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References

  • 1
    Richardson DJ & Watmough NJ (1999) Inorganic nitrogen metabolism in bacteria. Curr Opin Chem Biol 3, 207219.
  • 2
    Simon J (2002) Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol Rev 26, 285309.
  • 3
    Kern M & Simon J (2009) Electron transport chains and bioenergetics of respiratory nitrogen metabolism in Wolinella succinogenes and other Epsilonproteobacteria. Biochim Biophys Acta 1787, 646656.
  • 4
    Kern M, Volz J & Simon J (2011) The oxidative and nitrosative stress defence network of Wolinella succinogenes: cytochrome c nitrite reductase mediates the stress response to nitrite, nitric oxide, hydroxylamine and hydrogen peroxide. Environ Microbiol 13, 24782494.
  • 5
    Pereira IA, LeGall J, Xavier AV & Teixeira M (2000) Characterization of a heme c nitrite reductase from a non-ammonifying microorganism Desulfovibrio vulgaris Hildenborough. Biochim Biophys Acta, 1481, 119130.
  • 6
    Einsle O, Messerschmidt A, Stach P, Bourenkov GP, Bartunik HD, Huber R & Kroneck PM (1999) Structure of cytochrome c nitrite reductase. Nature 400, 476480.
  • 7
    Einsle O, Stach P, Messerschmidt A, Simon J, Kroger A, Huber R & Kroneck PM (2000) Cytochrome c nitrite reductase from Wolinella succinogenes. Structure at 1.6 A resolution, inhibitor binding, and heme-packing motifs. J Biol Chem 275, 3960839616.
  • 8
    Stach P, Einsle O, Schumacher W, Kurun E & Kroneck PM (2000) Bacterial cytochrome c nitrite reductase: new structural and functional aspects. J Inorg Biochem 79, 381385.
  • 9
    Bamford VA, Angove HC, Seward HE, Thomson AJ, Cole JA, Butt JN, Hemmings AM & Richardson DJ (2002) Structure and spectroscopy of the periplasmic cytochrome c nitrite reductase from Escherichia coli. Biochemistry 41, 29212931.
  • 10
    Cunha CA, Macieira S, Dias JM, Almeida G, Goncalves LL, Costa C, Lampreia J, Huber R, Moura JJ, Moura I et al. (2003) Cytochrome c nitrite reductase from Desulfovibrio desulfuricans ATCC 27774. The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA). J Biol Chem 278, 1745517465.
  • 11
    Almeida MG, Macieira S, Goncalves LL, Huber R, Cunha CA, Romao MJ, Costa C, Lampreia J, Moura JJ & Moura I (2003) The isolation and characterization of cytochrome c nitrite reductase subunits (NrfA and NrfH) from Desulfovibrio desulfuricans ATCC 27774. Re-evaluation of the spectroscopic data and redox properties. Eur J Biochem 270, 39043915.
  • 12
    Rodrigues ML, Oliveira TF, Pereira IA & Archer M (2006) X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination. EMBO J 25, 59515960.
  • 13
    Rodrigues ML, Scott KA, Sansom MS, Pereira IA & Archer M (2008) Quinol oxidation by c-type cytochromes: structural characterization of the menaquinol binding site of NrfHA. J Mol Biol 381, 341350.
  • 14
    Klotz MG, Schmid MC, Strous M, op den Camp HJ, Jetten MS & Hooper AB (2008) Evolution of an octahaem cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria. Environ Microbiol 10, 31503163.
  • 15
    Sorokin DY, Antipov AN & Kuenen JG (2003) Complete denitrification in coculture of obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria from a hypersaline soda lake. Arch Microbiol 180, 127133.
  • 16
    Sorokin DY, Touruva TP, Sjollema KA & Kuenen JG (2003) Thioalkalivibrio nitratireducens sp. nov., a nitrate-reducing member of an autotrophic denitrifying consortium from a soda lake. Int J Syst Evol Microbiol 53, 17791783.
  • 17
    Tikhonova TV, Slutsky A, Antipov AN, Boyko KM, Polyakov KM, Sorokin DY, Zvyagilskaya RA & Popov VO (2006) Molecular and catalytic properties of a novel cytochrome c nitrite reductase from nitrate-reducing haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio nitratireducens. Biochim Biophys Acta 1764, 715723.
  • 18
    Tikhonova TV, Slutskaya ES, Filimonenkov AA, Boyko KM, Kleimenov SY, Konarev PV, Polyakov KM, Svergun DI, Trofimov AA, Khomenkov VG et al. (2008) Isolation and oligomeric composition of cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. Biochemistry (Mosc) 73, 164170.
  • 19
    Trofimov AA, Polyakov KM, Boyko KM, Tikhonova TV, Safonova TN, Tikhonov AV, Popov AN & Popov VO (2010) Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide. Acta Crystallogr D Biol Crystallogr 66, 10431047.
  • 20
    Polyakov KM, Boyko KM, Tikhonova TV, Slutsky A, Antipov AN, Zvyagilskaya RA, Popov AN, Bourenkov GP, Lamzin VS & Popov VO (2009) High-resolution structural analysis of a novel octaheme cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. J Mol Biol 389, 846862.
  • 21
    Trofimov AA, Polyakov KM, Boyko KM, Filimonenkov AA, Dorovatovskii PV, Tikhonova TV, Popov VO & Kovalchuk MV (2010) Structure of octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens in a complex with phosphate. Crystallogr Rep 55, 5864.
