KEGG   PATHWAY: rva00020
Entry
rva00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Rhodomicrobium vannielii
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
rva00020  Citrate cycle (TCA cycle)
rva00020

Module
rva_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:rva00020]
rva_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:rva00020]
rva_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:rva00020]
rva_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:rva00020]
rva_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:rva00020]
Other DBs
GO: 0006099
Organism
Rhodomicrobium vannielii [GN:rva]
Gene
Rvan_3206  citrate synthase I [KO:K01647] [EC:2.3.3.1]
Rvan_1154  aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
Rvan_1988  aconitate hydratase 2 [KO:K01682] [EC:4.2.1.3 4.2.1.99]
Rvan_1989  isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
Rvan_0651  2-oxoglutarate dehydrogenase, E1 subunit [KO:K00164] [EC:1.2.4.2]
Rvan_0652  2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
Rvan_1330  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Rvan_0653  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Rvan_0650  succinyl-CoA synthetase, alpha subunit [KO:K01902] [EC:6.2.1.5]
Rvan_3431  CoA-binding domain protein [KO:K01902] [EC:6.2.1.5]
Rvan_0647  succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
Rvan_3430  Succinate--CoA ligase (ADP-forming) [KO:K01903] [EC:6.2.1.5]
Rvan_0941  succinate CoA transferase [KO:K18118] [EC:2.8.3.18]
Rvan_0093  succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
Rvan_1599  succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
Rvan_0095  succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
Rvan_0094  succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
Rvan_3006  fumarate reductase, flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
Rvan_3007  succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00245] [EC:1.3.5.1]
Rvan_3008  fumarate reductase subunit C [KO:K00246]
Rvan_3009  fumarate reductase D subunit [KO:K00247]
Rvan_1966  fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
Rvan_0646  malate dehydrogenase, NAD-dependent [KO:K00024] [EC:1.1.1.37]
Rvan_0659  phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
Rvan_1335  pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit [KO:K00161] [EC:1.2.4.1]
Rvan_1333  Transketolase central region [KO:K00162] [EC:1.2.4.1]
Rvan_1331  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
rva00010  Glycolysis / Gluconeogenesis
rva00053  Ascorbate and aldarate metabolism
rva00061  Fatty acid biosynthesis
rva00071  Fatty acid degradation
rva00190  Oxidative phosphorylation
rva00220  Arginine biosynthesis
rva00250  Alanine, aspartate and glutamate metabolism
rva00280  Valine, leucine and isoleucine degradation
rva00350  Tyrosine metabolism
rva00470  D-Amino acid metabolism
rva00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   

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