ENTRY       ath00910                    Pathway
NAME        Nitrogen metabolism - Arabidopsis thaliana (thale cress)
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). 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 ath00910  Nitrogen metabolism
MODULE      ath_M00531  Assimilatory nitrate reduction, nitrate => ammonia [PATH:ath00910]
DBLINKS     GO: 0006807
ORGANISM    Arabidopsis thaliana (thale cress) [GN:ath]
GENE        AT4G37550  Acetamidase/Formamidase family protein [KO:K01455] [EC:3.5.1.49]
            AT4G37560  Acetamidase/Formamidase family protein [KO:K01455] [EC:3.5.1.49]
            AT1G08100  NRT2.2; nitrate transporter 2.2 [KO:K02575]
            AT1G08090  NRT2:1; nitrate transporter 2:1 [KO:K02575]
            AT5G14570  NRT2.7; high affinity nitrate transporter 2.7 [KO:K02575]
            AT5G60770  NRT2.4; nitrate transporter 2.4 [KO:K02575]
            AT3G45060  NRT2.6; high affinity nitrate transporter 2.6 [KO:K02575]
            AT5G60780  NRT2.3; nitrate transporter 2.3 [KO:K02575]
            AT1G12940  NRT2.5; nitrate transporter2.5 [KO:K02575]
            AT1G37130  NIA2; nitrate reductase 2 [KO:K10534] [EC:1.7.1.1 1.7.1.2 1.7.1.3]
            AT1G77760  NIA1; nitrate reductase 1 [KO:K10534] [EC:1.7.1.1 1.7.1.2 1.7.1.3]
            AT2G15620  NIR1; nitrite reductase 1 [KO:K00366] [EC:1.7.7.1]
            AT3G44320  NIT3; nitrilase 3 [KO:K01501] [EC:3.5.5.1]
            AT3G44300  NIT2; nitrilase 2 [KO:K01501] [EC:3.5.5.1]
            AT3G44310  NIT1; nitrilase 1 [KO:K01501] [EC:3.5.5.1]
            AT5G07440  GDH2; glutamate dehydrogenase 2 [KO:K00261] [EC:1.4.1.3]
            AT5G18170  GDH1; glutamate dehydrogenase 1 [KO:K00261] [EC:1.4.1.3]
            AT3G03910  GDH3; glutamate dehydrogenase 3 [KO:K00261] [EC:1.4.1.3]
            AT1G51720  Amino acid dehydrogenase family protein [KO:K00262] [EC:1.4.1.4]
            AT5G37600  GSR_1; uncharacterized protein [KO:K01915] [EC:6.3.1.2]
            AT3G17820  GLN1.3; glutamine synthetase 1.3 [KO:K01915] [EC:6.3.1.2]
            AT1G48470  GLN1;5; glutamine synthetase 1;5 [KO:K01915] [EC:6.3.1.2]
            AT5G35630  GS2; glutamine synthetase 2 [KO:K01915] [EC:6.3.1.2]
            AT5G16570  GLN1;4; glutamine synthetase 1;4 [KO:K01915] [EC:6.3.1.2]
            AT1G66200  GSR2; uncharacterized protein [KO:K01915] [EC:6.3.1.2]
            AT5G53460  GLT1; NADH-dependent glutamate synthase 1 [KO:K00264] [EC:1.4.1.14]
            AT2G41220  GLU2; glutamate synthase 2 [KO:K00284] [EC:1.4.7.1]
            AT5G04140  GLU1; glutamate synthase 1 [KO:K00284] [EC:1.4.7.1]
            AT3G23490  CYN; cyanase [KO:K01725] [EC:4.2.1.104]
            AT5G14740  CA2; carbonic anhydrase 2 [KO:K01673] [EC:4.2.1.1]
            AT1G23730  BCA3; beta carbonic anhydrase 3 [KO:K01673] [EC:4.2.1.1]
            AT3G01500  CA1; carbonic anhydrase 1 [KO:K01673] [EC:4.2.1.1]
            AT1G58180  BCA6; beta carbonic anhydrase 6 [KO:K01673] [EC:4.2.1.1]
            AT1G70410  BCA4; beta carbonic anhydrase 4 [KO:K01673] [EC:4.2.1.1]
            AT4G33580  BCA5; beta carbonic anhydrase 5 [KO:K01673] [EC:4.2.1.1]
            AT3G52720  ACA1; alpha carbonic anhydrase 1 [KO:K01674] [EC:4.2.1.1]
            AT4G21000  ACA6; alpha carbonic anhydrase 6 [KO:K01674] [EC:4.2.1.1]
            AT1G08080  ACA7; alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            AT1G08065  ACA5; alpha carbonic anhydrase 5 [KO:K01674] [EC:4.2.1.1]
            AT4G20990  ACA4; alpha carbonic anhydrase 4 [KO:K01674] [EC:4.2.1.1]
            AT5G04180  ACA3; alpha carbonic anhydrase 3 [KO:K01674] [EC:4.2.1.1]
            AT2G28210  ACA2; alpha carbonic anhydrase 2 [KO:K01674] [EC:4.2.1.1]
            AT5G56330  ACA8; alpha carbonic anhydrase 8 [KO:K01674] [EC:4.2.1.1]
COMPOUND    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   PMID:14702404
  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   PMID:17408485
  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   PMID:11004450
  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   PMID:15528644
  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   PMID:11921398
  AUTHORS   Stolz JF, Basu P
  TITLE     Evolution of nitrate reductase: molecular and structural variations on a common function.
  JOURNAL   Chembiochem 3:198-206 (2002)
            DOI:10.1002/1439-7633(20020301)3:2/3<198::AID-CBIC198>3.0.CO;2-C
REFERENCE   PMID:18021072
  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   PMID:19247843
  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   PMID:22221911
  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   PMID:26610024
  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   PMID:26610025
  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
REL_PATHWAY ath00220  Arginine biosynthesis
            ath00250  Alanine, aspartate and glutamate metabolism
            ath00460  Cyanoamino acid metabolism
            ath00630  Glyoxylate and dicarboxylate metabolism
KO_PATHWAY  ko00910
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