KEGG   PATHWAY: ndk00020
Entry
ndk00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Nocardioides dokdonensis
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
ndk00020  Citrate cycle (TCA cycle)
ndk00020

Module
ndk_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:ndk00020]
ndk_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:ndk00020]
ndk_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:ndk00020]
ndk_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:ndk00020]
ndk_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:ndk00020]
Other DBs
GO: 0006099
Organism
Nocardioides dokdonensis [GN:ndk]
Gene
I601_0196  cfiB; 2-oxoglutarate carboxylase small subunit [KO:K01958] [EC:6.4.1.1]
I601_0223  lpdC; Dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
I601_0252  [KO:K00241]
I601_0253  frdA; Fumarate reductase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
I601_0254  frdB; Fumarate reductase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
I601_0262  icd; Isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
I601_0266  mdh_1; Malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
I601_0276  sucD_1; Succinyl-CoA ligase [ADP-forming] subunit alpha [KO:K01902] [EC:6.2.1.5]
I601_0277  sucC; Succinyl-CoA ligase [ADP-forming] subunit beta [KO:K01903] [EC:6.2.1.5]
I601_0379  aceE_1; Pyruvate dehydrogenase E1 component [KO:K00163] [EC:1.2.4.1]
I601_0696  citA; Citrate synthase 1 [KO:K01647] [EC:2.3.3.1]
I601_0767  korA; 2-oxoglutarate oxidoreductase subunit KorA [KO:K00174] [EC:1.2.7.3 1.2.7.11]
I601_0768  korB; 2-oxoglutarate oxidoreductase subunit KorB [KO:K00175] [EC:1.2.7.3 1.2.7.11]
I601_1185  pdhD_1; Dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
I601_1186  pdhC_2; Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex [KO:K00627] [EC:2.3.1.12]
I601_1187  bfmBAB; 2-oxoisovalerate dehydrogenase subunit beta [KO:K00162] [EC:1.2.4.1]
I601_1188  pdhA; Pyruvate dehydrogenase E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
I601_1411  pckG; Phosphoenolpyruvate carboxykinase [GTP] [KO:K01596] [EC:4.1.1.32]
I601_1957  aarA; Citrate synthase [KO:K01647] [EC:2.3.3.1]
I601_2038  fumC; Fumarate hydratase class II [KO:K01679] [EC:4.2.1.2]
I601_2041  fumA; Fumarate hydratase class I, aerobic [KO:K01676] [EC:4.2.1.2]
I601_2088  aceE_2; Pyruvate dehydrogenase E1 component [KO:K00163] [EC:1.2.4.1]
I601_2881  aceF; Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex [KO:K00627] [EC:2.3.1.12]
I601_2882  pdhD_2; Dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
I601_3569  acnA; Aconitate hydratase [KO:K27802]
I601_3716  aceE_3; Pyruvate dehydrogenase E1 component [KO:K00163] [EC:1.2.4.1]
I601_3950  kgd; Multifunctional 2-oxoglutarate metabolism enzyme [KO:K01616] [EC:2.2.1.5 4.1.1.71 1.2.4.2 2.3.1.61]
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
ndk00010  Glycolysis / Gluconeogenesis
ndk00061  Fatty acid biosynthesis
ndk00071  Fatty acid degradation
ndk00190  Oxidative phosphorylation
ndk00220  Arginine biosynthesis
ndk00250  Alanine, aspartate and glutamate metabolism
ndk00280  Valine, leucine and isoleucine degradation
ndk00350  Tyrosine metabolism
ndk00470  D-Amino acid metabolism
ndk00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   

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