  • 22
    Trofimov AA, Polyakov KM, Tikhonova TV, Tikhonov AV, Safonova TN, Boyko KM, Dorovatovsky PV & Popov VO (2012) Covalent modifications of catalytic tyrosine in octaheme cytochrome c nitrite reductase and their effect on the enzyme activity. Acta Crystallogr D Biol Crystallogr 68, 144153.
  • 23
    Sorokin DY, Tourova TP, Lysenko AM, Mityushina LL & Kuenen JG (2002) Thioalkalivibrio thiocyanoxidans sp. nov. and Thioalkalivibrio paradoxus sp. nov., novel alkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria capable of growth on thiocyanate, from soda lakes. Int J Syst Evol Microbiol 52, 657664.
  • 24
    Clarke TA, Hemmings AM, Burlat B, Butt JN, Cole JA & Richardson DJ (2006) Comparison of the structural and kinetic properties of the cytochrome c nitrite reductases from Escherichia coli, Wolinella succinogenes, Sulfurospirillum deleyianum and Desulfovibrio desulfuricans. Biochem Soc Trans 34, 143145.
  • 25
    Pereira IC, Abreu IA, Xavier AV, LeGall J & Teixeira M (1996) Nitrite reductase from Desulfovibrio desulfuricans (ATCC 27774) a heterooligomer heme protein with sulfite reductase activity. Biochem Biophys Res Commun 224, 611618.
  • 26
    Lukat P, Rudolf M, Stach P, Messerschmidt A, Kroneck PMH, Simon J & Einsle O (2008) Binding and reduction of sulfite by cytochrome c nitrite reductase. Biochemistry 47, 20802086.
  • 27
    Liu MC & Peck HD Jr (1981) The isolation of a hexaheme cytochrome from Desulfovibrio desulfuricans and its identification as a new type of nitrite reductase. J Biol Chem 256, 1315913164.
  • 28
    Kemp GL, Clarke TA, Marritt SJ, Lockwood C, Poock SR, Hemmings AM, Richardson DJ, Cheesman MR & Butt JN (2010) Kinetic and thermodynamic resolution of the interactions between sulfite and the pentahaem cytochrome NrfA from Escherichia coli. Biochem J 431, 7380.
  • 29
    Bykov D & Neese F (2011) Substrate binding and activation in the active site of cytochrome c nitrite reductase: a density functional study. J Biol Inorg Chem 16, 417430.
  • 30
    Himo F, Noodleman L, Blomberg MRA & Siegbahn PEM (2002) Relative acidities of ortho-substituted phenols, as model for modified tyrosines in proteins. J Phys Chem 106, 87578761.
  • 31
    Whittaker MM, Chuang YY & Whittaker JW (1993) Models for the redox active site in galactose oxidase. J Am Chem Soc 115, 1002910035.
  • 32
    Itoh S, Takayama S, Arakawa R, Furuta A, Komatsu M, Ishida A, Takamuku S & Fukuzumi S (1997) Active site models for galactose oxidase. Electronic effect of the thioether group in the novel organic cofactor. Inorg Chem 36, 14071416.
  • 33
    Sorokin DY, Lysenko AM, Mityushina LL, Tourova TP, Jones BE, Rainey FA, Robertson LA & Kuenen JG (2001) Thioalkalimicrobium aerophilum gen. nov., sp. nov. and Thioalkalimicrobium sibericum sp. nov., and Thioalkalivibrio versutus gen. nov., sp. nov., Thioalkalivibrio nitratis sp. nov., novel and Thioalkalivibrio denitrificancs sp. nov., novel obligately alkaliphilic and obligately chemolithoautotrophic sulfur-oxidizing bacteria from soda lakes. Int J Syst Evol Microbiol 51, 565580.
  • 34
    Pfennig N & Lippert KD (1966) Utilisation of molecular hydrogen by Chlorobium thiosulfatophilum. Growth and CO2-fixation. Arch Microbiol 55, 245256.
  • 35
    Laemmli UK (1970) Cleavage of structural proteins during the assembly of the 533 head of bacteriophage T4. Nature, 227, 680685.
  • 36
    Bradford M (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72, 248254.
  • 37
    Berry EA & Trumpower BL (1987) Simultaneous determination of hemes a, b, and c from pyridine hemochrome spectra. Anal Biochem 161, 115.
  • 38
    Nicolas DJD & Nason A (1957) Determination of nitrate and nitrite. Methods Enzymol 3, 981984.
  • 39
    Ochman H, Gerber AS & Hartl DL (1988) Genetic applications of an inverse polymerase chain reaction. Genetics 120, 621623.
  • 40
    Poirot O, O'Toole E & Notredame C (2003) Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res 31, 35033506.
  • 41
    Smirnova EA, Kislitsyn YuA, Sosfenov NI, Lyashenko AV, Popov AN, Baidus AN, Timofeev I & Kuranova IP (2009) Protein crystal growth on the Russian segment of the International Space Station. Crystallogr Rep 54, 901911.
  • 42
    Kabsch W (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Crystallogr 26, 795800.
  • 43
    Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67, 235242.
  • 44
    Murshudov GN, Vagin AA & Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53, 240255.
  • 45
    Emsley P & Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 21262132.