KEGG   PATHWAY: vpe00020
Entry
vpe00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Variovorax paradoxus EPS
Description
The citrate cycle (TCA cycle, Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA, the activated form of acetate, derived from glycolysis and pyruvate oxidation for carbohydrates and from beta oxidation of fatty acids. The two-carbon acetyl group in acetyl-CoA is transferred to the four-carbon compound of oxaloacetate to form the six-carbon compound of citrate. In a series of reactions two carbons in citrate are oxidized to CO2 and the reaction pathway supplies NADH for use in the oxidative phosphorylation and other metabolic processes. The pathway also supplies important precursor metabolites including 2-oxoglutarate. At the end of the cycle the remaining four-carbon part is transformed back to oxaloacetate. According to the genome sequence data, many organisms seem to lack genes for the full cycle [MD:M00009], but contain genes for specific segments [MD:M00010 M00011].
Class
Metabolism; Carbohydrate metabolism
Pathway map
vpe00020  Citrate cycle (TCA cycle)
vpe00020

Module
vpe_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:vpe00020]
vpe_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:vpe00020]
vpe_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:vpe00020]
vpe_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:vpe00020]
vpe_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:vpe00020]
Other DBs
GO: 0006099
Organism
Variovorax paradoxus EPS [GN:vpe]
Gene
Varpa_1410  citrate synthase [KO:K01647] [EC:2.3.3.1]
Varpa_5723  Citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
Varpa_5724  Citrate synthase [KO:K01647] [EC:2.3.3.1]
Varpa_5343  citrate synthase [KO:K01647] [EC:2.3.3.1]
Varpa_1569  citrate synthase I [KO:K01647] [EC:2.3.3.1]
Varpa_1593  aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
Varpa_1580  aconitate hydratase 2 [KO:K01682] [EC:4.2.1.3 4.2.1.99]
Varpa_1457  isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
Varpa_3278  isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
Varpa_4752  Isocitrate dehydrogenase (NAD(+)) [KO:K00030] [EC:1.1.1.41]
Varpa_3719  2-oxoglutarate dehydrogenase, E1 subunit [KO:K00164] [EC:1.2.4.2]
Varpa_3718  2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
Varpa_3727  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Varpa_3717  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Varpa_2456  pyruvate flavodoxin/ferredoxin oxidoreductase domain protein [KO:K00174] [EC:1.2.7.3 1.2.7.11]
Varpa_2457  2-oxoglutarate synthase [KO:K00175] [EC:1.2.7.3 1.2.7.11]
Varpa_5914  succinyl-CoA synthetase, alpha subunit [KO:K01902] [EC:6.2.1.5]
Varpa_5195  succinyl-CoA synthetase, alpha subunit [KO:K01902] [EC:6.2.1.5]
Varpa_5915  succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
Varpa_5196  succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
Varpa_1572  succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
Varpa_1571  succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
Varpa_1574  succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
Varpa_1573  succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
Varpa_3414  hydro-lyase, Fe-S type, tartrate/fumarate subfamily, alpha subunit [KO:K01676] [EC:4.2.1.2]
Varpa_3410  fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
Varpa_1576  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
Varpa_0172  Phosphoenolpyruvate carboxykinase (GTP) [KO:K01596] [EC:4.1.1.32]
Varpa_5865  2-oxo-acid dehydrogenase E1 subunit, homodimeric type [KO:K00163] [EC:1.2.4.1]
Varpa_3730  2-oxo-acid dehydrogenase E1 subunit, homodimeric type [KO:K00163] [EC:1.2.4.1]
Varpa_3729  pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase [KO:K00627] [EC:2.3.1.12]
Compound
C00022  Pyruvate
C00024  Acetyl-CoA
C00026  2-Oxoglutarate
C00036  Oxaloacetate
C00042  Succinate
C00068  Thiamin diphosphate
C00074  Phosphoenolpyruvate
C00091  Succinyl-CoA
C00122  Fumarate
C00149  (S)-Malate
C00158  Citrate
C00311  Isocitrate
C00417  cis-Aconitate
C05125  2-(alpha-Hydroxyethyl)thiamine diphosphate
C05379  Oxalosuccinate
C05381  3-Carboxy-1-hydroxypropyl-ThPP
C15972  Enzyme N6-(lipoyl)lysine
C15973  Enzyme N6-(dihydrolipoyl)lysine
C16254  [Dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine
C16255  [Dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine
Reference
  Authors
Nishizuka Y (ed).
  Title
[Metabolic Maps] (In Japanese)
  Journal
Tokyo Kagaku Dojin (1980)
Reference
  Authors
Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds).
  Title
[Cellular Functions and Metabolic Maps] (In Japanese)
  Journal
Tokyo Kagaku Dojin (1997)
Reference
  Authors
Michal G.
  Title
Biochemical Pathways
  Journal
Wiley (1999)
Related
pathway
vpe00010  Glycolysis / Gluconeogenesis
vpe00053  Ascorbate and aldarate metabolism
vpe00061  Fatty acid biosynthesis
vpe00071  Fatty acid degradation
vpe00190  Oxidative phosphorylation
vpe00220  Arginine biosynthesis
vpe00250  Alanine, aspartate and glutamate metabolism
vpe00280  Valine, leucine and isoleucine degradation
vpe00350  Tyrosine metabolism
vpe00470  D-Amino acid metabolism
vpe00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   

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