KEGG   PATHWAY: oml00020
Entry
oml00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Oryzias melastigma (Indian medaka)
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
oml00020  Citrate cycle (TCA cycle)
oml00020

Module
oml_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:oml00020]
oml_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:oml00020]
oml_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:oml00020]
oml_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:oml00020]
oml_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:oml00020]
Other DBs
GO: 0006099
Organism
Oryzias melastigma (Indian medaka) [GN:oml]
Gene
112159816  cs; citrate synthase, mitochondrial [KO:K01647] [EC:2.3.3.1]
112153948  ATP-citrate synthase isoform X1 [KO:K01648] [EC:2.3.3.8]
112146149  aclya; ATP-citrate synthase [KO:K01648] [EC:2.3.3.8]
112140640  aco1; cytoplasmic aconitate hydratase [KO:K01681] [EC:4.2.1.3]
112154323  aco2; aconitate hydratase, mitochondrial [KO:K01681] [EC:4.2.1.3]
112139874  idh1; isocitrate dehydrogenase [NADP] cytoplasmic [KO:K00031] [EC:1.1.1.42]
112161066  isocitrate dehydrogenase [NADP], mitochondrial [KO:K00031] [EC:1.1.1.42]
112152846  idh2; isocitrate dehydrogenase [NADP], mitochondrial [KO:K00031] [EC:1.1.1.42]
112160487  idh3a; isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial isoform X1 [KO:K00030] [EC:1.1.1.41]
112145365  idh3b; isocitrate dehydrogenase [NAD] subunit beta, mitochondrial isoform X1 [KO:K00030] [EC:1.1.1.41]
112158665  idh3g; isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial [KO:K00030] [EC:1.1.1.41]
112159856  isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial isoform X1 [KO:K00030] [EC:1.1.1.41]
112163122  ogdhb; 2-oxoglutarate dehydrogenase, mitochondrial [KO:K00164] [EC:1.2.4.2]
112138440  ogdha; oxoglutarate (alpha-ketoglutarate) dehydrogenase a (lipoamide) [KO:K00164] [EC:1.2.4.2]
112162677  dlst; dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial [KO:K00658] [EC:2.3.1.61]
112141240  dldh; dihydrolipoyl dehydrogenase, mitochondrial [KO:K00382] [EC:1.8.1.4]
112157230  suclg1; succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial [KO:K01899] [EC:6.2.1.4 6.2.1.5]
112155268  sucla2; succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial [KO:K01900] [EC:6.2.1.4 6.2.1.5]
112145145  suclg2; succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial [KO:K01900] [EC:6.2.1.4 6.2.1.5]
112143854  sdha; succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial [KO:K00234] [EC:1.3.5.1]
112151104  succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial isoform X2 [KO:K00235] [EC:1.3.5.1]
112145238  sdhb; succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial [KO:K00235] [EC:1.3.5.1]
112150596  sdhc; succinate dehydrogenase cytochrome b560 subunit, mitochondrial isoform X1 [KO:K00236]
112149803  sdhdb; succinate dehydrogenase [ubiquinone] cytochrome b small subunit B, mitochondrial [KO:K00237]
112139659  succinate dehydrogenase [ubiquinone] cytochrome b small subunit B, mitochondrial-like [KO:K00237]
112150318  fh; fumarate hydratase, mitochondrial [KO:K01679] [EC:4.2.1.2]
112161617  mdh1ab; malate dehydrogenase 1Ab, NAD (soluble) [KO:K00025] [EC:1.1.1.37]
112157096  malate dehydrogenase, cytoplasmic isoform X1 [KO:K00025] [EC:1.1.1.37]
112143314  mdh2; malate dehydrogenase, mitochondrial [KO:K00026] [EC:1.1.1.37]
112156404  pyruvate carboxylase, mitochondrial isoform X2 [KO:K01958] [EC:6.4.1.1]
112151237  pck2; phosphoenolpyruvate carboxykinase [GTP], mitochondrial isoform X1 [KO:K01596] [EC:4.1.1.32]
112145622  pck1; phosphoenolpyruvate carboxykinase, cytosolic [GTP] [KO:K01596] [EC:4.1.1.32]
112140226  pdha1a; pyruvate dehydrogenase E1 subunit alpha 1a [KO:K00161] [EC:1.2.4.1]
112158967  pyruvate dehydrogenase E1 component subunit alpha, mitochondrial isoform X1 [KO:K00161] [EC:1.2.4.1]
112144778  pdhb; pyruvate dehydrogenase E1 component subunit beta, mitochondrial [KO:K00162] [EC:1.2.4.1]
112142745  dlat; dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial [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
oml00010  Glycolysis / Gluconeogenesis
oml00053  Ascorbate and aldarate metabolism
oml00061  Fatty acid biosynthesis
oml00062  Fatty acid elongation
oml00071  Fatty acid degradation
oml00190  Oxidative phosphorylation
oml00220  Arginine biosynthesis
oml00250  Alanine, aspartate and glutamate metabolism
oml00280  Valine, leucine and isoleucine degradation
oml00350  Tyrosine metabolism
oml00470  D-Amino acid metabolism
oml00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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