KEGG   PATHWAY: vum00020
Entry
vum00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Vigna umbellata (ricebean)
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
vum00020  Citrate cycle (TCA cycle)
vum00020

Module
vum_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:vum00020]
vum_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:vum00020]
Other DBs
GO: 0006099
Organism
Vigna umbellata (ricebean) [GN:vum]
Gene
124820455  ATP-citrate synthase alpha chain protein 1 [KO:K01648] [EC:2.3.3.8]
124845877  ATP-citrate synthase beta chain protein 1-like isoform X1 [KO:K01648] [EC:2.3.3.8]
124848000  LOW QUALITY PROTEIN: ATP-citrate synthase alpha chain protein 2-like [KO:K01648] [EC:2.3.3.8]
124839205  ATP-citrate synthase alpha chain protein 1-like [KO:K01648] [EC:2.3.3.8]
124841717  ATP-citrate synthase beta chain protein 1 [KO:K01648] [EC:2.3.3.8]
124841733  ATP-citrate synthase beta chain protein 2-like [KO:K01648] [EC:2.3.3.8]
124820435  aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
124822414  aconitate hydratase, cytoplasmic-like isoform X1 [KO:K01681] [EC:4.2.1.3]
124848445  aconitate hydratase, cytoplasmic-like [KO:K01681] [EC:4.2.1.3]
124823627  isocitrate dehydrogenase [NADP], chloroplastic/mitochondrial-like isoform X1 [KO:K00031] [EC:1.1.1.42]
124839202  isocitrate dehydrogenase [NADP]-like [KO:K00031] [EC:1.1.1.42]
124839204  isocitrate dehydrogenase [NADP]-like [KO:K00031] [EC:1.1.1.42]
124839262  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
124821421  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial-like isoform X1 [KO:K00030] [EC:1.1.1.41]
124835307  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial isoform X1 [KO:K00030] [EC:1.1.1.41]
124838665  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial-like [KO:K00030] [EC:1.1.1.41]
124830733  isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial [KO:K00030] [EC:1.1.1.41]
124832733  2-oxoglutarate dehydrogenase, mitochondrial [KO:K00164] [EC:1.2.4.2]
124843235  LOW QUALITY PROTEIN: 2-oxoglutarate dehydrogenase, mitochondrial-like [KO:K00164] [EC:1.2.4.2]
124835379  leghemoglobin reductase [KO:K00382] [EC:1.8.1.4]
124847262  dihydrolipoyl dehydrogenase 2, chloroplastic [KO:K00382] [EC:1.8.1.4]
124836797  dihydrolipoyl dehydrogenase 1, chloroplastic-like [KO:K00382] [EC:1.8.1.4]
124835527  succinate--CoA ligase [ADP-forming] subunit alpha-1, mitochondrial-like [KO:K01899] [EC:6.2.1.4 6.2.1.5]
124835533  succinate--CoA ligase [ADP-forming] subunit alpha, mitochondrial isoform X1 [KO:K01899] [EC:6.2.1.4 6.2.1.5]
124840720  succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial [KO:K01900] [EC:6.2.1.4 6.2.1.5]
124824409  succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial [KO:K00234] [EC:1.3.5.1]
124826513  succinate dehydrogenase [ubiquinone] flavoprotein subunit 1, mitochondrial [KO:K00234] [EC:1.3.5.1]
124838696  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 2, mitochondrial-like [KO:K00235] [EC:1.3.5.1]
124822418  uncharacterized protein LOC124822418 [KO:K00236]
124825532  succinate dehydrogenase subunit 4, mitochondrial [KO:K25801]
124844972  fumarate hydratase, mitochondrial-like [KO:K01679] [EC:4.2.1.2]
124843600  fumarate hydratase 1, mitochondrial-like [KO:K01679] [EC:4.2.1.2]
124843608  fumarate hydratase 1, mitochondrial [KO:K01679] [EC:4.2.1.2]
124843944  malate dehydrogenase, cytoplasmic [KO:K00025] [EC:1.1.1.37]
124842792  malate dehydrogenase, cytoplasmic-like isoform X1 [KO:K00025] [EC:1.1.1.37]
124824694  LOW QUALITY PROTEIN: malate dehydrogenase 2, peroxisomal-like [KO:K00026] [EC:1.1.1.37]
124826986  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
124830779  malate dehydrogenase, mitochondrial [KO:K00026] [EC:1.1.1.37]
124832691  phosphoenolpyruvate carboxykinase (ATP) 1-like [KO:K01610] [EC:4.1.1.49]
124822051  phosphoenolpyruvate carboxykinase (ATP) 1-like [KO:K01610] [EC:4.1.1.49]
124837116  pyruvate dehydrogenase E1 component subunit alpha, mitochondrial-like [KO:K00161] [EC:1.2.4.1]
124841215  pyruvate dehydrogenase E1 component subunit alpha-3, chloroplastic-like [KO:K00161] [EC:1.2.4.1]
124830615  pyruvate dehydrogenase E1 component subunit alpha, mitochondrial [KO:K00161] [EC:1.2.4.1]
124843145  pyruvate dehydrogenase E1 component subunit alpha-3, chloroplastic-like [KO:K00161] [EC:1.2.4.1]
124835013  pyruvate dehydrogenase E1 component subunit beta-like [KO:K00162] [EC:1.2.4.1]
124849205  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial [KO:K00162] [EC:1.2.4.1]
124822900  dihydrolipoyllysine-residue acetyltransferase component 1 of pyruvate dehydrogenase complex, mitochondrial isoform X1 [KO:K00627] [EC:2.3.1.12]
124835631  dihydrolipoyllysine-residue acetyltransferase component 3 of pyruvate dehydrogenase complex, mitochondrial-like [KO:K00627] [EC:2.3.1.12]
124838372  dihydrolipoyllysine-residue acetyltransferase component 5 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
124843197  dihydrolipoyllysine-residue acetyltransferase component 4 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
124831690  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
vum00010  Glycolysis / Gluconeogenesis
vum00053  Ascorbate and aldarate metabolism
vum00061  Fatty acid biosynthesis
vum00062  Fatty acid elongation
vum00071  Fatty acid degradation
vum00190  Oxidative phosphorylation
vum00220  Arginine biosynthesis
vum00250  Alanine, aspartate and glutamate metabolism
vum00280  Valine, leucine and isoleucine degradation
vum00350  Tyrosine metabolism
vum00470  D-Amino acid metabolism
vum00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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