KEGG   PATHWAY: vri00020
Entry
vri00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Vitis riparia (riverbank grape)
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
vri00020  Citrate cycle (TCA cycle)
vri00020

Module
vri_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:vri00020]
vri_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:vri00020]
vri_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:vri00020]
Other DBs
GO: 0006099
Organism
Vitis riparia (riverbank grape) [GN:vri]
Gene
117926507  citrate synthase, glyoxysomal [KO:K01647] [EC:2.3.3.1]
117928738  citrate synthase, mitochondrial [KO:K01647] [EC:2.3.3.1]
117922866  ATP-citrate synthase alpha chain protein 1 [KO:K01648] [EC:2.3.3.8]
117914565  ATP-citrate synthase beta chain protein 2 isoform X1 [KO:K01648] [EC:2.3.3.8]
117930821  ATP-citrate synthase alpha chain protein 2 [KO:K01648] [EC:2.3.3.8]
117913627  aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
117926812  aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
117908908  aconitate hydratase, cytoplasmic-like isoform X1 [KO:K01681] [EC:4.2.1.3]
117912817  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
117931359  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
117908406  isocitrate dehydrogenase [NADP]-like [KO:K00031] [EC:1.1.1.42]
117920740  isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial [KO:K00030] [EC:1.1.1.41]
117911313  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial isoform X1 [KO:K00030] [EC:1.1.1.41]
117912970  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial-like [KO:K00030] [EC:1.1.1.41]
117928084  2-oxoglutarate dehydrogenase, mitochondrial [KO:K00164] [EC:1.2.4.2]
117923705  dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 1, mitochondrial-like [KO:K00658] [EC:2.3.1.61]
117914863  dihydrolipoyl dehydrogenase 2, chloroplastic-like [KO:K00382] [EC:1.8.1.4]
117914956  dihydrolipoyl dehydrogenase, mitochondrial [KO:K00382] [EC:1.8.1.4]
117929810  dihydrolipoyl dehydrogenase 2, chloroplastic-like isoform X1 [KO:K00382] [EC:1.8.1.4]
117923605  succinate--CoA ligase [ADP-forming] subunit alpha-1, mitochondrial-like [KO:K01899] [EC:6.2.1.4 6.2.1.5]
117905001  LOW QUALITY PROTEIN: succinate--CoA ligase [ADP-forming] subunit alpha, mitochondrial-like [KO:K01899] [EC:6.2.1.4 6.2.1.5]
117918693  succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial [KO:K01900] [EC:6.2.1.4 6.2.1.5]
117912845  succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial [KO:K00234] [EC:1.3.5.1]
117919211  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 3, mitochondrial [KO:K00235] [EC:1.3.5.1]
117930832  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 1, mitochondrial [KO:K00235] [EC:1.3.5.1]
117918518  fumarate hydratase 1, mitochondrial [KO:K01679] [EC:4.2.1.2]
117931402  fumarate hydratase 1, mitochondrial-like isoform X1 [KO:K01679] [EC:4.2.1.2]
117917722  malate dehydrogenase, cytoplasmic [KO:K00025] [EC:1.1.1.37]
117917723  malate dehydrogenase, cytoplasmic-like [KO:K00025] [EC:1.1.1.37]
117931734  malate dehydrogenase, cytoplasmic-like isoform X1 [KO:K00025] [EC:1.1.1.37]
117931745  malate dehydrogenase, cytoplasmic-like isoform X1 [KO:K00025] [EC:1.1.1.37]
117909644  malate dehydrogenase, mitochondrial-like [KO:K00026] [EC:1.1.1.37]
117911303  malate dehydrogenase, glyoxysomal [KO:K00026] [EC:1.1.1.37]
117923908  malate dehydrogenase, mitochondrial [KO:K00026] [EC:1.1.1.37]
117904394  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
117918935  malate dehydrogenase, glyoxysomal-like [KO:K00026] [EC:1.1.1.37]
117930858  malate dehydrogenase, chloroplastic-like [KO:K00026] [EC:1.1.1.37]
117918430  phosphoenolpyruvate carboxykinase (ATP)-like isoform X1 [KO:K01610] [EC:4.1.1.49]
117922231  pyruvate dehydrogenase E1 component subunit alpha, mitochondrial-like [KO:K00161] [EC:1.2.4.1]
117915666  pyruvate dehydrogenase E1 component subunit alpha, mitochondrial [KO:K00161] [EC:1.2.4.1]
117932378  pyruvate dehydrogenase E1 component subunit alpha-3, chloroplastic [KO:K00161] [EC:1.2.4.1]
117913390  pyruvate dehydrogenase E1 component subunit beta-3, chloroplastic-like [KO:K00162] [EC:1.2.4.1]
117925665  pyruvate dehydrogenase E1 component subunit beta-3, chloroplastic-like [KO:K00162] [EC:1.2.4.1]
117903965  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial-like [KO:K00162] [EC:1.2.4.1]
117919833  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial [KO:K00162] [EC:1.2.4.1]
117922242  dihydrolipoyllysine-residue acetyltransferase component 2 of pyruvate dehydrogenase complex, mitochondrial [KO:K00627] [EC:2.3.1.12]
117925731  dihydrolipoyllysine-residue acetyltransferase component 2 of pyruvate dehydrogenase complex, mitochondrial-like isoform X1 [KO:K00627] [EC:2.3.1.12]
117928878  dihydrolipoyllysine-residue acetyltransferase component 1 of pyruvate dehydrogenase complex, mitochondrial [KO:K00627] [EC:2.3.1.12]
117918191  dihydrolipoyllysine-residue acetyltransferase component 4 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
117907742  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
vri00010  Glycolysis / Gluconeogenesis
vri00053  Ascorbate and aldarate metabolism
vri00061  Fatty acid biosynthesis
vri00062  Fatty acid elongation
vri00071  Fatty acid degradation
vri00190  Oxidative phosphorylation
vri00220  Arginine biosynthesis
vri00250  Alanine, aspartate and glutamate metabolism
vri00280  Valine, leucine and isoleucine degradation
vri00350  Tyrosine metabolism
vri00470  D-Amino acid metabolism
vri00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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