KEGG   PATHWAY: snap00020
Entry
snap00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Sphingomonas naphthae
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
snap00020  Citrate cycle (TCA cycle)
snap00020

Module
snap_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:snap00020]
snap_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:snap00020]
snap_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:snap00020]
snap_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:snap00020]
snap_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:snap00020]
Other DBs
GO: 0006099
Organism
Sphingomonas naphthae [GN:snap]
Gene
PQ455_09015  citrate synthase [KO:K01647] [EC:2.3.3.1]
PQ455_18395  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
PQ455_16050  bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
PQ455_07670  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
PQ455_02275  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
PQ455_11410  2-oxo acid dehydrogenase subunit E2 [KO:K00658] [EC:2.3.1.61]
PQ455_02270  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
PQ455_04480  2-oxo acid dehydrogenase subunit E2 [KO:K00658] [EC:2.3.1.61]
PQ455_15210  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
PQ455_02260  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
PQ455_02280  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
PQ455_16305  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
PQ455_15360  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
PQ455_00265  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
PQ455_15350  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
PQ455_15355  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
PQ455_12090  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
PQ455_14135  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
PQ455_02290  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
PQ455_09820  phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
PQ455_04720  transketolase [KO:K00163] [EC:1.2.4.1]
PQ455_18520  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
PQ455_18515  pyruvate dehydrogenase complex E1 component subunit beta [KO:K00162] [EC:1.2.4.1]
PQ455_15225  pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase [KO:K00627] [EC:2.3.1.12]
PQ455_15570  2-oxo acid dehydrogenase subunit E2 [KO:K00627] [EC:2.3.1.12]
PQ455_04725  dihydrolipoamide acetyltransferase family protein [KO:K00627] [EC:2.3.1.12]
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
snap00010  Glycolysis / Gluconeogenesis
snap00053  Ascorbate and aldarate metabolism
snap00061  Fatty acid biosynthesis
snap00071  Fatty acid degradation
snap00190  Oxidative phosphorylation
snap00220  Arginine biosynthesis
snap00250  Alanine, aspartate and glutamate metabolism
snap00280  Valine, leucine and isoleucine degradation
snap00350  Tyrosine metabolism
snap00470  D-Amino acid metabolism
snap00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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