KEGG   PATHWAY: amd00020
Entry
amd00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Amycolatopsis mediterranei U32
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
amd00020  Citrate cycle (TCA cycle)
amd00020

Module
amd_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:amd00020]
amd_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:amd00020]
amd_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:amd00020]
amd_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:amd00020]
amd_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:amd00020]
Other DBs
GO: 0006099
Organism
Amycolatopsis mediterranei U32 [GN:amd]
Gene
AMED_0540  korB; 2-oxoglutarate ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
AMED_0541  korA; 2-oxoglutarate ferredoxin oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
AMED_0802  sucC; succinyl-CoA synthetase beta subunit [KO:K01903] [EC:6.2.1.5]
AMED_0803  sucD; succinyl-CoA synthetase alpha subunit [KO:K01902] [EC:6.2.1.5]
AMED_0833  icd; isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
AMED_0849  sdhB; succinate dehydrogenase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
AMED_0850  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
AMED_0851  sdhD; succinate dehydrogenase hydrophobic membrane anchor protein [KO:K00242]
AMED_0852  sdhC; succinate dehydrogenase cytochrome b-556 subunit [KO:K00241]
AMED_1761  pyc; pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
AMED_1985  aceE; pyruvate dehydrogenase E1 component [KO:K00163] [EC:1.2.4.1]
AMED_2113  aceE; pyruvate dehydrogenase E1 component [KO:K00163] [EC:1.2.4.1]
AMED_2168  sucB; 2-oxoglutarate dehydrogenase E2 component [KO:K00627] [EC:2.3.1.12]
AMED_2169  pdhD; dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
AMED_2352  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
AMED_2353  sdhB; succinate dehydrogenase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
AMED_2567  [KO:K01676] [EC:4.2.1.2]
AMED_3219  sdhC; succinate dehydrogenase cytochrome b-556 subunit [KO:K00241]
AMED_3220  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
AMED_3221  sdhB; succinate dehydrogenase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
AMED_4569  sucD; succinyl-CoA synthetase alpha subunit [KO:K01902] [EC:6.2.1.5]
AMED_4570  sucC; succinyl-CoA synthetase beta subunit [KO:K01903] [EC:6.2.1.5]
AMED_4640  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
AMED_4853  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
AMED_4955  acnA; aconitate hydratase 1 [KO:K27802]
AMED_6934  pdhD; dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
AMED_7278  fumA; fumarate hydratase subunit alpha [KO:K01677] [EC:4.2.1.2]
AMED_7279  fumB; fumarate hydratase subunit beta [KO:K01678] [EC:4.2.1.2]
AMED_7949  kgd; 2-oxoglutarate decarboxylase [KO:K01616] [EC:2.2.1.5 4.1.1.71 1.2.4.2 2.3.1.61]
AMED_8062  fumC; fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
AMED_8426  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
AMED_8451  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
AMED_9253  pckA; phosphoenolpyruvate carboxykinase [KO:K01596] [EC:4.1.1.32]
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
amd00010  Glycolysis / Gluconeogenesis
amd00053  Ascorbate and aldarate metabolism
amd00061  Fatty acid biosynthesis
amd00071  Fatty acid degradation
amd00190  Oxidative phosphorylation
amd00220  Arginine biosynthesis
amd00250  Alanine, aspartate and glutamate metabolism
amd00280  Valine, leucine and isoleucine degradation
amd00350  Tyrosine metabolism
amd00470  D-Amino acid metabolism
amd00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   

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