KEGG   PATHWAY: atr00020
Entry
atr00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Amborella trichopoda
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
atr00020  Citrate cycle (TCA cycle)
atr00020

Module
atr_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:atr00020]
atr_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:atr00020]
atr_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:atr00020]
Other DBs
GO: 0006099
Organism
Amborella trichopoda [GN:atr]
Gene
18427432  citrate synthase, mitochondrial [KO:K01647] [EC:2.3.3.1]
18437501  citrate synthase, glyoxysomal [KO:K01647] [EC:2.3.3.1]
18440864  citrate synthase, mitochondrial isoform X1 [KO:K01647] [EC:2.3.3.1]
18430021  ATP-citrate synthase alpha chain protein 2 isoform X1 [KO:K01648] [EC:2.3.3.8]
18431257  ATP-citrate synthase beta chain protein 2 [KO:K01648] [EC:2.3.3.8]
18430455  LOW QUALITY PROTEIN: ATP-citrate synthase alpha chain protein 2 [KO:K01648] [EC:2.3.3.8]
18424196  aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
18425876  aconitate hydratase, cytoplasmic [KO:K01681] [EC:4.2.1.3]
18430862  isocitrate dehydrogenase [NADP] isoform X3 [KO:K00031] [EC:1.1.1.42]
18448410  isocitrate dehydrogenase [NADP] isoform X2 [KO:K00031] [EC:1.1.1.42]
18424254  isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial [KO:K00030] [EC:1.1.1.41]
18431455  LOW QUALITY PROTEIN: isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial-like [KO:K00030] [EC:1.1.1.41]
18441411  isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial [KO:K00030] [EC:1.1.1.41]
18438344  2-oxoglutarate dehydrogenase, mitochondrial [KO:K00164] [EC:1.2.4.2]
18440187  dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 1, mitochondrial [KO:K00658] [EC:2.3.1.61]
18431228  LOW QUALITY PROTEIN: dihydrolipoyl dehydrogenase 2, chloroplastic [KO:K00382] [EC:1.8.1.4]
18448186  dihydrolipoyl dehydrogenase, mitochondrial isoform X1 [KO:K00382] [EC:1.8.1.4]
18437335  dihydrolipoyl dehydrogenase, mitochondrial [KO:K00382] [EC:1.8.1.4]
18437566  LOW QUALITY PROTEIN: succinate--CoA ligase [ADP-forming] subunit alpha, mitochondrial [KO:K01899] [EC:6.2.1.4 6.2.1.5]
18447203  LOW QUALITY PROTEIN: succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial [KO:K01900] [EC:6.2.1.4 6.2.1.5]
18445831  succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial [KO:K00234] [EC:1.3.5.1]
18442000  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 2, mitochondrial [KO:K00235] [EC:1.3.5.1]
18422451  succinate dehydrogenase [ubiquinone] iron-sulfur subunit 3, mitochondrial [KO:K00235] [EC:1.3.5.1]
18430144  fumarate hydratase 1, mitochondrial [KO:K01679] [EC:4.2.1.2]
18428843  malate dehydrogenase, cytoplasmic [KO:K00025] [EC:1.1.1.37]
105420834  malate dehydrogenase, cytoplasmic [KO:K00025] [EC:1.1.1.37]
18422244  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
18440828  malate dehydrogenase, chloroplastic [KO:K00026] [EC:1.1.1.37]
18442455  malate dehydrogenase, glyoxysomal [KO:K00026] [EC:1.1.1.37]
18442196  malate dehydrogenase, mitochondrial [KO:K00026] [EC:1.1.1.37]
18437478  LOW QUALITY PROTEIN: phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
18429777  pyruvate dehydrogenase E1 component subunit alpha, mitochondrial [KO:K00161] [EC:1.2.4.1]
18448759  pyruvate dehydrogenase E1 component subunit alpha-3, chloroplastic [KO:K00161] [EC:1.2.4.1]
18428486  LOW QUALITY PROTEIN: pyruvate dehydrogenase E1 component subunit alpha-3, chloroplastic [KO:K00161] [EC:1.2.4.1]
18427331  pyruvate dehydrogenase E1 component subunit beta [KO:K00162] [EC:1.2.4.1]
18434431  pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial isoform X1 [KO:K00162] [EC:1.2.4.1]
18426345  dihydrolipoyllysine-residue acetyltransferase component 2 of pyruvate dehydrogenase complex, mitochondrial isoform X1 [KO:K00627] [EC:2.3.1.12]
18429064  dihydrolipoyllysine-residue acetyltransferase component 4 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
18441063  dihydrolipoyllysine-residue acetyltransferase component 5 of pyruvate dehydrogenase complex, chloroplastic [KO:K00627] [EC:2.3.1.12]
18441494  dihydrolipoyllysine-residue acetyltransferase component 1 of pyruvate dehydrogenase complex, mitochondrial 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
atr00010  Glycolysis / Gluconeogenesis
atr00053  Ascorbate and aldarate metabolism
atr00061  Fatty acid biosynthesis
atr00062  Fatty acid elongation
atr00071  Fatty acid degradation
atr00190  Oxidative phosphorylation
atr00220  Arginine biosynthesis
atr00250  Alanine, aspartate and glutamate metabolism
atr00280  Valine, leucine and isoleucine degradation
atr00350  Tyrosine metabolism
atr00470  D-Amino acid metabolism
atr00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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