2.02012-08-15 08:51:33 -06002015-09-17 15:41:55 -0600ECMDB21652M2MDB002046Ferricytochrome cCytochrome c, or Cyt c, is a small heme protein and a component of the oxidative phosphorylation electron transport chain. The heme group of cytochrome c accepts electrons from the Cytochrome b-c1 complex (Complex III) and transfers electrons to the Cytochrome oxidase complex (Complex IV). Cyt c is capable of undergoing oxidation and reduction, but does not bind oxygen. Cytochrome c is a highly conserved protein across the spectrum of species, found in plants, animals, and many unicellular organisms. This, along with its small size (molecular weight about 12,000 daltons), makes it useful in studies of cladistics. Its primary structure consists of a chain of about 100 amino acids. (Wikipedia)Cytochrome cCytochrome c (JAN)Ferricytochrome cHolocytochrome cC42H68O13780.993780.46599225λ²-iron(2+) ion 3-[15-(1-{[2-amino-2-(methyl-C-hydroxycarbonimidoyl)ethyl]sulfanyl}ethyl)-10-(1-{[2-amino-3-(methylazanidyl)-3-oxopropyl]sulfanyl}ethyl)-20-(2-carboxyethyl)-5,9,14,19-tetramethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(21),2,4,6,8,10,12,14,16(22),17,19-undecaen-4-yl]propanoateλ²-iron(2+) ion 3-[15-(1-{[2-amino-2-(methyl-C-hydroxycarbonimidoyl)ethyl]sulfanyl}ethyl)-10-(1-{[2-amino-3-(methylazanidyl)-3-oxopropyl]sulfanyl}ethyl)-20-(2-carboxyethyl)-5,9,14,19-tetramethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(21),2,4,6,8,10,12,14,16(22),17,19-undecaen-4-yl]propanoate9007-43-6CC(CC\C=C(/C)COC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O)C1CCC2(C)C3CC=C4C(CCC(O)C4(C)C)C3(C)C(=O)CC12CInChI=1S/C42H68O13/c1-21(19-52-37-36(51)34(49)32(47)27(55-37)20-53-38-35(50)33(48)31(46)26(18-43)54-38)9-8-10-22(2)23-15-16-40(5)28-13-11-24-25(12-14-29(44)39(24,3)4)42(28,7)30(45)17-41(23,40)6/h9,11,22-23,25-29,31-38,43-44,46-51H,8,10,12-20H2,1-7H3/b21-9+FHOKVOIILRHONR-ZVBGSRNCSA-NSolidlogp1.77logs-4.81solubility1.45e-02 g/llogp0.88pka_strongest_acidic3.48pka_strongest_basic9.23iupacλ²-iron(2+) ion 3-[15-(1-{[2-amino-2-(methyl-C-hydroxycarbonimidoyl)ethyl]sulfanyl}ethyl)-10-(1-{[2-amino-3-(methylazanidyl)-3-oxopropyl]sulfanyl}ethyl)-20-(2-carboxyethyl)-5,9,14,19-tetramethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(21),2,4,6,8,10,12,14,16(22),17,19-undecaen-4-yl]propanoateaverage_mass780.993mono_mass780.46599225smilesCC(CC\C=C(/C)COC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O)C1CCC2(C)C3CC=C4C(CCC(O)C4(C)C)C3(C)C(=O)CC12CformulaC42H68O13inchiInChI=1S/C42H68O13/c1-21(19-52-37-36(51)34(49)32(47)27(55-37)20-53-38-35(50)33(48)31(46)26(18-43)54-38)9-8-10-22(2)23-15-16-40(5)28-13-11-24-25(12-14-29(44)39(24,3)4)42(28,7)30(45)17-41(23,40)6/h9,11,22-23,25-29,31-38,43-44,46-51H,8,10,12-20H2,1-7H3/b21-9+inchikeyFHOKVOIILRHONR-ZVBGSRNCSA-Npolar_surface_area245.72refractivity240.33polarizability93.79rotatable_bond_count16acceptor_count12donor_count6physiological_charge-1formal_charge0Nitrogen metabolism
The biological process of the nitrogen cycle is a complex interplay among many microorganisms catalyzing different reactions, where nitrogen is found in various oxidation states ranging from +5 in nitrate to -3 in ammonia.
The ability of fixing atmospheric nitrogen by the nitrogenase enzyme complex is present in restricted prokaryotes (diazotrophs). The other reduction pathways are assimilatory nitrate reduction and dissimilatory nitrate reduction both for conversion to ammonia, and denitrification. Denitrification is a respiration in which nitrate or nitrite is reduced as a terminal electron acceptor under low oxygen or anoxic conditions, producing gaseous nitrogen compounds (N2, NO and N2O) to the atmosphere.
Nitrate can be introduced into the cytoplasm through a nitrate:nitrite antiporter NarK or a nitrate / nitrite transporter NarU. Nitrate is then reduced by a Nitrate Reductase resulting in the release of water, an acceptor and a Nitrite. Nitrite can also be introduced into the cytoplasm through a nitrate:nitrite antiporter NarK
Nitrite can be reduced a NADPH dependent nitrite reductase resulting in water and NAD and Ammonia.
