1oah Citations

Cytochrome c nitrite reductase from Desulfovibrio desulfuricans ATCC 27774. The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA).

Abstract

The gene encoding cytochrome c nitrite reductase (NrfA) from Desulfovibrio desulfuricans ATCC 27774 was sequenced and the crystal structure of the enzyme was determined to 2.3-A resolution. In comparison with homologous structures, it presents structural differences mainly located at the regions surrounding the putative substrate inlet and product outlet, and includes a well defined second calcium site with octahedral geometry, coordinated to propionates of hemes 3 and 4, and caged by a loop non-existent in the previous structures. The highly negative electrostatic potential in the environment around hemes 3 and 4 suggests that the main role of this calcium ion may not be electrostatic but structural, namely in the stabilization of the conformation of the additional loop that cages it and influences the solvent accessibility of heme 4. The NrfA active site is similar to that of peroxidases with a nearby calcium site at the heme distal side nearly in the same location as occurs in the class II and class III peroxidases. This fact suggests that the calcium ion at the distal side of the active site in the NrfA enzymes may have a similar physiological role to that reported for the peroxidases.

Articles - 1oah mentioned but not cited (6)

  1. X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination. Rodrigues ML, Oliveira TF, Pereira IA, Archer M. EMBO J 25 5951-5960 (2006)
  2. Protein-Protein Interactions Mediated by Helical Tertiary Structure Motifs. Watkins AM, Wuo MG, Arora PS. J Am Chem Soc 137 11622-11630 (2015)
  3. Crystallization and preliminary structure determination of the membrane-bound complex cytochrome c nitrite reductase from Desulfovibrio vulgaris Hildenborough. Rodrigues ML, Oliveira T, Matias PM, Martins IC, Valente FM, Pereira IA, Archer M. Acta Crystallogr Sect F Struct Biol Cryst Commun 62 565-568 (2006)
  4. Measuring the cytochrome C nitrite reductase activity-practical considerations on the enzyme assays. Silveira CM, Besson S, Moura I, Moura JJ, Almeida MG. Bioinorg Chem Appl 634597 (2010)
  5. A New Paradigm of Multiheme Cytochrome Evolution by Grafting and Pruning Protein Modules. Soares R, Costa NL, Paquete CM, Andreini C, Louro RO. Mol Biol Evol 39 msac139 (2022)
  6. A quasi-reagentless point-of-care test for nitrite and unaffected by oxygen and cyanide. Monteiro T, Gomes S, Jubete E, Añorga L, Silveira CM, Almeida MG. Sci Rep 9 2622 (2019)


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  1. Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes. Shi L, Squier TC, Zachara JM, Fredrickson JK. Mol Microbiol 65 12-20 (2007)
  2. Mo and W bis-MGD enzymes: nitrate reductases and formate dehydrogenases. Moura JJ, Brondino CD, Trincão J, Romão MJ. J Biol Inorg Chem 9 791-799 (2004)
  3. Key bacterial multi-centered metal enzymes involved in nitrate and sulfate respiration. Fritz G, Einsle O, Rudolf M, Schiffer A, Kroneck PM. J Mol Microbiol Biotechnol 10 223-233 (2005)
  4. Nitrite biosensing via selective enzymes--a long but promising route. Almeida MG, Serra A, Silveira CM, Moura JJ. Sensors (Basel) 10 11530-11555 (2010)
  5. Enzymatic activity mastered by altering metal coordination spheres. Moura I, Pauleta SR, Moura JJ. J Biol Inorg Chem 13 1185-1195 (2008)
  6. Octaheme nitrite reductases: structure and properties. Tikhonova TV, Trofimov AA, Popov VO. Biochemistry (Mosc) 77 1129-1138 (2012)
  7. Characterization of the active site and calcium binding in cytochrome c nitrite reductases. Lockwood CW, Clarke TA, Butt JN, Hemmings AM, Richardson DJ. Biochem Soc Trans 39 1871-1875 (2011)
  8. Underexplored microbial metabolisms for enhanced nutrient recycling in agricultural soils. Bhowmik A, Cloutier M, Ball E, Bruns MA. AIMS Microbiol 3 826-845 (2017)
  9. Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen. Kroneck PMH. J Biol Inorg Chem 27 1-21 (2022)

