KEGG   PATHWAY: ypq00020
Entry
ypq00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Yersinia pseudotuberculosis ATCC 6904
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
ypq00020  Citrate cycle (TCA cycle)
ypq00020

Module
ypq_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:ypq00020]
ypq_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:ypq00020]
ypq_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:ypq00020]
ypq_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:ypq00020]
ypq_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:ypq00020]
Other DBs
GO: 0006099
Organism
Yersinia pseudotuberculosis ATCC 6904 [GN:ypq]
Gene
DJ40_1105  gltA; citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
DJ40_161  acnA; aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
DJ40_1656  acnB; aconitate hydratase 2 [KO:K01682] [EC:4.2.1.3 4.2.1.99]
DJ40_4107  icd; isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
DJ40_1100  sucA; oxoglutarate dehydrogenase (succinyl-transferring), E1 component [KO:K00164] [EC:1.2.4.2]
DJ40_1099  sucB; dihydrolipoyllysine-residue succinyltransferase, E2 component of oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
DJ40_1657  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
DJ40_2305  putative dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
DJ40_1097  sucD; succinyl-CoA ligase [ADP-forming] subunit alpha [KO:K01902] [EC:6.2.1.5]
DJ40_1098  sucC; succinyl-CoA ligase [ADP-forming] subunit beta [KO:K01903] [EC:6.2.1.5]
DJ40_1102  sdhA; succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
DJ40_1101  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
DJ40_1104  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
DJ40_1103  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
DJ40_1994  frdA; fumarate reductase, flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
DJ40_1995  frdB; fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
DJ40_1996  frdC; fumarate reductase subunit C [KO:K00246]
DJ40_1997  frdD; fumarate reductase subunit D [KO:K00247]
DJ40_1577  fumA; fumarate hydratase class I, aerobic [KO:K01676] [EC:4.2.1.2]
DJ40_121  fumC; fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
DJ40_1944  mdh; malate dehydrogenase, NAD-dependent [KO:K00024] [EC:1.1.1.37]
DJ40_2633  pckA; phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
DJ40_1659  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
DJ40_1658  aceF; dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
DJ40_55  nifJ; ferredoxin (flavodoxin) oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
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
ypq00010  Glycolysis / Gluconeogenesis
ypq00053  Ascorbate and aldarate metabolism
ypq00061  Fatty acid biosynthesis
ypq00071  Fatty acid degradation
ypq00190  Oxidative phosphorylation
ypq00220  Arginine biosynthesis
ypq00250  Alanine, aspartate and glutamate metabolism
ypq00280  Valine, leucine and isoleucine degradation
ypq00350  Tyrosine metabolism
ypq00470  D-Amino acid metabolism
ypq00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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