KEGG   PATHWAY: pavi00020
Entry
pavi00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Prunus avium (sweet cherry)
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
pavi00020  Citrate cycle (TCA cycle)
pavi00020

Module
pavi_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:pavi00020]
pavi_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:pavi00020]
pavi_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:pavi00020]
Other DBs
GO: 0006099
Organism
Prunus avium (sweet cherry) [GN:pavi]
Gene
110744480  citrate synthase, glyoxysomal [KO:K01647] [EC:2.3.3.1]
110772125  citrate synthase, mitochondrial isoform X1 [KO:K01647] [EC:2.3.3.1]
110752176  ATP-citrate synthase alpha chain protein 2 [KO:K01648] [EC:2.3.3.8]
110753199  ATP-citrate synthase alpha chain protein 2 [KO:K01648] [EC:2.3.3.8]
110771135  ATP-citrate synthase beta chain protein 2 [KO:K01648] [EC:2.3.3.8]
110764244  aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
110761354  aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
110762040  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
110765103  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
110746469  isocitrate dehydrogenase [NADP]-like isoform X1 [KO:K00031] [EC:1.1.1.42]
110754745  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial-like isoform X1 [KO:K00030] [EC:1.1.1.41]
110744334  isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial [KO:K00030] [EC:1.1.1.41]
110772763  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial [KO:K00030] [EC:1.1.1.41]
110756644  LOW QUALITY PROTEIN: 2-oxoglutarate dehydrogenase, mitochondrial-like [KO:K00164] [EC:1.2.4.2]
110756645  LOW QUALITY PROTEIN: 2-oxoglutarate dehydrogenase, mitochondrial-like [KO:K00164] [EC:1.2.4.2]
110764273  dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 2, mitochondrial-like [KO:K00658] [EC:2.3.1.61]
110752818  dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 2, mitochondrial-like [KO:K00658] [EC:2.3.1.61]
110751855  dihydrolipoyl dehydrogenase, mitochondrial [KO:K00382] [EC:1.8.1.4]
110763925  dihydrolipoyl dehydrogenase 1, chloroplastic-like [KO:K00382] [EC:1.8.1.4]
110759962  dihydrolipoyl dehydrogenase, mitochondrial-like [KO:K00382] [EC:1.8.1.4]
110747169  succinate--CoA ligase [ADP-forming] subunit alpha-2, mitochondrial isoform X1 [KO:K01899] [EC:6.2.1.4 6.2.1.5]
110757482  succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial [KO:K01900] [EC:6.2.1.4 6.2.1.5]
110773605  succinate dehydrogenase [ubiquinone] flavoprotein subunit 1, mitochondrial [KO:K00234] [EC:1.3.5.1]
110755946  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 2, mitochondrial-like [KO:K00235] [EC:1.3.5.1]
110768786  LOW QUALITY PROTEIN: succinate dehydrogenase [ubiquinone] iron-sulfur subunit 3, mitochondrial-like [KO:K00235] [EC:1.3.5.1]
110768787  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 3, mitochondrial-like [KO:K00235] [EC:1.3.5.1]
110749388  fumarate hydratase 1, mitochondrial [KO:K01679] [EC:4.2.1.2]
110748944  malate dehydrogenase [KO:K00025] [EC:1.1.1.37]
110748679  malate dehydrogenase, cytoplasmic-like [KO:K00025] [EC:1.1.1.37]
110760310  malate dehydrogenase, cytoplasmic-like isoform X1 [KO:K00025] [EC:1.1.1.37]
110771779  malate dehydrogenase, mitochondrial [KO:K00026] [EC:1.1.1.37]
110745262  malate dehydrogenase, glyoxysomal-like [KO:K00026] [EC:1.1.1.37]
110762351  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
110755010  malate dehydrogenase, mitochondrial-like [KO:K00026] [EC:1.1.1.37]
110757231  malate dehydrogenase, glyoxysomal [KO:K00026] [EC:1.1.1.37]
110763885  phosphoenolpyruvate carboxykinase (ATP)-like isoform X1 [KO:K01610] [EC:4.1.1.49]
110772055  LOW QUALITY PROTEIN: phosphoenolpyruvate carboxykinase (ATP)-like [KO:K01610] [EC:4.1.1.49]
110760796  pyruvate dehydrogenase E1 component subunit alpha, mitochondrial [KO:K00161] [EC:1.2.4.1]
110764047  pyruvate dehydrogenase E1 component subunit alpha-3, chloroplastic [KO:K00161] [EC:1.2.4.1]
110774041  pyruvate dehydrogenase E1 component subunit beta-3, chloroplastic-like [KO:K00162] [EC:1.2.4.1]
110745104  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial [KO:K00162] [EC:1.2.4.1]
110765520  dihydrolipoyllysine-residue acetyltransferase component 1 of pyruvate dehydrogenase complex, mitochondrial [KO:K00627] [EC:2.3.1.12]
110756244  dihydrolipoyllysine-residue acetyltransferase component 5 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
110759460  dihydrolipoyllysine-residue acetyltransferase component 3 of pyruvate dehydrogenase complex, mitochondrial-like [KO:K00627] [EC:2.3.1.12]
110757160  dihydrolipoyllysine-residue acetyltransferase component 4 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
pavi00010  Glycolysis / Gluconeogenesis
pavi00053  Ascorbate and aldarate metabolism
pavi00061  Fatty acid biosynthesis
pavi00062  Fatty acid elongation
pavi00071  Fatty acid degradation
pavi00190  Oxidative phosphorylation
pavi00220  Arginine biosynthesis
pavi00250  Alanine, aspartate and glutamate metabolism
pavi00280  Valine, leucine and isoleucine degradation
pavi00350  Tyrosine metabolism
pavi00470  D-Amino acid metabolism
pavi00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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