KEGG   PATHWAY: hydr00020
Entry
hydr00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Hydrogenophaga sp. SNF1
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
hydr00020  Citrate cycle (TCA cycle)
hydr00020

Module
hydr_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:hydr00020]
hydr_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:hydr00020]
hydr_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:hydr00020]
hydr_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:hydr00020]
hydr_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:hydr00020]
Other DBs
GO: 0006099
Organism
Hydrogenophaga sp. SNF1 [GN:hydr]
Gene
SOM08_00790  [KO:K01596] [EC:4.1.1.32]
SOM08_02405  mdeB; alpha-ketoglutarate dehydrogenase [KO:K00163] [EC:1.2.4.1]
SOM08_09430  [KO:K01679] [EC:4.2.1.2]
SOM08_13225  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
SOM08_13230  aceF; dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
SOM08_13235  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
SOM08_13335  [KO:K00164] [EC:1.2.4.2]
SOM08_13340  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
SOM08_13345  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
SOM08_13875  [KO:K00031] [EC:1.1.1.42]
SOM08_13885  icd; NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
SOM08_14345  [KO:K01676] [EC:4.2.1.2]
SOM08_15965  acnA; aconitate hydratase AcnA [KO:K27802]
SOM08_15995  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
SOM08_16010  [KO:K00024] [EC:1.1.1.37]
SOM08_16020  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
SOM08_16025  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
SOM08_16030  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
SOM08_16035  [KO:K00240] [EC:1.3.5.1]
SOM08_16045  [KO:K01647] [EC:2.3.3.1]
SOM08_22170  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
SOM08_22175  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
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
hydr00010  Glycolysis / Gluconeogenesis
hydr00053  Ascorbate and aldarate metabolism
hydr00061  Fatty acid biosynthesis
hydr00071  Fatty acid degradation
hydr00190  Oxidative phosphorylation
hydr00220  Arginine biosynthesis
hydr00250  Alanine, aspartate and glutamate metabolism
hydr00280  Valine, leucine and isoleucine degradation
hydr00350  Tyrosine metabolism
hydr00470  D-Amino acid metabolism
hydr00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   

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