KEGG   PATHWAY: agz00020
Entry
agz00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Agarivorans sp. TSD2052
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
agz00020  Citrate cycle (TCA cycle)
agz00020

Module
agz_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:agz00020]
agz_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:agz00020]
agz_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:agz00020]
agz_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:agz00020]
agz_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:agz00020]
Other DBs
GO: 0006099
Organism
Agarivorans sp. TSD2052 [GN:agz]
Gene
M0C34_11310  citrate synthase [KO:K01647] [EC:2.3.3.1]
M0C34_17020  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
M0C34_04565  icd; NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
M0C34_08440  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
M0C34_13075  isocitrate dehydrogenase [KO:K00030] [EC:1.1.1.41]
M0C34_11285  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
M0C34_11280  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
M0C34_17030  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
M0C34_20345  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
M0C34_11270  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
M0C34_11275  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
M0C34_11295  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
M0C34_11290  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
M0C34_11305  sdhC; succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
M0C34_11300  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
M0C34_17810  frdA; fumarate reductase (quinol) flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
M0C34_17815  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
M0C34_17820  fumarate reductase subunit C [KO:K00246]
M0C34_17825  frdD; fumarate reductase subunit FrdD [KO:K00247]
M0C34_10950  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
M0C34_16970  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
M0C34_18850  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
M0C34_17040  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
M0C34_17035  aceF; pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
M0C34_13625  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
agz00010  Glycolysis / Gluconeogenesis
agz00053  Ascorbate and aldarate metabolism
agz00061  Fatty acid biosynthesis
agz00071  Fatty acid degradation
agz00190  Oxidative phosphorylation
agz00220  Arginine biosynthesis
agz00250  Alanine, aspartate and glutamate metabolism
agz00280  Valine, leucine and isoleucine degradation
agz00350  Tyrosine metabolism
agz00470  D-Amino acid metabolism
agz00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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