KEGG   PATHWAY: prk00020
Entry
prk00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Pedobacter riviphilus
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
prk00020  Citrate cycle (TCA cycle)
prk00020

Module
prk_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:prk00020]
prk_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:prk00020]
prk_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:prk00020]
prk_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:prk00020]
Other DBs
GO: 0006099
Organism
Pedobacter riviphilus [GN:prk]
Gene
H9N25_08860  citrate synthase [KO:K01647] [EC:2.3.3.1]
H9N25_15960  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
H9N25_15955  bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
H9N25_02695  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
H9N25_16985  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
H9N25_09680  2-oxo acid dehydrogenase subunit E2 [KO:K00658] [EC:2.3.1.61]
H9N25_16980  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
H9N25_05495  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
H9N25_21075  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
H9N25_23025  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
H9N25_15110  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
H9N25_04600  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
H9N25_22005  fumarate reductase/succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
H9N25_22010  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
H9N25_22000  succinate dehydrogenase cytochrome b subunit [KO:K00241]
H9N25_22765  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
H9N25_03320  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
H9N25_00485  mqo; malate dehydrogenase (quinone) [KO:K00116] [EC:1.1.5.4]
H9N25_16645  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
H9N25_00475  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
H9N25_22415  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
H9N25_18895  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
H9N25_18190  pyruvate dehydrogenase complex E1 component subunit beta [KO:K00162] [EC:1.2.4.1]
H9N25_18900  2-oxo acid dehydrogenase subunit E2 [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
prk00010  Glycolysis / Gluconeogenesis
prk00053  Ascorbate and aldarate metabolism
prk00061  Fatty acid biosynthesis
prk00071  Fatty acid degradation
prk00190  Oxidative phosphorylation
prk00220  Arginine biosynthesis
prk00250  Alanine, aspartate and glutamate metabolism
prk00280  Valine, leucine and isoleucine degradation
prk00350  Tyrosine metabolism
prk00470  D-Amino acid metabolism
prk00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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