KEGG   PATHWAY: sera00020
Entry
sera00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Prodigiosinella confusarubida ATCC 39006
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
sera00020  Citrate cycle (TCA cycle)
sera00020

Module
sera_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:sera00020]
sera_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:sera00020]
sera_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:sera00020]
sera_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:sera00020]
sera_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:sera00020]
Other DBs
GO: 0006099
Organism
Prodigiosinella confusarubida ATCC 39006 [GN:sera]
Gene
Ser39006_009790  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
Ser39006_018120  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
Ser39006_012310  acnA; aconitate hydratase AcnA [KO:K27802] [EC:4.2.1.3 4.2.1.99]
Ser39006_006310  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
Ser39006_011325  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
Ser39006_014710  isocitrate dehydrogenase (NADP(+)) [KO:K00031] [EC:1.1.1.42]
Ser39006_018095  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
Ser39006_018090  dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
Ser39006_006300  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
Ser39006_018080  succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
Ser39006_018085  ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
Ser39006_018105  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
Ser39006_018100  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
Ser39006_018115  succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
Ser39006_018110  sdhD; succinate:quinone oxidoreductase subunit D [KO:K00242]
Ser39006_005225  fumarate reductase flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
Ser39006_005220  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
Ser39006_005215  fumarate reductase subunit FrdC [KO:K00246]
Ser39006_005210  fumarate reductase subunit FrdD [KO:K00247]
Ser39006_020920  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
Ser39006_013645  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
Ser39006_022180  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
Ser39006_000640  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
Ser39006_006290  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
Ser39006_006295  aceF; pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
Ser39006_022430  acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit [KO:K00627] [EC:2.3.1.12]
Ser39006_021415  nifJ; pyruvate:ferredoxin (flavodoxin) oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
Ser39006_015455  nifJ; pyruvate:ferredoxin (flavodoxin) oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
Ser39006_005325  nifJ; pyruvate:ferredoxin (flavodoxin) oxidoreductase [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
sera00010  Glycolysis / Gluconeogenesis
sera00053  Ascorbate and aldarate metabolism
sera00061  Fatty acid biosynthesis
sera00071  Fatty acid degradation
sera00190  Oxidative phosphorylation
sera00220  Arginine biosynthesis
sera00250  Alanine, aspartate and glutamate metabolism
sera00280  Valine, leucine and isoleucine degradation
sera00350  Tyrosine metabolism
sera00470  D-Amino acid metabolism
sera00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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