KEGG   PATHWAY: plyc00020
Entry
plyc00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Paenibacillus lycopersici
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
plyc00020  Citrate cycle (TCA cycle)
plyc00020

Module
plyc_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:plyc00020]
plyc_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:plyc00020]
plyc_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:plyc00020]
plyc_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:plyc00020]
Other DBs
GO: 0006099
Organism
Paenibacillus lycopersici [GN:plyc]
Gene
GXP70_05765  2-methylcitrate synthase [KO:K01659] [EC:2.3.3.5]
GXP70_09380  citZ; citrate synthase [KO:K01659] [EC:2.3.3.5]
GXP70_04395  acnA; aconitate hydratase AcnA [KO:K27802] [EC:4.2.1.3 4.2.1.99]
GXP70_09385  icd; NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
GXP70_17630  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
GXP70_17625  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
GXP70_17865  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
GXP70_11300  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
GXP70_12985  2-oxoacid:acceptor oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
GXP70_12990  2-oxoacid:ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
GXP70_12515  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
GXP70_12510  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
GXP70_08900  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
GXP70_08905  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
GXP70_08895  succinate dehydrogenase [KO:K00241]
GXP70_22640  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
GXP70_23735  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
GXP70_09390  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
GXP70_01555  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
GXP70_17880  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
GXP70_17875  alpha-ketoacid dehydrogenase subunit beta [KO:K00162] [EC:1.2.4.1]
GXP70_17870  2-oxo acid dehydrogenase subunit E2 [KO:K00627] [EC:2.3.1.12]
GXP70_17770  pyruvate synthase [KO:K00169] [EC:1.2.7.1]
GXP70_17775  4Fe-4S dicluster domain-containing protein [KO:K00172] [EC:1.2.7.1]
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
plyc00010  Glycolysis / Gluconeogenesis
plyc00053  Ascorbate and aldarate metabolism
plyc00061  Fatty acid biosynthesis
plyc00071  Fatty acid degradation
plyc00190  Oxidative phosphorylation
plyc00220  Arginine biosynthesis
plyc00250  Alanine, aspartate and glutamate metabolism
plyc00280  Valine, leucine and isoleucine degradation
plyc00350  Tyrosine metabolism
plyc00470  D-Amino acid metabolism
plyc00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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