KEGG   PATHWAY: idc00020
Entry
idc00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Ideonella dechloratans
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
idc00020  Citrate cycle (TCA cycle)
idc00020

Module
idc_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:idc00020]
idc_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:idc00020]
idc_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:idc00020]
idc_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:idc00020]
idc_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:idc00020]
Other DBs
GO: 0006099
Organism
Ideonella dechloratans [GN:idc]
Gene
LRM40_07920  gltA; citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
LRM40_09380  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
LRM40_07860  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
LRM40_10500  icd; NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
LRM40_11185  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
LRM40_11180  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
LRM40_09220  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
LRM40_11175  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
LRM40_16860  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
LRM40_16855  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
LRM40_13475  acetyl-CoA hydrolase/transferase family protein [KO:K18118] [EC:2.8.3.18]
LRM40_07905  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
LRM40_07910  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
LRM40_07895  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
LRM40_07900  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
LRM40_11455  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
LRM40_00290  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
LRM40_07885  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
LRM40_01160  phosphoenolpyruvate carboxykinase (GTP) [KO:K01596] [EC:4.1.1.32]
LRM40_09210  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
LRM40_09215  aceF; dihydrolipoyllysine-residue acetyltransferase [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
idc00010  Glycolysis / Gluconeogenesis
idc00053  Ascorbate and aldarate metabolism
idc00061  Fatty acid biosynthesis
idc00071  Fatty acid degradation
idc00190  Oxidative phosphorylation
idc00220  Arginine biosynthesis
idc00250  Alanine, aspartate and glutamate metabolism
idc00280  Valine, leucine and isoleucine degradation
idc00350  Tyrosine metabolism
idc00470  D-Amino acid metabolism
idc00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

DBGET integrated database retrieval system