KEGG   PATHWAY: aly00020
Entry
aly00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Arabidopsis lyrata (lyrate rockcress)
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
aly00020  Citrate cycle (TCA cycle)
aly00020

Module
aly_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:aly00020]
aly_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:aly00020]
aly_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:aly00020]
aly_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:aly00020]
aly_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:aly00020]
Other DBs
GO: 0006099
Organism
Arabidopsis lyrata (lyrate rockcress) [GN:aly]
Gene
9314306  citrate synthase 2, peroxisomal [KO:K01647] [EC:2.3.3.1]
9312603  citrate synthase 5, mitochondrial isoform X1 [KO:K01647] [EC:2.3.3.1]
9316174  citrate synthase 4, mitochondrial [KO:K01647] [EC:2.3.3.1]
9317939  citrate synthase 3, peroxisomal [KO:K01647] [EC:2.3.3.1]
9314305  LOW QUALITY PROTEIN: citrate synthase 1, peroxisomal [KO:K01647] [EC:2.3.3.1]
9318551  ATP-citrate synthase beta chain protein 1 [KO:K01648] [EC:2.3.3.8]
9322651  ATP-citrate synthase alpha chain protein 2 [KO:K01648] [EC:2.3.3.8]
9328568  ATP-citrate synthase alpha chain protein 3 [KO:K01648] [EC:2.3.3.8]
9325888  ATP-citrate synthase alpha chain protein 1 [KO:K01648] [EC:2.3.3.8]
9300060  ATP-citrate synthase beta chain protein 2 [KO:K01648] [EC:2.3.3.8]
110229838  aconitate hydratase 3, mitochondrial [KO:K01681] [EC:4.2.1.3]
9319771  aconitate hydratase 3, mitochondrial [KO:K01681] [EC:4.2.1.3]
9303604  aconitate hydratase 2, mitochondrial [KO:K01681] [EC:4.2.1.3]
9305129  LOW QUALITY PROTEIN: aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
9306509  aconitate hydratase 3, mitochondrial [KO:K01681] [EC:4.2.1.3]
9323052  LOW QUALITY PROTEIN: cytosolic isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
9330628  peroxisomal isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
9309747  isocitrate dehydrogenase [NADP], chloroplastic/mitochondrial [KO:K00031] [EC:1.1.1.42]
9320108  isocitrate dehydrogenase [NAD] regulatory subunit 2, mitochondrial isoform X1 [KO:K00030] [EC:1.1.1.41]
9305145  isocitrate dehydrogenase [NAD] regulatory subunit 3, mitochondrial [KO:K00030] [EC:1.1.1.41]
9329788  LOW QUALITY PROTEIN: putative isocitrate dehydrogenase [NAD] subunit-like 4 [KO:K00030] [EC:1.1.1.41]
9307093  isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial [KO:K00030] [EC:1.1.1.41]
9320824  isocitrate dehydrogenase [NAD] catalytic subunit 6, mitochondrial [KO:K00030] [EC:1.1.1.41]
9303153  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial [KO:K00030] [EC:1.1.1.41]
9302761  2-oxoglutarate dehydrogenase, mitochondrial [KO:K00164] [EC:1.2.4.2]
9314101  2-oxoglutarate dehydrogenase, mitochondrial [KO:K00164] [EC:1.2.4.2]
9300449  dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 1, mitochondrial [KO:K00658] [EC:2.3.1.61]
9305659  dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 2, mitochondrial isoform X1 [KO:K00658] [EC:2.3.1.61]
9319102  dihydrolipoyl dehydrogenase 1, chloroplastic [KO:K00382] [EC:1.8.1.4]
9321261  dihydrolipoyl dehydrogenase 2, mitochondrial [KO:K00382] [EC:1.8.1.4]
9306249  dihydrolipoyl dehydrogenase 2, chloroplastic [KO:K00382] [EC:1.8.1.4]
9330152  dihydrolipoyl dehydrogenase 1, mitochondrial [KO:K00382] [EC:1.8.1.4]
9310186  succinate--CoA ligase [ADP-forming] subunit alpha-2, mitochondrial [KO:K01899] [EC:6.2.1.4 6.2.1.5]
9307386  succinate--CoA ligase [ADP-forming] subunit alpha-1, mitochondrial [KO:K01899] [EC:6.2.1.4 6.2.1.5]
