KEGG   PATHWAY: vvi00020
Entry
vvi00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Vitis vinifera (wine 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
vvi00020  Citrate cycle (TCA cycle)
vvi00020

Module
vvi_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:vvi00020]
vvi_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:vvi00020]
vvi_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:vvi00020]
vvi_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:vvi00020]
vvi_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:vvi00020]
Other DBs
GO: 0006099
Organism
Vitis vinifera (wine grape) [GN:vvi]
Gene
100255795  citrate synthase, glyoxysomal [KO:K01647] [EC:2.3.3.1]
100261432  citrate synthase, mitochondrial isoform X2 [KO:K01647] [EC:2.3.3.1]
100255189  ATP-citrate synthase alpha chain protein 1 isoform X2 [KO:K01648] [EC:2.3.3.8]
100240939  ATP-citrate synthase alpha chain protein 2 [KO:K01648] [EC:2.3.3.8]
100267071  ATP-citrate synthase beta chain protein 2 [KO:K01648] [EC:2.3.3.8]
100242027  aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
100256776  aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
100253811  aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
100249290  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
100243260  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
100261578  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
100263635  isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial [KO:K00030] [EC:1.1.1.41]
100253697  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial isoform X1 [KO:K00030] [EC:1.1.1.41]
100242228  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial isoform X1 [KO:K00030] [EC:1.1.1.41]
100254754  uncharacterized protein LOC100254754 [KO:K00164] [EC:1.2.4.2]
100244395  dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 1, mitochondrial [KO:K00658] [EC:2.3.1.61]
100251123  dihydrolipoyl dehydrogenase 2, chloroplastic isoform X2 [KO:K00382] [EC:1.8.1.4]
100246037  dihydrolipoyl dehydrogenase, mitochondrial [KO:K00382] [EC:1.8.1.4]
100246616  dihydrolipoyl dehydrogenase 2, chloroplastic [KO:K00382] [EC:1.8.1.4]
100261358  succinate--CoA ligase [ADP-forming] subunit alpha-1, mitochondrial [KO:K01899] [EC:6.2.1.4 6.2.1.5]
100261494  succinate--CoA ligase [ADP-forming] subunit alpha, mitochondrial [KO:K01899] [EC:6.2.1.4 6.2.1.5]
100248061  succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial [KO:K01900] [EC:6.2.1.4 6.2.1.5]
100254718  succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial [KO:K00234] [EC:1.3.5.1]
100244487  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 3, mitochondrial [KO:K00235] [EC:1.3.5.1]
100262907  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 1, mitochondrial [KO:K00235] [EC:1.3.5.1]
7498669  sdh3; succinate dehydrogenase subunit 3 [KO:K00236]
7498540  sdh4; succinate dehydrogenase subunit 4 [KO:K25801]
100264013  fumarate hydratase 1, mitochondrial [KO:K01679] [EC:4.2.1.2]
100256208  fumarate hydratase 1, mitochondrial [KO:K01679] [EC:4.2.1.2]
100248145  malate dehydrogenase, cytoplasmic [KO:K00025] [EC:1.1.1.37]
100253273  malate dehydrogenase, cytoplasmic [KO:K00025] [EC:1.1.1.37]
100256452  malate dehydrogenase isoform X4 [KO:K00025] [EC:1.1.1.37]
100260994  malate dehydrogenase, glyoxysomal [KO:K00026] [EC:1.1.1.37]
100247511  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
100265585  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
100253724  malate dehydrogenase, mitochondrial [KO:K00026] [EC:1.1.1.37]
100232859  MDH; malate dehydrogenase [KO:K00026] [EC:1.1.1.37]
100232924  malate dehydrogenase, glyoxysomal [KO:K00026] [EC:1.1.1.37]
100256754  phosphoenolpyruvate carboxykinase (ATP) 1 isoform X1 [KO:K01610] [EC:4.1.1.49]
100263880  pyruvate dehydrogenase E1 component subunit alpha, mitochondrial [KO:K00161] [EC:1.2.4.1]
100243322  pyruvate dehydrogenase E1 component subunit alpha, mitochondrial [KO:K00161] [EC:1.2.4.1]
100264423  pyruvate dehydrogenase E1 component subunit alpha-3, chloroplastic [KO:K00161] [EC:1.2.4.1]
100264409  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial [KO:K00162] [EC:1.2.4.1]
100259931  LOW QUALITY PROTEIN: pyruvate dehydrogenase E1 component subunit beta-3, chloroplastic-like [KO:K00162] [EC:1.2.4.1]
100247469  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial [KO:K00162] [EC:1.2.4.1]
100250049  pyruvate dehydrogenase E1 component subunit beta-3, chloroplastic [KO:K00162] [EC:1.2.4.1]
100251405  dihydrolipoyllysine-residue acetyltransferase component 2 of pyruvate dehydrogenase complex, mitochondrial [KO:K00627] [EC:2.3.1.12]
100249200  dihydrolipoyllysine-residue acetyltransferase component 3 of pyruvate dehydrogenase complex, mitochondrial isoform X4 [KO:K00627] [EC:2.3.1.12]
100243846  dihydrolipoyllysine-residue acetyltransferase component 1 of pyruvate dehydrogenase complex, mitochondrial isoform X1 [KO:K00627] [EC:2.3.1.12]
100245266  dihydrolipoyllysine-residue acetyltransferase component 5 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
100261197  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
vvi00010  Glycolysis / Gluconeogenesis
vvi00053  Ascorbate and aldarate metabolism
vvi00061  Fatty acid biosynthesis
vvi00062  Fatty acid elongation
vvi00071  Fatty acid degradation
vvi00190  Oxidative phosphorylation
vvi00220  Arginine biosynthesis
vvi00250  Alanine, aspartate and glutamate metabolism
vvi00280  Valine, leucine and isoleucine degradation
vvi00350  Tyrosine metabolism
vvi00470  D-Amino acid metabolism
vvi00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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