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  1. Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195. Nonaka H, Keresztes G, Shinoda Y, Ikenaga Y, Abe M, Naito K, Inatomi K, Furukawa K, Inui M, Yukawa H. J Bacteriol 188 2262-2274 (2006)
  2. High-resolution structural analysis of a novel octaheme cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. Polyakov KM, Boyko KM, Tikhonova TV, Slutsky A, Antipov AN, Zvyagilskaya RA, Popov AN, Bourenkov GP, Lamzin VS, Popov VO. J Mol Biol 389 846-862 (2009)
  3. The crystal structure of the pentahaem c-type cytochrome NrfB and characterization of its solution-state interaction with the pentahaem nitrite reductase NrfA. Clarke TA, Cole JA, Richardson DJ, Hemmings AM. Biochem J 406 19-30 (2007)
  4. The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states. Coelho C, González PJ, Moura JG, Moura I, Trincão J, João Romão M. J Mol Biol 408 932-948 (2011)
  5. 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. Kern M, Volz J, Simon J. Environ Microbiol 13 2478-2494 (2011)
  6. 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. Almeida MG, Macieira S, Gonçalves LL, Gonçalves LL, Huber R, Cunha CA, Romão MJ, Costa C, Lampreia J, Moura JJ, Moura I. Eur J Biochem 270 3904-3915 (2003)
  7. Redundancy and modularity in membrane-associated dissimilatory nitrate reduction in Bacillus. Heylen K, Keltjens J. Front Microbiol 3 371 (2012)
  8. A needle in a haystack: the active site of the membrane-bound complex cytochrome c nitrite reductase. Almeida MG, Silveira CM, Guigliarelli B, Bertrand P, Moura JJ, Moura I, Léger C. FEBS Lett 581 284-288 (2007)
  9. Kinetic and product distribution analysis of NO* reductase activity in Nitrosomonas europaea hydroxylamine oxidoreductase. Kostera J, Youngblut MD, Slosarczyk JM, Pacheco AA. J Biol Inorg Chem 13 1073-1083 (2008)
  10. Laue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system. Youngblut M, Judd ET, Srajer V, Sayyed B, Goelzer T, Elliott SJ, Schmidt M, Pacheco AA. J Biol Inorg Chem 17 647-662 (2012)
  11. c-Type cytochrome biogenesis can occur via a natural Ccm system lacking CcmH, CcmG, and the heme-binding histidine of CcmE. Goddard AD, Stevens JM, Rao F, Mavridou DA, Chan W, Richardson DJ, Allen JW, Ferguson SJ. J Biol Chem 285 22882-22889 (2010)
  12. Kinetic and thermodynamic resolution of the interactions between sulfite and the pentahaem cytochrome NrfA from Escherichia coli. Kemp GL, Clarke TA, Marritt SJ, Lockwood C, Poock SR, Hemmings AM, Richardson DJ, Cheesman MR, Butt JN. Biochem J 431 73-80 (2010)
  13. Substrate binding and activation in the active site of cytochrome c nitrite reductase: a density functional study. Bykov D, Neese F. J Biol Inorg Chem 16 417-430 (2011)
  14. Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species. Tikhonova T, Tikhonov A, Trofimov A, Polyakov K, Boyko K, Cherkashin E, Rakitina T, Sorokin D, Popov V. FEBS J 279 4052-4061 (2012)
  15. Reductive activation of the heme iron-nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study. Bykov D, Neese F. J Biol Inorg Chem 17 741-760 (2012)
  16. Heme-bound nitroxyl, hydroxylamine, and ammonia ligands as intermediates in the reaction cycle of cytochrome c nitrite reductase: a theoretical study. Bykov D, Plog M, Neese F. J Biol Inorg Chem 19 97-112 (2014)
  17. Contrasting catalytic profiles of multiheme nitrite reductases containing CxxCK heme-binding motifs. Doyle RM, Marritt SJ, Gwyer JD, Lowe TG, Tikhonova TV, Popov VO, Cheesman MR, Butt JN. J Biol Inorg Chem 18 655-667 (2013)
  18. Covalent modifications of the catalytic tyrosine in octahaem cytochrome c nitrite reductase and their effect on the enzyme activity. Trofimov AA, Polyakov KM, Tikhonova TV, Tikhonov AV, Safonova TN, Boyko KM, Dorovatovskii PV, Popov VO. Acta Crystallogr D Biol Crystallogr 68 144-153 (2012)
  19. Cytochrome c nitrite reductase from the bacterium Geobacter lovleyi represents a new NrfA subclass. Campeciño J, Lagishetty S, Wawrzak Z, Sosa Alfaro V, Lehnert N, Reguera G, Hu J, Hegg EL. J Biol Chem 295 11455-11465 (2020)
  20. Shewanella oneidensis cytochrome c nitrite reductase (ccNiR) does not disproportionate hydroxylamine to ammonia and nitrite, despite a strongly favorable driving force. Youngblut M, Pauly DJ, Stein N, Walters D, Conrad JA, Moran GR, Bennett B, Pacheco AA. Biochemistry 53 2136-2144 (2014)
  21. In meso crystal structure of a novel membrane-associated octaheme cytochrome c from the Crenarchaeon Ignicoccus hospitalis. Parey K, Fielding AJ, Sörgel M, Rachel R, Huber H, Ziegler C, Rajendran C. FEBS J 283 3807-3820 (2016)
  22. Influence of the heme distal pocket on nitrite binding orientation and reactivity in Sperm Whale myoglobin. Tse W, Whitmore N, Cheesman MR, Watmough NJ. Biochem J 478 927-942 (2021)
  23. Isolation and oligomeric composition of cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. Tikhonova TV, Slutskaya ES, Filimonenkov AA, Boyko KM, Kleimenov SY, Konarev PV, Polyakov KM, Svergun DI, Trofimov AA, Khomenkov VG, Zvyagilskaya RA, Popov VO. Biochemistry (Mosc) 73 164-170 (2008)
  24. Correlations between the Electronic Properties of Shewanella oneidensis Cytochrome c Nitrite Reductase (ccNiR) and Its Structure: Effects of Heme Oxidation State and Active Site Ligation. Stein N, Love D, Judd ET, Elliott SJ, Bennett B, Pacheco AA. Biochemistry 54 3749-3758 (2015)
  25. Molecular interactions between multihaem cytochromes: probing the protein-protein interactions between pentahaem cytochromes of a nitrite reductase complex. Lockwood C, Butt JN, Clarke TA, Richardson DJ. Biochem Soc Trans 39 263-268 (2011)
  26. Properties and structure of a low-potential, penta-heme cytochrome c552 from a thermophilic purple sulfur photosynthetic bacterium Thermochromatium tepidum. Chen JH, Yu LJ, Boussac A, Wang-Otomo ZY, Kuang T, Shen JR. Photosynth Res 139 281-293 (2019)
  27. Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes. Saghaï A, Pold G, Jones CM, Hallin S. Nat Commun 14 8249 (2023)