KEGG   PATHWAY: pds00020
Entry
pds00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Photobacterium damselae subsp. damselae
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
pds00020  Citrate cycle (TCA cycle)
pds00020

Module
pds_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:pds00020]
pds_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:pds00020]
pds_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:pds00020]
pds_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:pds00020]
pds_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:pds00020]
Other DBs
GO: 0006099
Organism
Photobacterium damselae subsp. damselae [GN:pds]
Gene
CAY62_04125  citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
CAY62_12175  bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
CAY62_09140  isocitrate dehydrogenase (NADP(+)) [KO:K00031] [EC:1.1.1.42]
CAY62_04150  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
CAY62_04155  dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
CAY62_12195  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
CAY62_13200  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
CAY62_04165  succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
CAY62_04160  succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
CAY62_04140  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
CAY62_04145  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
CAY62_04130  succinate dehydrogenase cytochrome b556 large subunit [KO:K00241]
CAY62_04135  succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
CAY62_00705  fumarate reductase (quinol) flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
CAY62_00700  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
CAY62_00695  fumarate reductase subunit C [KO:K00246]
CAY62_00690  fumarate reductase subunit D [KO:K00247]
CAY62_07980  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
CAY62_15175  aspA; aspartate ammonia-lyase [KO:K01679] [EC:4.2.1.2]
CAY62_01175  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
CAY62_00125  phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
CAY62_12205  pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
CAY62_12200  aceF; pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
CAY62_09400  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
pds00010  Glycolysis / Gluconeogenesis
pds00053  Ascorbate and aldarate metabolism
pds00061  Fatty acid biosynthesis
pds00071  Fatty acid degradation
pds00190  Oxidative phosphorylation
pds00220  Arginine biosynthesis
pds00250  Alanine, aspartate and glutamate metabolism
pds00280  Valine, leucine and isoleucine degradation
pds00350  Tyrosine metabolism
pds00470  D-Amino acid metabolism
pds00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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