KEGG   PATHWAY: sly00020
Entry
sly00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Solanum lycopersicum (tomato)
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
sly00020  Citrate cycle (TCA cycle)
sly00020

Module
sly_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:sly00020]
sly_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:sly00020]
sly_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:sly00020]
sly_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:sly00020]
sly_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:sly00020]
Other DBs
GO: 0006099
Organism
Solanum lycopersicum (tomato) [GN:sly]
Gene
101249011  citrate synthase, mitochondrial [KO:K01647] [EC:2.3.3.1]
101260902  citrate synthase, glyoxysomal [KO:K01647] [EC:2.3.3.1]
101258079  citrate synthase 3, peroxisomal-like [KO:K01647] [EC:2.3.3.1]
101263147  ATP-citrate synthase beta chain protein 2-like [KO:K01648] [EC:2.3.3.8]
101261460  ATP-citrate synthase alpha chain protein 3 [KO:K01648] [EC:2.3.3.8]
101258745  ATP-citrate synthase alpha chain protein 2 isoform X3 [KO:K01648] [EC:2.3.3.8]
101267503  ATP-citrate synthase beta chain protein 2 [KO:K01648] [EC:2.3.3.8]
101246135  ATP-citrate synthase alpha chain protein 2 [KO:K01648] [EC:2.3.3.8]
101248455  aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
101254008  aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
101268602  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
101255848  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
101248445  isocitrate dehydrogenase [NADP] isoform X1 [KO:K00031] [EC:1.1.1.42]
101253647  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial-like [KO:K00030] [EC:1.1.1.41]
101251730  ICDH1; isocitrate dehydrogenase [NAD] regulatory subunit 1 [KO:K00030] [EC:1.1.1.41]
101246168  3-isopropylmalate dehydrogenase, chloroplastic [KO:K00030] [EC:1.1.1.41]
101246460  3-isopropylmalate dehydrogenase, chloroplastic isoform X1 [KO:K00030] [EC:1.1.1.41]
101264112  2-oxoglutarate dehydrogenase, mitochondrial [KO:K00164] [EC:1.2.4.2]
101259749  LOW QUALITY PROTEIN: 2-oxoglutarate dehydrogenase, mitochondrial [KO:K00164] [EC:1.2.4.2]
101258624  alpha-kGDH; alpha - ketoglutarate dehydrogenase subunit E2 [KO:K00658] [EC:2.3.1.61]
101268590  dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 2, mitochondrial [KO:K00658] [EC:2.3.1.61]
101245293  dihydrolipoyl dehydrogenase 2, chloroplastic [KO:K00382] [EC:1.8.1.4]
101246429  dihydrolipoyl dehydrogenase 1, chloroplastic isoform X1 [KO:K00382] [EC:1.8.1.4]
101245444  dihydrolipoyl dehydrogenase, mitochondrial [KO:K00382] [EC:1.8.1.4]
544237  dihydrolipoamide dehydrogenase precursor [KO:K00382] [EC:1.8.1.4]
543860  SCOA; succinate--CoA ligase [ADP-forming] subunit alpha-1, mitochondrial [KO:K01899] [EC:6.2.1.4 6.2.1.5]
543943  succinate--CoA ligase [ADP-forming] subunit alpha-2, mitochondrial [KO:K01899] [EC:6.2.1.4 6.2.1.5]
543863  succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial [KO:K01900] [EC:6.2.1.4 6.2.1.5]
101256641  succinate dehydrogenase [ubiquinone] flavoprotein subunit 1, mitochondrial [KO:K00234] [EC:1.3.5.1]
101253277  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 3, mitochondrial-like [KO:K00235] [EC:1.3.5.1]
101252979  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 3, mitochondrial-like [KO:K00235] [EC:1.3.5.1]
100736507  succinate dehydrogenase [KO:K00235] [EC:1.3.5.1]
34678300  sdh3; succinate dehydrogenase subunit 3 [KO:K00236]
34678270  sdh4; succinate dehydrogenase subunit 4 [KO:K25801]
101265278  fumarate hydratase 1, mitochondrial [KO:K01679] [EC:4.2.1.2]
101243791  fumarate hydratase 1, mitochondrial isoform X1 [KO:K01679] [EC:4.2.1.2]
101253131  malate dehydrogenase [KO:K00025] [EC:1.1.1.37]
778330  cMDH; cytosolic malate dehydrogenase [KO:K00025] [EC:1.1.1.37]
101249428  malate dehydrogenase, glyoxysomal [KO:K00026] [EC:1.1.1.37]
101258932  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
101258530  mMDH2; malate dehydrogenase, mitochondrial [KO:K00026] [EC:1.1.1.37]
778285  mMDH1; mitochondrial malate dehydrogenase [KO:K00026] [EC:1.1.1.37]
778286  gMDH; glyoxisomal malate dehydrogenase [KO:K00026] [EC:1.1.1.37]
101248141  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
101252671  phosphoenolpyruvate carboxykinase (ATP)-like [KO:K01610] [EC:4.1.1.49]
543812  phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
101258551  pyruvate dehydrogenase E1 component subunit alpha, mitochondrial [KO:K00161] [EC:1.2.4.1]
101256654  pyruvate dehydrogenase E1 component subunit alpha-3, chloroplastic [KO:K00161] [EC:1.2.4.1]
101256355  pyruvate dehydrogenase E1 component subunit alpha-3, chloroplastic [KO:K00161] [EC:1.2.4.1]
543639  pyruvate dehydrogenase E1 component subunit alpha, mitochondrial [KO:K00161] [EC:1.2.4.1]
101248181  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial [KO:K00162] [EC:1.2.4.1]
101254693  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial-like [KO:K00162] [EC:1.2.4.1]
101252977  pyruvate dehydrogenase E1 component subunit beta-3, chloroplastic-like isoform X1 [KO:K00162] [EC:1.2.4.1]
101266731  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial [KO:K00162] [EC:1.2.4.1]
101268205  pyruvate dehydrogenase E1 component subunit beta-3, chloroplastic-like [KO:K00162] [EC:1.2.4.1]
101257033  dihydrolipoyllysine-residue acetyltransferase component 1 of pyruvate dehydrogenase complex, mitochondrial isoform X2 [KO:K00627] [EC:2.3.1.12]
101264480  dihydrolipoyllysine-residue acetyltransferase component 5 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
101257857  dihydrolipoyllysine-residue acetyltransferase component 4 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
101244498  dihydrolipoyllysine-residue acetyltransferase component 2 of pyruvate dehydrogenase complex, mitochondrial-like isoform X1 [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
sly00010  Glycolysis / Gluconeogenesis
sly00053  Ascorbate and aldarate metabolism
sly00061  Fatty acid biosynthesis
sly00062  Fatty acid elongation
sly00071  Fatty acid degradation
sly00190  Oxidative phosphorylation
sly00220  Arginine biosynthesis
sly00250  Alanine, aspartate and glutamate metabolism
sly00280  Valine, leucine and isoleucine degradation
sly00350  Tyrosine metabolism
sly00470  D-Amino acid metabolism
sly00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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