Nitrite can interact with hydrogen ion, ferrocytochrome c through a cytochrome c-552 ferricytochrome resulting in the release of ferricytochrome c, water and ammonia
Another process by which ammonia is produced is by a reversible reaction of hydroxylamine with a reduced acceptor through a hydroxylamine reductase resulting in an acceptor, water and ammonia.
Water and carbon dioxide react through a carbonate dehydratase resulting in carbamic acid. This compound reacts spontaneously with hydrogen ion resulting in the release of carbon dioxide and ammonia. Carbon dioxide can interact with water through a carbonic anhydrase resulting in hydrogen carbonate. This compound interacts with cyanate and hydrogen ion through a cyanate hydratase resulting in a carbamic acid.
Ammonia can be metabolized by reacting with L-glutamine and ATP driven glutamine synthetase resulting in ADP, phosphate and L-glutamine. The latter compound reacts with oxoglutaric acid and hydrogen ion through a NADPH dependent glutamate synthase resulting in the release of NADP and L-glutamic acid. L-glutamic acid reacts with water through a NADP-specific glutamate dehydrogenase resulting in the release of oxoglutaric acid, NADPH, hydrogen ion and ammonia.
PW000755ec00910MetabolicPyruvate metabolismec00620Microbial metabolism in diverse environmentsec01120Metabolic pathwayseco01100Specdb::MsMs1327069Specdb::MsMs1327070Specdb::MsMs1327071Specdb::MsMs1441405Specdb::MsMs1441406Specdb::MsMs1441407HMDB12920439171C0012515991Cytochrome_cRespiratory nitrate reductase 1 alpha chainP09152NARG_ECOLInarGhttp://ecmdb.ca/proteins/P09152.xmlCytochrome c-552P0ABK9NRFA_ECOLInrfAhttp://ecmdb.ca/proteins/P0ABK9.xmlRespiratory nitrate reductase 2 gamma chainP0AF32NARV_ECOLInarVhttp://ecmdb.ca/proteins/P0AF32.xmlRespiratory nitrate reductase 1 beta chainP11349NARH_ECOLInarHhttp://ecmdb.ca/proteins/P11349.xmlRespiratory nitrate reductase 1 gamma chainP11350NARI_ECOLInarIhttp://ecmdb.ca/proteins/P11350.xmlProbable nitrate reductase molybdenum cofactor assembly chaperone NarWP19317NARW_ECOLInarWhttp://ecmdb.ca/proteins/P19317.xmlRespiratory nitrate reductase 2 beta chainP19318NARY_ECOLInarYhttp://ecmdb.ca/proteins/P19318.xmlRespiratory nitrate reductase 2 alpha chainP19319NARZ_ECOLInarZhttp://ecmdb.ca/proteins/P19319.xmlL-lactate dehydrogenase [cytochrome]P33232LLDD_ECOLIlldDhttp://ecmdb.ca/proteins/P33232.xmlPeriplasmic nitrate reductaseP33937NAPA_ECOLInapAhttp://ecmdb.ca/proteins/P33937.xmlProbable cytochrome c peroxidaseP37197YHJA_ECOLIyhjAhttp://ecmdb.ca/proteins/P37197.xmlNitrate reductase molybdenum cofactor assembly chaperone NarJP0AF26NARJ_ECOLInarJhttp://ecmdb.ca/proteins/P0AF26.xmlheme lyase (NrfEFG) for insertion of heme into c552, subunit NrfEP32710nrfEhttp://ecmdb.ca/proteins/P32710.xmlL-Lactic acid + 2 Ferricytochrome c > Pyruvic acid +2 Ferrocytochrome c +2 Hydrogen ionAmmonia + 2 Water + 6 Ferricytochrome c > Nitrite +6 Ferrocytochrome c +7 Hydrogen ion2 Ferrocytochrome c + Hydrogen peroxide >2 Ferricytochrome c +2 WaterL-Lactic acid + 2 Ferricytochrome c + Ferricytochrome c <> Pyruvic acid +2 Ferrocytochrome c +2 Hydrogen ion + Ferrocytochrome cR00196Ammonia + 2 Water + 6 Ferricytochrome c + Ferricytochrome c <> Nitrite +6 Ferrocytochrome c +6 Hydrogen ion + Ferrocytochrome cR05712Ferrocytochrome c + Hydrogen peroxide <> Ferricytochrome c + WaterR00017 Nitrite + 6 ferrocytochrome c + 7 Hydrogen ion + Nitrite + 6 Ferrocytochrome c <> Ammonia +6 ferricytochrome c +2 Water +6 Ferricytochrome cPW_R002428L-Lactic acid + 2 Ferricytochrome c <> Pyruvic acid +2 Ferrocytochrome c +2 Hydrogen ionL-Lactic acid + 2 Ferricytochrome c <> Pyruvic acid +2 Ferrocytochrome c +2 Hydrogen ion