KEGG   PATHWAY: yre00020
Entry
yre00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Yokenella regensburgei
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
yre00020  Citrate cycle (TCA cycle)
yre00020

Module
yre_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:yre00020]
yre_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:yre00020]
yre_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:yre00020]
yre_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:yre00020]
yre_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:yre00020]
Other DBs
GO: 0006099
Organism
Yokenella regensburgei [GN:yre]
Gene
HEC60_00725  citrate synthase [KO:K01647] [EC:2.3.3.1]
HEC60_04700  acnA; aconitate hydratase AcnA [KO:K27802] [EC:4.2.1.3 4.2.1.99]
HEC60_21785  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
HEC60_03010  icd; NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
HEC60_00750  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
HEC60_00755  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
HEC60_21765  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
HEC60_00765  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
HEC60_00760  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
HEC60_00740  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
HEC60_00745  sdhB; succinate dehydrogenase iron-sulfur subunit SdhB [KO:K00240] [EC:1.3.5.1]
HEC60_00730  sdhC; succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
HEC60_00735  sdhD; succinate dehydrogenase membrane anchor subunit [KO:K00242]
HEC60_19770  frdA; fumarate reductase (quinol) flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
HEC60_19765  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
HEC60_19760  frdC; fumarate reductase subunit FrdC [KO:K00246]
HEC60_19755  frdD; fumarate reductase subunit FrdD [KO:K00247]
HEC60_00060  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
HEC60_20920  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
HEC60_06350  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
HEC60_06340  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
HEC60_06755  fumD; fumarate hydratase FumD [KO:K01675] [EC:4.2.1.2]
HEC60_15620  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
HEC60_05690  mqo; malate dehydrogenase (quinone) [KO:K00116] [EC:1.1.5.4]
HEC60_10520  mqo; malate dehydrogenase (quinone) [KO:K00116] [EC:1.1.5.4]
HEC60_16420  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
HEC60_21755  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
HEC60_21760  aceF; pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
HEC60_05010  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
yre00010  Glycolysis / Gluconeogenesis
yre00053  Ascorbate and aldarate metabolism
yre00061  Fatty acid biosynthesis
yre00071  Fatty acid degradation
yre00190  Oxidative phosphorylation
yre00220  Arginine biosynthesis
yre00250  Alanine, aspartate and glutamate metabolism
yre00280  Valine, leucine and isoleucine degradation
yre00350  Tyrosine metabolism
yre00470  D-Amino acid metabolism
yre00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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