KEGG   PATHWAY: nfa00910
Entry
nfa00910                    Pathway                                
Name
Nitrogen metabolism - Nocardia farcinica IFM 10152
Description
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 core nitrogen cycle involves four reduction pathways and two oxidation pathways. Nitrogen fixation [MD:M00175] is the process of reducing atmospheric molecular nitrogen to ammonia, a biologically useful reduced form incorporated into amino acids and other vital compounds. 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 [MD:M00531] and dissimilatory nitrate reduction [MD:M00530] both for conversion to ammonia, and denitrification [MD:M00529]. 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. The two oxidation pathways are nitrification [MD:M00528] and anaerobic ammonium oxidation (anammox) [MD:M00973]. Nitrification is the oxidation of ammonia (NH3) with oxygen into nitrite followed by the oxidation of nitrite into nitrate. The first step is performed by ammonia-oxidizing microorganisms (e.g., Nitrosomonas and Nitrosococcus) and the second step by nitrite-oxidizing microorganisms (e.g., Nitrobacter). Anammox is a biochemical process of oxidizing ammonium (NH4+) into dinitrogen gas (N2) using nitrite as an electron acceptor. It occurs in the anammoxosome, a membrane bound compartment inside the cytoplasm, of anammox bacteria (e.g., Planctomycetes).
Class
Metabolism; Energy metabolism
Pathway map
nfa00910  Nitrogen metabolism
nfa00910

Module
nfa_M00530  Dissimilatory nitrate reduction, nitrate => ammonia [PATH:nfa00910]
Other DBs
GO: 0006807
Organism
Nocardia farcinica IFM 10152 [GN:nfa]
Gene
NFA_45620  narK; putative nitrite transporter [KO:K02575]
NFA_45650  narU; putative nitrite extrusion protein [KO:K02575]
NFA_45490  narG; putative nitrate reductase alpha subunit [KO:K00370] [EC:1.7.5.1 1.7.99.-]
NFA_45500  narH; putative nitrate reductase beta subunit [KO:K00371] [EC:1.7.5.1 1.7.99.-]
NFA_45520  narI; putative nitrate reductase gamma subunit [KO:K00374] [EC:1.7.5.1 1.7.99.-]
NFA_45610  nirB; putative nitrite reductase (NAD(P)H) subunit [KO:K00362] [EC:1.7.1.15]
NFA_45600  nirD; putative nitrite reductase (NAD(P)H) subunit [KO:K00363] [EC:1.7.1.15]
NFA_30840  putative dioxygenase [KO:K00459] [EC:1.13.12.16]
NFA_7150  putative dioxygenase [KO:K00459] [EC:1.13.12.16]
NFA_34970  putative dioxygenase [KO:K00459] [EC:1.13.12.16]
NFA_32690  putative nitrilase [KO:K01501] [EC:3.5.5.1]
NFA_12260  hypothetical protein [KO:K15371] [EC:1.4.1.2]
NFA_13060  putative NAD-dependent glutamate dehydrogenase [KO:K15371] [EC:1.4.1.2]
NFA_45920  putative glutamate dehydrogenase [KO:K00262] [EC:1.4.1.4]
NFA_16600  glnA; putative glutamine synthetase [KO:K01915] [EC:6.3.1.2]
NFA_16670  glnA2; putative glutamine synthetase [KO:K01915] [EC:6.3.1.2]
NFA_21040  glnA3; putative glutamine synthetase [KO:K01915] [EC:6.3.1.2]
NFA_960  gltB; putative glutamate synthase large subunit [KO:K00265] [EC:1.4.1.13]
NFA_970  gltD; putative glutamate synthase small subunit [KO:K00266] [EC:1.4.1.13]
NFA_4300  putative carbonic anhydrase [KO:K01673] [EC:4.2.1.1]
PNF1_540  putative transporter [KO:K01673] [EC:4.2.1.1]
NFA_37150  putative transporter [KO:K01673] [EC:4.2.1.1]
Compound
C00007  Oxygen
C00011  CO2
C00014  Ammonia
C00025  L-Glutamate
C00058  Formate
C00064  L-Glutamine
C00088  Nitrite
C00169  Carbamoyl phosphate
C00192  Hydroxylamine
C00244  Nitrate
C00288  HCO3-
C00488  Formamide
C00533  Nitric oxide
C00697  Nitrogen
C00726  Nitrile
C00887  Nitrous oxide
C01417  Cyanate
C01563  Carbamate
C05361  Hydrazine
C06058  Nitroalkane
Reference
  Authors
Scott JD, Ludwig RA
  Title
Azorhizobium caulinodans electron-transferring flavoprotein N electrochemically couples pyruvate dehydrogenase complex activity to N2 fixation.
  Journal
Microbiology 150:117-26 (2004)
DOI:10.1099/mic.0.26603-0
Reference
  Authors
Kneip C, Lockhart P, Voss C, Maier UG
  Title
Nitrogen fixation in eukaryotes--new models for symbiosis.
  Journal
BMC Evol Biol 7:55 (2007)
DOI:10.1186/1471-2148-7-55
Reference
  Authors
Whittaker M, Bergmann D, Arciero D, Hooper AB
  Title
Electron transfer during the oxidation of ammonia by the chemolithotrophic bacterium Nitrosomonas europaea.
  Journal
Biochim Biophys Acta 1459:346-55 (2000)
DOI:10.1016/S0005-2728(00)00171-7
Reference
  Authors
Cabello P, Roldan MD, Moreno-Vivian C
  Title
Nitrate reduction and the nitrogen cycle in archaea.
  Journal
Microbiology 150:3527-46 (2004)
DOI:10.1099/mic.0.27303-0
Reference
  Authors
Stolz JF, Basu P
  Title
Evolution of nitrate reductase: molecular and structural variations on a common function.
  Journal
Reference
  Authors
Morozkina EV, Zvyagilskaya RA
  Title
Nitrate reductases: structure, functions, and effect of stress factors.
  Journal
Biochemistry (Mosc) 72:1151-60 (2007)
DOI:10.1134/S0006297907100124
Reference
  Authors
Jetten MS, Niftrik L, Strous M, Kartal B, Keltjens JT, Op den Camp HJ
  Title
Biochemistry and molecular biology of anammox bacteria.
  Journal
Crit Rev Biochem Mol Biol 44:65-84 (2009)
DOI:10.1080/10409230902722783
Reference
  Authors
Luesken FA, Wu ML, Op den Camp HJ, Keltjens JT, Stunnenberg H, Francoijs KJ, Strous M, Jetten MS
  Title
Effect of oxygen on the anaerobic methanotroph 'Candidatus Methylomirabilis oxyfera': kinetic and transcriptional analysis.
  Journal
Environ Microbiol 14:1024-34 (2012)
DOI:10.1111/j.1462-2920.2011.02682.x
Reference
  Authors
Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M
  Title
Complete nitrification by Nitrospira bacteria.
  Journal
Nature 528:504-9 (2015)
DOI:10.1038/nature16461
Reference
  Authors
van Kessel MA, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJ, Kartal B, Jetten MS, Lucker S
  Title
Complete nitrification by a single microorganism.
  Journal
Nature 528:555-9 (2015)
DOI:10.1038/nature16459
Related
pathway
nfa00220  Arginine biosynthesis
nfa00250  Alanine, aspartate and glutamate metabolism
nfa00460  Cyanoamino acid metabolism
nfa00630  Glyoxylate and dicarboxylate metabolism
nfa00680  Methane metabolism
nfa00720  Other carbon fixation pathways
KO pathway
ko00910   
LinkDB

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