KEGG   PATHWAY: vap00020
Entry
vap00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Variovorax paradoxus S110
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
vap00020  Citrate cycle (TCA cycle)
vap00020

Module
vap_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:vap00020]
vap_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:vap00020]
vap_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:vap00020]
vap_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:vap00020]
vap_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:vap00020]
Other DBs
GO: 0006099
Organism
Variovorax paradoxus S110 [GN:vap]
Gene
Vapar_5653  citrate synthase [KO:K01647] [EC:2.3.3.1]
Vapar_5753  Citrate synthase [KO:K01647] [EC:2.3.3.1]
Vapar_4823  citrate synthase [KO:K01647] [EC:2.3.3.1]
Vapar_1425  citrate synthase I [KO:K01647] [EC:2.3.3.1]
Vapar_1313  citrate synthase [KO:K01647] [EC:2.3.3.1]
Vapar_1440  aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
Vapar_6188  aconitate hydratase domain protein [KO:K01681] [EC:4.2.1.3]
Vapar_1436  aconitate hydratase 2 [KO:K01682] [EC:4.2.1.3 4.2.1.99]
Vapar_2649  isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
Vapar_4079  Isocitrate dehydrogenase (NAD(+)) [KO:K00030] [EC:1.1.1.41]
Vapar_2171  2-oxoglutarate dehydrogenase, E1 subunit [KO:K00164] [EC:1.2.4.2]
Vapar_2172  2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
Vapar_5336  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Vapar_2165  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Vapar_2173  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Vapar_5478  pyruvate flavodoxin/ferredoxin oxidoreductase domain protein [KO:K00174] [EC:1.2.7.3 1.2.7.11]
Vapar_5477  thiamine pyrophosphate protein domain protein TPP-binding [KO:K00175] [EC:1.2.7.3 1.2.7.11]
Vapar_4481  succinyl-CoA synthetase, alpha subunit [KO:K01902] [EC:6.2.1.5]
Vapar_5191  succinyl-CoA synthetase, alpha subunit [KO:K01902] [EC:6.2.1.5]
Vapar_4482  succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
Vapar_5192  succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
Vapar_1428  succinate dehydrogenase or fumarate reductase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
Vapar_1427  succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
Vapar_1430  succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
Vapar_1429  succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
Vapar_5615  fumarate reductase/succinate dehydrogenase flavoprotein domain protein [KO:K00244] [EC:1.3.5.1]
Vapar_5618  succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00245] [EC:1.3.5.1]
Vapar_5617  conserved hypothetical protein [KO:K00246]
Vapar_5616  succinate dehydrogenase, cytochrome b subunit [KO:K00247]
Vapar_2518  hydro-lyase, Fe-S type, tartrate/fumarate subfamily, alpha subunit [KO:K01676] [EC:4.2.1.2]
Vapar_2522  fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
Vapar_1432  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
Vapar_0147  Phosphoenolpyruvate carboxykinase (GTP) [KO:K01596] [EC:4.1.1.32]
Vapar_5334  2-oxo-acid dehydrogenase E1 subunit, homodimeric type [KO:K00163] [EC:1.2.4.1]
Vapar_2162  2-oxo-acid dehydrogenase E1 subunit, homodimeric type [KO:K00163] [EC:1.2.4.1]
Vapar_5149  alpha-ketoglutarate dehydrogenase [KO:K00163] [EC:1.2.4.1]
Vapar_5335  catalytic domain of components of various dehydrogenase complexes [KO:K00627] [EC:2.3.1.12]
Vapar_2163  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
vap00010  Glycolysis / Gluconeogenesis
vap00053  Ascorbate and aldarate metabolism
vap00061  Fatty acid biosynthesis
vap00071  Fatty acid degradation
vap00190  Oxidative phosphorylation
vap00220  Arginine biosynthesis
vap00250  Alanine, aspartate and glutamate metabolism
vap00280  Valine, leucine and isoleucine degradation
vap00350  Tyrosine metabolism
vap00470  D-Amino acid metabolism
vap00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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