KEGG   PATHWAY: ymo00020
Entry
ymo00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Yersinia mollaretii
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
ymo00020  Citrate cycle (TCA cycle)
ymo00020

Module
ymo_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:ymo00020]
ymo_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:ymo00020]
ymo_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:ymo00020]
ymo_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:ymo00020]
ymo_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:ymo00020]
Other DBs
GO: 0006099
Organism
Yersinia mollaretii [GN:ymo]
Gene
HRD69_11565  citrate synthase [KO:K01647] [EC:2.3.3.1]
HRD69_15285  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
HRD69_09240  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
HRD69_17135  icd; NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
HRD69_11590  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
HRD69_11595  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
HRD69_04670  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
HRD69_09225  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
HRD69_11605  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
HRD69_11600  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
HRD69_11580  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
HRD69_11585  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
HRD69_11570  sdhC; succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
HRD69_11575  sdhD; succinate dehydrogenase membrane anchor subunit [KO:K00242]
HRD69_07680  frdA; fumarate reductase (quinol) flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
HRD69_07675  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
HRD69_07670  frdC; fumarate reductase subunit FrdC [KO:K00246]
HRD69_07665  frdD; fumarate reductase subunit FrdD [KO:K00247]
HRD69_09905  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
HRD69_15590  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
HRD69_07935  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
HRD69_06535  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
HRD69_09215  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
HRD69_09220  aceF; pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
HRD69_15990  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
ymo00010  Glycolysis / Gluconeogenesis
ymo00053  Ascorbate and aldarate metabolism
ymo00061  Fatty acid biosynthesis
ymo00071  Fatty acid degradation
ymo00190  Oxidative phosphorylation
ymo00220  Arginine biosynthesis
ymo00250  Alanine, aspartate and glutamate metabolism
ymo00280  Valine, leucine and isoleucine degradation
ymo00350  Tyrosine metabolism
ymo00470  D-Amino acid metabolism
ymo00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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