KEGG   PATHWAY: ypy00020
Entry
ypy00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Yersinia pseudotuberculosis YPIII (serotype O:3)
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
ypy00020  Citrate cycle (TCA cycle)
ypy00020

Module
ypy_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:ypy00020]
ypy_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:ypy00020]
ypy_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:ypy00020]
ypy_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:ypy00020]
ypy_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:ypy00020]
Other DBs
GO: 0006099
Organism
Yersinia pseudotuberculosis YPIII (serotype O:3) [GN:ypy]
Gene
YPK_2973  citrate synthase I [KO:K01647] [EC:2.3.3.1]
YPK_2030  aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
YPK_3487  aconitate hydratase 2 [KO:K01682] [EC:4.2.1.3 4.2.1.99]
YPK_1723  isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
YPK_2968  2-oxoglutarate dehydrogenase, E1 subunit [KO:K00164] [EC:1.2.4.2]
YPK_2967  2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
YPK_3489  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
YPK_4081  pyridine nucleotide-disulphide oxidoreductase dimerisation region [KO:K00382] [EC:1.8.1.4]
YPK_2965  succinyl-CoA synthetase, alpha subunit [KO:K01902] [EC:6.2.1.5]
YPK_2966  succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
YPK_2970  succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
YPK_2969  succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
YPK_2972  succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
YPK_2971  succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
YPK_3813  fumarate reductase, flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
YPK_3814  succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00245] [EC:1.3.5.1]
YPK_3815  fumarate reductase subunit C [KO:K00246]
YPK_3816  fumarate reductase D subunit [KO:K00247]
YPK_3404  hydro-lyase, Fe-S type, tartrate/fumarate subfamily, beta subunit [KO:K01676] [EC:4.2.1.2]
YPK_1985  fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
YPK_3761  malate dehydrogenase, NAD-dependent [KO:K00024] [EC:1.1.1.37]
YPK_0174  Phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
YPK_3491  2-oxo-acid dehydrogenase E1 subunit, homodimeric type [KO:K00163] [EC:1.2.4.1]
YPK_3490  pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase [KO:K00627] [EC:2.3.1.12]
YPK_1913  pyruvate flavodoxin/ferredoxin oxidoreductase domain protein [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
ypy00010  Glycolysis / Gluconeogenesis
ypy00053  Ascorbate and aldarate metabolism
ypy00061  Fatty acid biosynthesis
ypy00071  Fatty acid degradation
ypy00190  Oxidative phosphorylation
ypy00220  Arginine biosynthesis
ypy00250  Alanine, aspartate and glutamate metabolism
ypy00280  Valine, leucine and isoleucine degradation
ypy00350  Tyrosine metabolism
ypy00470  D-Amino acid metabolism
ypy00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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