KEGG   PATHWAY: dfn00020
Entry
dfn00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Dickeya fangzhongdai DSM 101947
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
dfn00020  Citrate cycle (TCA cycle)
dfn00020

Module
dfn_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:dfn00020]
dfn_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:dfn00020]
dfn_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dfn00020]
dfn_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:dfn00020]
dfn_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dfn00020]
Other DBs
GO: 0006099
Organism
Dickeya fangzhongdai DSM 101947 [GN:dfn]
Gene
CVE23_06845  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
CVE23_13215  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
CVE23_18700  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
CVE23_15435  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
CVE23_12050  isocitrate dehydrogenase (NADP(+)) [KO:K00031] [EC:1.1.1.42]
CVE23_06870  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
CVE23_06875  dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
CVE23_18730  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
CVE23_06885  succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
CVE23_06880  ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
CVE23_06860  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
CVE23_06865  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
CVE23_06850  succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
CVE23_06855  sdhD; succinate:quinone oxidoreductase subunit D [KO:K00242]
CVE23_19910  fumarate reductase (quinol) flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
CVE23_19915  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
CVE23_19920  fumarate reductase subunit FrdC [KO:K00246]
CVE23_19925  fumarate reductase subunit FrdD [KO:K00247]
CVE23_04690  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
CVE23_11190  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
CVE23_03500  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
CVE23_15035  mqo; malate dehydrogenase (quinone) [KO:K00116] [EC:1.1.5.4]
CVE23_20585  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
CVE23_18740  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
CVE23_18735  aceF; pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
CVE23_04120  nifJ; pyruvate:ferredoxin (flavodoxin) oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
CVE23_19800  nifJ; pyruvate:ferredoxin (flavodoxin) oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
CVE23_09225  nifJ; pyruvate:ferredoxin (flavodoxin) oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
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
dfn00010  Glycolysis / Gluconeogenesis
dfn00053  Ascorbate and aldarate metabolism
dfn00061  Fatty acid biosynthesis
dfn00071  Fatty acid degradation
dfn00190  Oxidative phosphorylation
dfn00220  Arginine biosynthesis
dfn00250  Alanine, aspartate and glutamate metabolism
dfn00280  Valine, leucine and isoleucine degradation
dfn00350  Tyrosine metabolism
dfn00470  D-Amino acid metabolism
dfn00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

DBGET integrated database retrieval system