9320268  succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial [KO:K01900] [EC:6.2.1.4 6.2.1.5]
9302813  succinate dehydrogenase [ubiquinone] flavoprotein subunit 1, mitochondrial [KO:K00234] [EC:1.3.5.1]
9320201  succinate dehydrogenase [ubiquinone] flavoprotein subunit 2, mitochondrial [KO:K00234] [EC:1.3.5.1]
9304714  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 2, mitochondrial [KO:K00235] [EC:1.3.5.1]
9313115  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 1, mitochondrial [KO:K00235] [EC:1.3.5.1]
9302725  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 3, mitochondrial [KO:K00235] [EC:1.3.5.1]
9307450  succinate dehydrogenase subunit 3-1, mitochondrial isoform X1 [KO:K00236]
9318138  succinate dehydrogenase subunit 4, mitochondrial [KO:K25801]
9316376  fumarate hydratase 1, mitochondrial [KO:K01679] [EC:4.2.1.2]
9300161  fumarate hydratase 2, chloroplastic [KO:K01679] [EC:4.2.1.2]
9302237  malate dehydrogenase 3, cytoplasmic [KO:K00025] [EC:1.1.1.37]
9299740  malate dehydrogenase 2, cytoplasmic [KO:K00025] [EC:1.1.1.37]
9328278  malate dehydrogenase 1, cytoplasmic [KO:K00025] [EC:1.1.1.37]
9314701  malate dehydrogenase 1, peroxisomal isoform X1 [KO:K00026] [EC:1.1.1.37]
9318975  malate dehydrogenase 2, mitochondrial isoform X1 [KO:K00026] [EC:1.1.1.37]
9309482  malate dehydrogenase 2, glyoxysomal [KO:K00026] [EC:1.1.1.37]
9311912  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
9330491  malate dehydrogenase 1, mitochondrial [KO:K00026] [EC:1.1.1.37]
9301045  phosphoenolpyruvate carboxykinase (ATP) isoform X1 [KO:K01610] [EC:4.1.1.49]
9305033  phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
9322716  pyruvate dehydrogenase E1 component subunit alpha-1, mitochondrial [KO:K00161] [EC:1.2.4.1]
9329391  pyruvate dehydrogenase E1 component subunit alpha-2, mitochondrial [KO:K00161] [EC:1.2.4.1]
9325449  pyruvate dehydrogenase E1 component subunit alpha-3, chloroplastic [KO:K00161] [EC:1.2.4.1]
9317413  pyruvate dehydrogenase E1 component subunit beta-3, chloroplastic [KO:K00162] [EC:1.2.4.1]
9326914  pyruvate dehydrogenase E1 component subunit beta-2, chloroplastic [KO:K00162] [EC:1.2.4.1]
9300156  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial [KO:K00162] [EC:1.2.4.1]
9313917  dihydrolipoyllysine-residue acetyltransferase component 1 of pyruvate dehydrogenase complex, mitochondrial [KO:K00627] [EC:2.3.1.12]
9321064  dihydrolipoyllysine-residue acetyltransferase component 2 of pyruvate dehydrogenase complex, mitochondrial [KO:K00627] [EC:2.3.1.12]
9330544  dihydrolipoyllysine-residue acetyltransferase component 3 of pyruvate dehydrogenase complex, mitochondrial [KO:K00627] [EC:2.3.1.12]
9313003  dihydrolipoyllysine-residue acetyltransferase component 4 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
9327165  dihydrolipoyllysine-residue acetyltransferase component 5 of pyruvate dehydrogenase complex, chloroplastic [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
aly00010  Glycolysis / Gluconeogenesis
aly00053  Ascorbate and aldarate metabolism
aly00061  Fatty acid biosynthesis
aly00062  Fatty acid elongation
aly00071  Fatty acid degradation
aly00190  Oxidative phosphorylation
aly00220  Arginine biosynthesis
aly00250  Alanine, aspartate and glutamate metabolism
aly00280  Valine, leucine and isoleucine degradation
aly00350  Tyrosine metabolism
aly00470  D-Amino acid metabolism
aly00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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