KEGG   PATHWAY: ppud00020
Entry
ppud00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Pseudomonas putida DLL-E4
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
ppud00020  Citrate cycle (TCA cycle)
ppud00020

Module
ppud_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:ppud00020]
ppud_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:ppud00020]
ppud_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:ppud00020]
ppud_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:ppud00020]
ppud_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:ppud00020]
Other DBs
GO: 0006099
Organism
Pseudomonas putida DLL-E4 [GN:ppud]
Gene
DW66_4038  type II citrate synthase [KO:K01647] [EC:2.3.3.1]
DW66_1968  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
DW66_2650  bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
DW66_2174  bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
DW66_3868  isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
DW66_3869  isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
DW66_4033  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
DW66_4032  dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
DW66_4031  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
DW66_4241  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
DW66_5788  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
DW66_4029  succinyl-CoA synthetase subunit alpha [KO:K01902] [EC:6.2.1.5]
DW66_4030  succinyl-CoA synthetase subunit beta [KO:K01903] [EC:6.2.1.5]
DW66_0131  succinate CoA transferase [KO:K18118] [EC:2.8.3.18]
DW66_4035  succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
DW66_4034  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
DW66_4037  succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
DW66_4036  succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
DW66_4684  Fe-S type hydro-lyase subunit alpha [KO:K01676] [EC:4.2.1.2]
DW66_0937  fumarate hydratase [KO:K01679] [EC:4.2.1.2]
DW66_1685  fumarate hydratase [KO:K01679] [EC:4.2.1.2]
DW66_0662  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
DW66_3257  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
DW66_1977  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
DW66_0770  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
DW66_0836  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
DW66_4411  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
DW66_5767  pyruvate carboxylase subunit A [KO:K01959] [EC:6.4.1.1]
DW66_5766  pyruvate carboxylase subunit B [KO:K01960] [EC:6.4.1.1]
DW66_0257  phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
DW66_0346  pyruvate dehydrogenase subunit E1 [KO:K00163] [EC:1.2.4.1]
DW66_0568  branched-chain alpha-keto acid dehydrogenase subunit E2 [KO:K00627] [EC:2.3.1.12]
DW66_0345  dihydrolipoamide acetyltransferase [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
ppud00010  Glycolysis / Gluconeogenesis
ppud00053  Ascorbate and aldarate metabolism
ppud00061  Fatty acid biosynthesis
ppud00071  Fatty acid degradation
ppud00190  Oxidative phosphorylation
ppud00220  Arginine biosynthesis
ppud00250  Alanine, aspartate and glutamate metabolism
ppud00280  Valine, leucine and isoleucine degradation
ppud00350  Tyrosine metabolism
ppud00470  D-Amino acid metabolism
ppud00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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