KEGG   PATHWAY: pym00020
Entry
pym00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Pseudomonas yamanorum
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
pym00020  Citrate cycle (TCA cycle)
pym00020

Module
pym_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:pym00020]
pym_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:pym00020]
pym_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:pym00020]
pym_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:pym00020]
pym_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:pym00020]
Other DBs
GO: 0006099
Organism
Pseudomonas yamanorum [GN:pym]
Gene
AK972_1574  Citrate synthase (si) [KO:K01647] [EC:2.3.3.1]
AK972_4255  Aconitate hydratase [KO:K01681] [EC:4.2.1.3]
AK972_2776  Aconitate hydratase 2 2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
AK972_3644  Isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
AK972_3645  Isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
AK972_1579  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
AK972_1580  Dihydrolipoamide succinyltransferase component (E2) of 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
AK972_1581  Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase [KO:K00382] [EC:1.8.1.4]
AK972_1819  Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase [KO:K00382] [EC:1.8.1.4]
AK972_1583  Succinyl-CoA ligase [ADP-forming] alpha chain [KO:K01902] [EC:6.2.1.5]
AK972_1582  Succinyl-CoA ligase [ADP-forming] beta chain [KO:K01903] [EC:6.2.1.5]
AK972_5821  Propionyl-CoA:succinyl-CoA transferase [KO:K18118] [EC:2.8.3.18]
AK972_1577  Succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
AK972_1578  Succinate dehydrogenase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
AK972_1575  Succinate dehydrogenase cytochrome b-556 subunit [KO:K00241]
AK972_1576  Succinate dehydrogenase hydrophobic membrane anchor protein [KO:K00242]
AK972_1072  Fumarate hydratase class I, aerobic [KO:K01676] [EC:4.2.1.2]
AK972_4004  Fumarate hydratase class II [KO:K01679] [EC:4.2.1.2]
AK972_0721  Fumarate hydratase class II [KO:K01679] [EC:4.2.1.2]
AK972_0751  Malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
AK972_4203  Malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
AK972_6003  Pyruvate carboxyl transferase subunit A [KO:K01959] [EC:6.4.1.1]
AK972_6004  Pyruvate carboxyl transferase subunit B [KO:K01960] [EC:6.4.1.1]
AK972_5680  Phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
AK972_5455  Pyruvate dehydrogenase E1 component [KO:K00163] [EC:1.2.4.1]
AK972_2513  Pyruvate dehydrogenase E1 component [KO:K00163] [EC:1.2.4.1]
AK972_1868  Pyruvate dehydrogenase E1 component [KO:K00163] [EC:1.2.4.1]
AK972_5456  Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex [KO:K00627] [EC:2.3.1.12]
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
pym00010  Glycolysis / Gluconeogenesis
pym00053  Ascorbate and aldarate metabolism
pym00061  Fatty acid biosynthesis
pym00071  Fatty acid degradation
pym00190  Oxidative phosphorylation
pym00220  Arginine biosynthesis
pym00250  Alanine, aspartate and glutamate metabolism
pym00280  Valine, leucine and isoleucine degradation
pym00350  Tyrosine metabolism
pym00470  D-Amino acid metabolism
pym00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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