2.0 2012-08-15 08:51:33 -0600 2015-09-17 15:41:55 -0600 ECMDB21652 M2MDB002046 Ferricytochrome c Cytochrome 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 c Cytochrome c (JAN) Ferricytochrome c Holocytochrome c C42H68O13 780.993 780.46599225 λ²-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]propanoate λ²-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]propanoate 9007-43-6 CC(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)CC12C InChI=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-N Solid logp 1.77 ALOGPS logs -4.81 ALOGPS solubility 1.45e-02 g/l ALOGPS logp 0.88 ChemAxon pka_strongest_acidic 3.48 ChemAxon pka_strongest_basic 9.23 ChemAxon iupac λ²-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]propanoate ChemAxon average_mass 780.993 ChemAxon mono_mass 780.46599225 ChemAxon smiles CC(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)CC12C ChemAxon formula C42H68O13 ChemAxon inchi InChI=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+ ChemAxon inchikey FHOKVOIILRHONR-ZVBGSRNCSA-N ChemAxon polar_surface_area 245.72 ChemAxon refractivity 240.33 ChemAxon polarizability 93.79 ChemAxon rotatable_bond_count 16 ChemAxon acceptor_count 12 ChemAxon donor_count 6 ChemAxon physiological_charge -1 ChemAxon formal_charge 0 ChemAxon Nitrogen 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. PW000755 ec00910 Metabolic Pyruvate metabolism ec00620 Microbial metabolism in diverse environments ec01120 Metabolic pathways eco01100 Specdb::MsMs 1327069 Specdb::MsMs 1327070 Specdb::MsMs 1327071 Specdb::MsMs 1441405 Specdb::MsMs 1441406 Specdb::MsMs 1441407 HMDB12920 439171 C00125 15991 Cytochrome_c Respiratory nitrate reductase 1 alpha chain P09152 NARG_ECOLI narG http://ecmdb.ca/proteins/P09152.xml Cytochrome c-552 P0ABK9 NRFA_ECOLI nrfA http://ecmdb.ca/proteins/P0ABK9.xml Respiratory nitrate reductase 2 gamma chain P0AF32 NARV_ECOLI narV http://ecmdb.ca/proteins/P0AF32.xml Respiratory nitrate reductase 1 beta chain P11349 NARH_ECOLI narH http://ecmdb.ca/proteins/P11349.xml Respiratory nitrate reductase 1 gamma chain P11350 NARI_ECOLI narI http://ecmdb.ca/proteins/P11350.xml Probable nitrate reductase molybdenum cofactor assembly chaperone NarW P19317 NARW_ECOLI narW http://ecmdb.ca/proteins/P19317.xml Respiratory nitrate reductase 2 beta chain P19318 NARY_ECOLI narY http://ecmdb.ca/proteins/P19318.xml Respiratory nitrate reductase 2 alpha chain P19319 NARZ_ECOLI narZ http://ecmdb.ca/proteins/P19319.xml L-lactate dehydrogenase [cytochrome] P33232 LLDD_ECOLI lldD http://ecmdb.ca/proteins/P33232.xml Periplasmic nitrate reductase P33937 NAPA_ECOLI napA http://ecmdb.ca/proteins/P33937.xml Probable cytochrome c peroxidase P37197 YHJA_ECOLI yhjA http://ecmdb.ca/proteins/P37197.xml Nitrate reductase molybdenum cofactor assembly chaperone NarJ P0AF26 NARJ_ECOLI narJ http://ecmdb.ca/proteins/P0AF26.xml heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE P32710 nrfE http://ecmdb.ca/proteins/P32710.xml L-Lactic acid + 2 Ferricytochrome c > Pyruvic acid +2 Ferrocytochrome c +2 Hydrogen ion Ammonia + 2 Water + 6 Ferricytochrome c > Nitrite +6 Ferrocytochrome c +7 Hydrogen ion 2 Ferrocytochrome c + Hydrogen peroxide >2 Ferricytochrome c +2 Water L-Lactic acid + 2 Ferricytochrome c + Ferricytochrome c <> Pyruvic acid +2 Ferrocytochrome c +2 Hydrogen ion + Ferrocytochrome c R00196 Ammonia + 2 Water + 6 Ferricytochrome c + Ferricytochrome c <> Nitrite +6 Ferrocytochrome c +6 Hydrogen ion + Ferrocytochrome c R05712 Ferrocytochrome c + Hydrogen peroxide <> Ferricytochrome c + Water R00017 Nitrite + 6 ferrocytochrome c + 7 Hydrogen ion + Nitrite + 6 Ferrocytochrome c <> Ammonia +6 ferricytochrome c +2 Water +6 Ferricytochrome c PW_R002428 L-Lactic acid + 2 Ferricytochrome c <> Pyruvic acid +2 Ferrocytochrome c +2 Hydrogen ion L-Lactic acid + 2 Ferricytochrome c <> Pyruvic acid +2 Ferrocytochrome c +2 Hydrogen ion