ENTRY       mtr00910                    Pathway
NAME        Nitrogen metabolism - Medicago truncatula (barrel medic)
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 mtr00910  Nitrogen metabolism
MODULE      mtr_M00531  Assimilatory nitrate reduction, nitrate => ammonia [PATH:mtr00910]
DBLINKS     GO: 0006807
ORGANISM    Medicago truncatula (barrel medic) [GN:mtr]
GENE        25493523  formamidase isoform X2 [KO:K01455] [EC:3.5.1.49]
            25501481  high affinity nitrate transporter 2.5 [KO:K02575]
            25492414  high-affinity nitrate transporter 2.1 [KO:K02575]
            25492416  high-affinity nitrate transporter 2.1 [KO:K02575]
            11410374  inducible nitrate reductase [NADH] 2 [KO:K10534] [EC:1.7.1.1 1.7.1.2 1.7.1.3]
            11415881  LOW QUALITY PROTEIN: inducible nitrate reductase [NADH] 2 [KO:K10534] [EC:1.7.1.1 1.7.1.2 1.7.1.3]
            11428809  nitrate reductase [NADH] [KO:K10534] [EC:1.7.1.1 1.7.1.2 1.7.1.3]
            11445727  ferredoxin--nitrite reductase, chloroplastic [KO:K00366] [EC:1.7.7.1]
            25498983  glutamate dehydrogenase 1 [KO:K00261] [EC:1.4.1.3]
            11433210  glutamate dehydrogenase 2 [KO:K00261] [EC:1.4.1.3]
            25493591  glutamate dehydrogenase 2 [KO:K00261] [EC:1.4.1.3]
            11414500  probable glutamate dehydrogenase 3 [KO:K00261] [EC:1.4.1.3]
            25500394  NADP-specific glutamate dehydrogenase isoform X1 [KO:K00262] [EC:1.4.1.4]
            11406645  glutamine synthetase cytosolic isozyme [KO:K01915] [EC:6.3.1.2]
            11431638  glutamine synthetase nodule isozyme [KO:K01915] [EC:6.3.1.2]
            120575736  glutamine synthetase leaf isozyme, chloroplastic-like [KO:K01915] [EC:6.3.1.2]
            25486062  glutamine synthetase leaf isozyme, chloroplastic [KO:K01915] [EC:6.3.1.2]
            11427840  glutamine synthetase nodule isozyme [KO:K01915] [EC:6.3.1.2]
            25482265  glutamate synthase [NADH], amyloplastic isoform X1 [KO:K00264] [EC:1.4.1.14]
            11415038  ferredoxin-dependent glutamate synthase, chloroplastic [KO:K00284] [EC:1.4.7.1]
            25482994  cyanate hydratase-like [KO:K01725] [EC:4.2.1.104]
            11433869  beta carbonic anhydrase 5, chloroplastic [KO:K01673] [EC:4.2.1.1]
            11429026  carbonic anhydrase 2 [KO:K01673] [EC:4.2.1.1]
            11432684  carbonic anhydrase 2 [KO:K01673] [EC:4.2.1.1]
            25501341  carbonic anhydrase 2 [KO:K01673] [EC:4.2.1.1]
            11407419  carbonic anhydrase 2 isoform X1 [KO:K01673] [EC:4.2.1.1]
            11435508  beta carbonic anhydrase 5, chloroplastic isoform X1 [KO:K01673] [EC:4.2.1.1]
            11428425  carbonic anhydrase, chloroplastic isoform X1 [KO:K01673] [EC:4.2.1.1]
            25480663  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            25499340  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            25480666  alpha carbonic anhydrase 7-like isoform X1 [KO:K01674] [EC:4.2.1.1]
            25483818  alpha carbonic anhydrase 1, chloroplastic [KO:K01674] [EC:4.2.1.1]
            25483819  alpha carbonic anhydrase 1, chloroplastic [KO:K01674] [EC:4.2.1.1]
            25483943  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            25483945  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            11415364  alpha carbonic anhydrase 4 [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 mtr00220  Arginine biosynthesis
            mtr00250  Alanine, aspartate and glutamate metabolism
            mtr00460  Cyanoamino acid metabolism
            mtr00630  Glyoxylate and dicarboxylate metabolism
KO_PATHWAY  ko00910
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