KEGG   PATHWAY: ypc00020
Entry
ypc00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Yersinia pseudotuberculosis 1
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
ypc00020  Citrate cycle (TCA cycle)
ypc00020

Module
ypc_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:ypc00020]
ypc_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:ypc00020]
ypc_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:ypc00020]
ypc_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:ypc00020]
ypc_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:ypc00020]
Other DBs
GO: 0006099
Organism
Yersinia pseudotuberculosis 1 [GN:ypc]
Gene
BZ23_728  gltA; citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
BZ23_1708  acnA; aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
BZ23_193  acnB; aconitate hydratase 2 [KO:K01682] [EC:4.2.1.3 4.2.1.99]
BZ23_2005  icd; isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
BZ23_733  sucA; oxoglutarate dehydrogenase (succinyl-transferring), E1 component [KO:K00164] [EC:1.2.4.2]
BZ23_734  sucB; dihydrolipoyllysine-residue succinyltransferase, E2 component of oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
BZ23_192  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
BZ23_3736  glucose inhibited division A family protein [KO:K00382] [EC:1.8.1.4]
BZ23_736  sucD; succinyl-CoA ligase [ADP-forming] subunit alpha [KO:K01902] [EC:6.2.1.5]
BZ23_735  sucC; succinyl-CoA ligase [ADP-forming] subunit beta [KO:K01903] [EC:6.2.1.5]
BZ23_731  sdhA; succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
BZ23_732  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
BZ23_729  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
BZ23_730  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
BZ23_4053  frdA; fumarate reductase, flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
BZ23_4052  frdB; fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
BZ23_4051  frdC; fumarate reductase subunit C [KO:K00246]
BZ23_4050  frdD; fumarate reductase subunit D [KO:K00247]
BZ23_271  fumA; fumarate hydratase class I, aerobic [KO:K01676] [EC:4.2.1.2]
BZ23_1753  fumC; fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
BZ23_4104  mdh; malate dehydrogenase, NAD-dependent [KO:K00024] [EC:1.1.1.37]
BZ23_3383  pckA; phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
BZ23_190  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
BZ23_191  aceF; dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
BZ23_1820  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
ypc00010  Glycolysis / Gluconeogenesis
ypc00053  Ascorbate and aldarate metabolism
ypc00061  Fatty acid biosynthesis
ypc00071  Fatty acid degradation
ypc00190  Oxidative phosphorylation
ypc00220  Arginine biosynthesis
ypc00250  Alanine, aspartate and glutamate metabolism
ypc00280  Valine, leucine and isoleucine degradation
ypc00350  Tyrosine metabolism
ypc00470  D-Amino acid metabolism
ypc00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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