KEGG   PATHWAY: yru00020
Entry
yru00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Yersinia ruckeri YRB
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
yru00020  Citrate cycle (TCA cycle)
yru00020

Module
yru_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:yru00020]
yru_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:yru00020]
yru_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:yru00020]
yru_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:yru00020]
yru_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:yru00020]
Other DBs
GO: 0006099
Organism
Yersinia ruckeri YRB [GN:yru]
Gene
BD65_3026  gltA; citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
BD65_298  acnA; aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
BD65_2584  acnB; aconitate hydratase 2 [KO:K01682] [EC:4.2.1.3 4.2.1.99]
BD65_90  icd; isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
BD65_3031  sucA; oxoglutarate dehydrogenase (succinyl-transferring), E1 component [KO:K00164] [EC:1.2.4.2]
BD65_3032  sucB; dihydrolipoyllysine-residue succinyltransferase, E2 component of oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
BD65_1813  pyridine nucleotide-disulfide oxidoreductase family protein [KO:K00382] [EC:1.8.1.4]
BD65_2582  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
BD65_3034  sucD; succinate-CoA ligase, alpha subunit [KO:K01902] [EC:6.2.1.5]
BD65_3033  sucC; succinyl-CoA ligase [ADP-forming] subunit beta [KO:K01903] [EC:6.2.1.5]
BD65_3029  sdhA; succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
BD65_3030  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
BD65_3027  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
BD65_3028  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
BD65_2279  frdA; fumarate reductase, flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
BD65_2278  frdB; fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
BD65_2277  frdC; fumarate reductase subunit C [KO:K00246]
BD65_2276  frdD; fumarate reductase subunit D [KO:K00247]
BD65_2706  fumA; fumarate hydratase class I, aerobic [KO:K01676] [EC:4.2.1.2]
BD65_331  fumC; fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
BD65_2332  mdh; malate dehydrogenase, NAD-dependent [KO:K00024] [EC:1.1.1.37]
BD65_1129  mqo; malate dehydrogenase [KO:K00116] [EC:1.1.5.4]
BD65_2145  pckA; phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
BD65_2580  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
BD65_2581  aceF; dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
BD65_391  nifJ; 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
yru00010  Glycolysis / Gluconeogenesis
yru00053  Ascorbate and aldarate metabolism
yru00061  Fatty acid biosynthesis
yru00071  Fatty acid degradation
yru00190  Oxidative phosphorylation
yru00220  Arginine biosynthesis
yru00250  Alanine, aspartate and glutamate metabolism
yru00280  Valine, leucine and isoleucine degradation
yru00350  Tyrosine metabolism
yru00470  D-Amino acid metabolism
yru00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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