KEGG   PATHWAY: osa00020
Entry
osa00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Oryza sativa japonica (Japanese rice) (RefSeq)
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
osa00020  Citrate cycle (TCA cycle)
osa00020

Module
osa_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:osa00020]
osa_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:osa00020]
osa_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:osa00020]
osa_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:osa00020]
osa_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:osa00020]
Other DBs
GO: 0006099
Organism
Oryza sativa japonica (Japanese rice) (RefSeq) [GN:osa]
Gene
4328812  citrate synthase 3, peroxisomal [KO:K01647] [EC:2.3.3.1]
4328598  citrate synthase 4, mitochondrial [KO:K01647] [EC:2.3.3.1]
4350660  citrate synthase 4, mitochondrial [KO:K01647] [EC:2.3.3.1]
4325777  ATP-citrate synthase beta chain protein 1 [KO:K01648] [EC:2.3.3.8]
4352549  ATP-citrate synthase alpha chain protein 3 [KO:K01648] [EC:2.3.3.8]
9272295  ATP-citrate synthase alpha chain protein 2 [KO:K01648] [EC:2.3.3.8]
9272485  ATP-citrate synthase subunit alpha chain protein 1 [KO:K01648] [EC:2.3.3.8]
4340833  putative aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
4331547  putative aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
9270306  putative aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
4336353  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
4339674  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
4327213  cytosolic isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
4324176  cytosolic isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
4336169  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial [KO:K00030] [EC:1.1.1.41]
4324442  isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial [KO:K00030] [EC:1.1.1.41]
4329858  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial isoform X1 [KO:K00030] [EC:1.1.1.41]
4335673  2-oxoglutarate dehydrogenase, mitochondrial [KO:K00164] [EC:1.2.4.2]
4344403  2-oxoglutarate dehydrogenase, mitochondrial [KO:K00164] [EC:1.2.4.2]
4335689  dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 1, mitochondrial isoform X1 [KO:K00658] [EC:2.3.1.61]
9266803  dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 1, mitochondrial [KO:K00658] [EC:2.3.1.61]
4326980  dihydrolipoyl dehydrogenase 1, mitochondrial [KO:K00382] [EC:1.8.1.4]
4337862  dihydrolipoyl dehydrogenase 1, chloroplastic [KO:K00382] [EC:1.8.1.4]
4326849  dihydrolipoyl dehydrogenase 1, chloroplastic [KO:K00382] [EC:1.8.1.4]
4337881  dihydrolipoyl dehydrogenase, mitochondrial [KO:K00382] [EC:1.8.1.4]
4343710  probable succinyl-CoA ligase [ADP-forming] subunit alpha, mitochondrial [KO:K01899] [EC:6.2.1.4 6.2.1.5]
4330016  succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial [KO:K01900] [EC:6.2.1.4 6.2.1.5]
4342350  succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial [KO:K00234] [EC:1.3.5.1]
4344541  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 1, mitochondrial isoform X2 [KO:K00235] [EC:1.3.5.1]
4346890  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 2, mitochondrial [KO:K00235] [EC:1.3.5.1]
4328125  succinate dehydrogenase subunit 3-1, mitochondrial [KO:K00236]
4343404  succinate dehydrogenase subunit 3-2, mitochondrial [KO:K00236]
4338591  succinate dehydrogenase subunit 4, mitochondrial-like [KO:K25801]
4326521  succinate dehydrogenase subunit 4, mitochondrial [KO:K25801]
4332774  fumarate hydratase 1, mitochondrial [KO:K01679] [EC:4.2.1.2]
4348905  malate dehydrogenase, cytoplasmic [KO:K00025] [EC:1.1.1.37]
4336595  malate dehydrogenase, cytoplasmic-like [KO:K00025] [EC:1.1.1.37]
4352871  malate dehydrogenase, glyoxysomal [KO:K00026] [EC:1.1.1.37]
4334274  malate dehydrogenase, glyoxysomal-like [KO:K00026] [EC:1.1.1.37]
4326249  malate dehydrogenase, mitochondrial [KO:K00026] [EC:1.1.1.37]
4327423  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
4345657  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
4339682  malate dehydrogenase, mitochondrial [KO:K00026] [EC:1.1.1.37]
4343993  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
4332293  phosphoenolpyruvate carboxykinase [ATP] [KO:K01610] [EC:4.1.1.49]
4348268  phosphoenolpyruvate carboxykinase [ATP] [KO:K01610] [EC:4.1.1.49]
4334968  pyruvate dehydrogenase E1 component subunit alpha-3, chloroplastic [KO:K00161] [EC:1.2.4.1]
4340640  pyruvate dehydrogenase E1 component subunit alpha-2, mitochondrial [KO:K00161] [EC:1.2.4.1]
4330673  pyruvate dehydrogenase E1 component subunit alpha-1, mitochondrial [KO:K00161] [EC:1.2.4.1]
4346159  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial [KO:K00162] [EC:1.2.4.1]
4352803  pyruvate dehydrogenase E1 component subunit beta-3, chloroplastic [KO:K00162] [EC:1.2.4.1]
4347531  pyruvate dehydrogenase E1 component subunit beta-2, mitochondrial [KO:K00162] [EC:1.2.4.1]
4333564  pyruvate dehydrogenase E1 component subunit beta-4, chloroplastic [KO:K00162] [EC:1.2.4.1]
4339859  dihydrolipoyllysine-residue acetyltransferase component 3 of pyruvate dehydrogenase complex, mitochondrial isoform X1 [KO:K00627] [EC:2.3.1.12]
4341113  dihydrolipoyllysine-residue acetyltransferase component 1 of pyruvate dehydrogenase complex, mitochondrial [KO:K00627] [EC:2.3.1.12]
4351678  dihydrolipoyllysine-residue acetyltransferase component 5 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
4343003  dihydrolipoyllysine-residue acetyltransferase component 2 of pyruvate dehydrogenase complex, mitochondrial isoform X1 [KO:K00627] [EC:2.3.1.12]
4328010  dihydrolipoyllysine-residue acetyltransferase component 2 of pyruvate dehydrogenase complex, mitochondrial [KO:K00627] [EC:2.3.1.12]
4345640  dihydrolipoyllysine-residue acetyltransferase component 4 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
4347022  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
osa00010  Glycolysis / Gluconeogenesis
osa00053  Ascorbate and aldarate metabolism
osa00061  Fatty acid biosynthesis
osa00062  Fatty acid elongation
osa00071  Fatty acid degradation
osa00190  Oxidative phosphorylation
osa00220  Arginine biosynthesis
osa00250  Alanine, aspartate and glutamate metabolism
osa00280  Valine, leucine and isoleucine degradation
osa00350  Tyrosine metabolism
osa00470  D-Amino acid metabolism
osa00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

DBGET integrated database retrieval system