2.0 2012-05-31 14:05:23 -0600 2015-09-13 12:56:14 -0600 ECMDB04114 M2MDB000616 Nitrogen Elemental nitrogen is a colorless, odorless, tasteless and mostly inert diatomic gas at standard conditions, constituting 78% by volume of Earth's atmosphere. Nitrogen occurs in all living organisms. In E. coli, nitrogen exists as a dissolved gas in the cell cytoplasm. E. coli is not able to "fix" nitrogen or readily incorporate it into metabolites. It is a constituent element of amino acids and therefore of proteins and nucleic acids (DNA and RNA). The characteristic odor of animal flesh decay is caused by nitrogen-containing long-chain amines, such as putrescine and cadaverine. Decay of organisms and their waste products may produce small amounts of nitrate, but most decay eventually returns nitrogen content to the atmosphere, as molecular nitrogen. The circulation of nitrogen from the atmosphere through organics and then back to the atmosphere is commonly referred to as the nitrogen cycle. Dinitrogen Nitrogen Nitrogen gas Nitrogen oxide NO2 N2 28.0134 28.00614801 diazyne nitrogen 7727-37-9 N#N InChI=1S/N2/c1-2 IJGRMHOSHXDMSA-UHFFFAOYSA-N Liquid Outer membrane Inner membrane melting_point -210.01 oC logp 0.31 ChemAxon iupac diazyne ChemAxon average_mass 28.0134 ChemAxon mono_mass 28.00614801 ChemAxon smiles N#N ChemAxon formula N2 ChemAxon inchi InChI=1S/N2/c1-2 ChemAxon inchikey IJGRMHOSHXDMSA-UHFFFAOYSA-N ChemAxon polar_surface_area 47.58 ChemAxon refractivity 26.23 ChemAxon polarizability 1.77 ChemAxon rotatable_bond_count 0 ChemAxon acceptor_count 2 ChemAxon donor_count 0 ChemAxon physiological_charge 0 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 Microbial metabolism in diverse environments ec01120 Phosphotransferase system (PTS) ec02060 Two-component system ec02020 Specdb::CMs 16976 Specdb::CMs 146987 Specdb::EiMs 1537 Specdb::MsMs 26156 Specdb::MsMs 26157 Specdb::MsMs 26158 Specdb::MsMs 32714 Specdb::MsMs 32715 Specdb::MsMs 32716 Specdb::MsMs 2881079 Specdb::MsMs 2881080 Specdb::MsMs 2881081 HMDB01371 947 922 C00697 17997 NITROGEN-OXIDE TFH Nitrogen Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. 22080510 Balafa C, Smith-Thomas L, Phillips J, Moustafa M, George E, Blount M, Nicol S, Westgate G, MacNeil S: Dopa oxidase activity in the hair, skin and ocular melanocytes is increased in the presence of stressed fibroblasts. Exp Dermatol. 2005 May;14(5):363-72. 15854130 Konya C, Sanada H, Sugama J, Kitayama Y, Ishikawa S, Togashi H, Tamura S: Skin debris and micro-organisms on the periwound skin of pressure ulcers and the influence of periwound cleansing on microbial flora. Ostomy Wound Manage. 2005 Jan;51(1):50-9. 15695835 http://hmdb.ca/system/metabolites/msds/000/001/233/original/HMDB01371.pdf?1358462997 Flavodoxin-1 P61949 FLAV_ECOLI fldA http://ecmdb.ca/proteins/P61949.xml Adenosine triphosphate + Nitrogen + 6 Reduced flavodoxin + Water <> Phosphate + ADP +6 Oxidized flavodoxin +2 Ammonia R05186 Adenosine triphosphate + Nitrogen + 6 a reduced flavodoxin + Water <> Phosphate + Adenosine diphosphate + an oxidized flavodoxin +2 Ammonia + ADP PW_R005170