KEGG   PATHWAY: bdi00020
Entry
bdi00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Brachypodium distachyon (stiff brome)
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
bdi00020  Citrate cycle (TCA cycle)
bdi00020

Module
bdi_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:bdi00020]
bdi_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:bdi00020]
bdi_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:bdi00020]
bdi_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:bdi00020]
bdi_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:bdi00020]
Other DBs
GO: 0006099
Organism
Brachypodium distachyon (stiff brome) [GN:bdi]
Gene
100821411  citrate synthase 4, mitochondrial [KO:K01647] [EC:2.3.3.1]
100838601  citrate synthase, glyoxysomal [KO:K01647] [EC:2.3.3.1]
100829187  ATP-citrate synthase beta chain protein 1 [KO:K01648] [EC:2.3.3.8]
100845535  ATP-citrate synthase alpha chain protein 2 [KO:K01648] [EC:2.3.3.8]
100839155  ATP-citrate synthase alpha chain protein 3 [KO:K01648] [EC:2.3.3.8]
100842898  putative aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
100838918  putative aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
100837485  cytosolic isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
100837048  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
100837775  cytosolic isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
100836887  isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial [KO:K00030] [EC:1.1.1.41]
100829621  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial [KO:K00030] [EC:1.1.1.41]
100843832  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial isoform X1 [KO:K00030] [EC:1.1.1.41]
100838957  2-oxoglutarate dehydrogenase, mitochondrial [KO:K00164] [EC:1.2.4.2]
100839262  2-oxoglutarate dehydrogenase, mitochondrial [KO:K00164] [EC:1.2.4.2]
100824660  dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 1, mitochondrial [KO:K00658] [EC:2.3.1.61]
100830109  dihydrolipoyl dehydrogenase, mitochondrial [KO:K00382] [EC:1.8.1.4]
100837564  dihydrolipoyl dehydrogenase 2, chloroplastic isoform X2 [KO:K00382] [EC:1.8.1.4]
100823154  dihydrolipoyl dehydrogenase 1, mitochondrial [KO:K00382] [EC:1.8.1.4]
100826755  dihydrolipoyl dehydrogenase 1, chloroplastic [KO:K00382] [EC:1.8.1.4]
100843332  succinate--CoA ligase [ADP-forming] subunit alpha, mitochondrial [KO:K01899] [EC:6.2.1.4 6.2.1.5]
100835038  succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial isoform X3 [KO:K01900] [EC:6.2.1.4 6.2.1.5]
100831380  succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial [KO:K00234] [EC:1.3.5.1]
100823502  succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial [KO:K00234] [EC:1.3.5.1]
100841750  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 1, mitochondrial isoform X2 [KO:K00235] [EC:1.3.5.1]
100839755  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 2, mitochondrial [KO:K00235] [EC:1.3.5.1]
100845567  succinate dehydrogenase subunit 3-2, mitochondrial [KO:K00236]
100828671  succinate dehydrogenase subunit 3-1, mitochondrial [KO:K00236]
100825203  succinate dehydrogenase subunit 4, mitochondrial [KO:K25801]
100846386  succinate dehydrogenase subunit 4, mitochondrial [KO:K25801]
100821540  fumarate hydratase 1, mitochondrial [KO:K01679] [EC:4.2.1.2]
100822821  malate dehydrogenase, cytoplasmic [KO:K00025] [EC:1.1.1.37]
100841049  malate dehydrogenase, cytoplasmic [KO:K00025] [EC:1.1.1.37]
100841882  malate dehydrogenase, glyoxysomal [KO:K00026] [EC:1.1.1.37]
100832550  malate dehydrogenase 1, mitochondrial [KO:K00026] [EC:1.1.1.37]
100831548  malate dehydrogenase 1, mitochondrial [KO:K00026] [EC:1.1.1.37]
100832576  malate dehydrogenase, glyoxysomal [KO:K00026] [EC:1.1.1.37]
100838923  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
100830661  phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
100821082  pyruvate dehydrogenase E1 component subunit alpha-2, mitochondrial [KO:K00161] [EC:1.2.4.1]
100841947  pyruvate dehydrogenase E1 component subunit alpha-1, mitochondrial [KO:K00161] [EC:1.2.4.1]
100843225  pyruvate dehydrogenase E1 component subunit alpha-3, chloroplastic [KO:K00161] [EC:1.2.4.1]
100827441  pyruvate dehydrogenase E1 component subunit beta-4, chloroplastic [KO:K00162] [EC:1.2.4.1]
100823497  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial [KO:K00162] [EC:1.2.4.1]
100845850  pyruvate dehydrogenase E1 component subunit beta-2, mitochondrial [KO:K00162] [EC:1.2.4.1]
100835788  pyruvate dehydrogenase E1 component subunit beta-3, chloroplastic [KO:K00162] [EC:1.2.4.1]
100830020  dihydrolipoyllysine-residue acetyltransferase component 3 of pyruvate dehydrogenase complex, mitochondrial [KO:K00627] [EC:2.3.1.12]
100823294  dihydrolipoyllysine-residue acetyltransferase component 2 of pyruvate dehydrogenase complex, mitochondrial isoform X4 [KO:K00627] [EC:2.3.1.12]
100825328  dihydrolipoyllysine-residue acetyltransferase component 4 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
100830979  dihydrolipoyllysine-residue acetyltransferase component 4 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
100846462  dihydrolipoyllysine-residue acetyltransferase component 5 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
100839523  dihydrolipoyllysine-residue acetyltransferase component 1 of pyruvate dehydrogenase complex, mitochondrial [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
bdi00010  Glycolysis / Gluconeogenesis
bdi00053  Ascorbate and aldarate metabolism
bdi00061  Fatty acid biosynthesis
bdi00062  Fatty acid elongation
bdi00071  Fatty acid degradation
bdi00190  Oxidative phosphorylation
bdi00220  Arginine biosynthesis
bdi00250  Alanine, aspartate and glutamate metabolism
bdi00280  Valine, leucine and isoleucine degradation
bdi00350  Tyrosine metabolism
bdi00470  D-Amino acid metabolism
bdi00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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