KEGG   PATHWAY: ypz00020
Entry
ypz00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Yersinia pestis Z176003
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
ypz00020  Citrate cycle (TCA cycle)
ypz00020

Module
ypz_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:ypz00020]
ypz_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:ypz00020]
ypz_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:ypz00020]
ypz_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:ypz00020]
ypz_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:ypz00020]
Other DBs
GO: 0006099
Organism
Yersinia pestis Z176003 [GN:ypz]
Gene
YPZ3_1006  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
YPZ3_1632  acnA; aconitate hydratase 1 [KO:K27802] [EC:4.2.1.3 4.2.1.99]
YPZ3_3012  acnB; aconitate hydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
YPZ3_2051  icdA; isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
YPZ3_1010  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
YPZ3_1011  sucB; dihydrolipoamide acetyltransferase [KO:K00658] [EC:2.3.1.61]
YPZ3_3458  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
YPZ3_3014  lpdA; dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
YPZ3_1013  sucD; succinyl-CoA synthetase alpha subunit [KO:K01902] [EC:6.2.1.5]
YPZ3_1012  sucC; succinyl-CoA synthetase subunit beta [KO:K01903] [EC:6.2.1.5]
YPZ3_1008  sdhA; succinate dehydrogenase catalytic subunit [KO:K00239] [EC:1.3.5.1]
YPZ3_1009  sdhB; succinate dehydrogenase catalytic subunit [KO:K00240] [EC:1.3.5.1]
YPZ3_1007  sdhD; succinate dehydrogenase cytochrome b556 small membrane subunit [KO:K00242]
YPZ3_0360  frdA; fumarate reductase [KO:K00244] [EC:1.3.5.1]
YPZ3_0359  frdB; succinate dehydrogenase [KO:K00245] [EC:1.3.5.1]
YPZ3_0358  frdC; fumarate reductase subunit C [KO:K00246]
YPZ3_0357  frdD; fumarate reductase subunit D [KO:K00247]
YPZ3_2937  fumA; fumarate hydratase, class I [KO:K01676] [EC:4.2.1.2]
YPZ3_1594  fumC; fumarate hydratase [KO:K01679] [EC:4.2.1.2]
YPZ3_3246  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
YPZ3_0118  pckA; phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
YPZ3_3016  aceE; pyruvate dehydrogenase E1 component [KO:K00163] [EC:1.2.4.1]
YPZ3_3015  aceF; dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex [KO:K00627] [EC:2.3.1.12]
YPZ3_1543  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
ypz00010  Glycolysis / Gluconeogenesis
ypz00053  Ascorbate and aldarate metabolism
ypz00061  Fatty acid biosynthesis
ypz00071  Fatty acid degradation
ypz00190  Oxidative phosphorylation
ypz00220  Arginine biosynthesis
ypz00250  Alanine, aspartate and glutamate metabolism
ypz00280  Valine, leucine and isoleucine degradation
ypz00350  Tyrosine metabolism
ypz00470  D-Amino acid metabolism
ypz00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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