliakov, A. V., Soulimane, T., et al. ( 2012) Structural insights into electron transfer in caa 3-type cytochrome oxidase. Nature 487, 514518.
  • 36
    Harrenga, A. and Michel H. ( 1999) The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction. J. Biol. Chem. 274, 3329633299.
  • 37
    Koepke, J., Olkhova, E., Angerer, H., Muller, H., Peng, G., et al. ( 2009) High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways. Biochim. Biophys. Acta 1787, 635645.
  • 38
    Svensson-Ek, M., Abramson, J., Larsson, G., Tornroth, S., Brzezinski, P., et al. ( 2002) The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides. J. Mol. Biol. 321, 329339.
  • 39
    Qin, L., Liu, J., Mills, D. A., Proshlyakov, D. A., Hiser, C., etal. ( 2009) Redox-dependent conformational changes in cytochrome C oxidase suggest a gating mechanism for proton uptake. Biochemistry 48, 51215130.
  • 40
    Aoyama, H., Muramoto, K., Shinzawa-Itoh, K., Hirata, K., Yamashita, E., et al. ( 2009) A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump. Proc. Natl. Acad. Sci. USA 106, 21652169.
  • 41
    Muramoto, K., Hirata, K., Shinzawa-Itoh, K., Yoko-o, S., Yamashita, E., et al. ( 2007) A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase. Proc. Natl. Acad. Sci. USA 104, 78817886.
  • 42
    Muramoto, K., Ohta, K., Shinzawa-Itoh, K., Kanda, K., Taniguchi, M., etal. ( 2010) Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate. Proc. Natl. Acad. Sci. USA 107, 77407745.
  • 43
    Yoshikawa, S., Shinzawa-Itoh, K., Nakashima, R., Yaono, R., Yamashita, E., etal. ( 1998) Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase. Science 280, 17231729.
  • 44
    Petrek, M., Otyepka, M., Banas, P., Kosinova, P., Koca, J., et al. ( 2006) CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 7, 316.
  • 45
    Pisliakov, A. V., Hino, T., Shiro, Y., and Sugita, Y. ( 2012) Molecular dynamics simulations reveal proton transfer pathways in cytochrome C-dependent nitric oxide reductase. PLoS Comput. Biol. 8, e1002674.
  • 46
    Salomonsson, L., Reimann, J., Tosha, T., Krause, N., Gonska, N., et al. ( 2012) Proton transfer in the quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus during reduction of oxygen. Biochim. Biophys. Acta 1817, 19141920.
  • 47
    Flock, U., Watmough, N. J., and Adelroth, P. ( 2005) Electron/proton coupling in bacterial nitric oxide reductase during reduction of oxygen. Biochemistry 44, 1071110719.
  • 48
    Ishigami, I., Nishigaki, K., Shinzawa-Itoh, K., Yoshikawa, S., Nakashima, S., et al. ( 2012) An intermediate conformational state during ligand binding to cytochrome c oxidase detected by time-resolved resonance Raman analyses of heme peripheral group. Chem. Lett. 2, 178180.