KEGG   PATHWAY: ypm00020
Entry
ypm00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Yersinia pestis 91001 (biovar Microtus)
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
ypm00020  Citrate cycle (TCA cycle)
ypm00020

Module
ypm_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:ypm00020]
ypm_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:ypm00020]
ypm_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:ypm00020]
ypm_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:ypm00020]
ypm_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:ypm00020]
Other DBs
GO: 0006099
Organism
Yersinia pestis 91001 (biovar Microtus) [GN:ypm]
Gene
YP_1048  gltA; citrate synthase GltA [KO:K01647] [EC:2.3.3.1]
YP_2019  acnA; aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
YP_0270  acnB; aconitate hydratase 2 [KO:K01682] [EC:4.2.1.3 4.2.1.99]
YP_1771  icdA; isocitrate dehydrogenase (NADP) [KO:K00031] [EC:1.1.1.42]
YP_1043  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
YP_1042  sucB; dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
YP_3131  lpd; putative pyridine nucleotide-disulfide oxidoreductase [KO:K00382] [EC:1.8.1.4]
YP_0268  lpdA; dihydrolipoamide dehydrogenase component of pyruvate dehydrogenase complex [KO:K00382] [EC:1.8.1.4]
YP_1040  sucD; succinyl-CoA synthetase alpha chain [KO:K01902] [EC:6.2.1.5]
YP_1041  sucC; succinyl-CoA synthetase beta chain [KO:K01903] [EC:6.2.1.5]
YP_1045  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
YP_1044  sdhB; succinate dehydrogenase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
YP_1047  sdhC; succinate dehydrogenase cytochrome b-556 subunit [KO:K00241]
YP_1046  sdhD; succinate dehydrogenase hydrophobic membrane anchor protein [KO:K00242]
YP_0515  frdA; fumarate reductase flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
YP_0514  frdB; fumarate reductase iron-sulfur protein [KO:K00245] [EC:1.3.5.1]
YP_0513  frdC; fumarate reductase hydrophobic protein [KO:K00246]
YP_0512  frdD; fumarate reductase hydrophobic protein [KO:K00247]
YP_0352  fumA; fumarate hydratase, class I [KO:K01676] [EC:4.2.1.2]
YP_2061  fumC; fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
YP_0567  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
YP_0139  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
YP_0265  aceE; pyruvate dehydrogenase E1 component [KO:K00163] [EC:1.2.4.1]
YP_0266  aceF; dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex [KO:K00627] [EC:2.3.1.12]
YP_2120  nifJ; putative pyruvate-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
ypm00010  Glycolysis / Gluconeogenesis
ypm00053  Ascorbate and aldarate metabolism
ypm00061  Fatty acid biosynthesis
ypm00071  Fatty acid degradation
ypm00190  Oxidative phosphorylation
ypm00220  Arginine biosynthesis
ypm00250  Alanine, aspartate and glutamate metabolism
ypm00280  Valine, leucine and isoleucine degradation
ypm00350  Tyrosine metabolism
ypm00470  D-Amino acid metabolism
ypm00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   

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