KEGG   PATHWAY: dfe00020
Entry
dfe00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Dyadobacter fermentans
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
dfe00020  Citrate cycle (TCA cycle)
dfe00020

Module
dfe_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:dfe00020]
dfe_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dfe00020]
dfe_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:dfe00020]
dfe_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dfe00020]
Other DBs
GO: 0006099
Organism
Dyadobacter fermentans [GN:dfe]
Gene
Dfer_0554  citrate synthase I [KO:K01647] [EC:2.3.3.1]
Dfer_1208  aconitate hydratase [KO:K27802] [EC:4.2.1.3 4.2.1.99]
Dfer_1209  Aconitase B, N-terminal protein [KO:K01682] [EC:4.2.1.3 4.2.1.99]
Dfer_3730  isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
Dfer_5752  2-oxoglutarate dehydrogenase, E1 subunit [KO:K00164] [EC:1.2.4.2]
Dfer_5753  2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
Dfer_0455  catalytic domain of components of various dehydrogenase complexes [KO:K00658] [EC:2.3.1.61]
Dfer_3995  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Dfer_2911  succinyl-CoA synthetase, alpha subunit [KO:K01902] [EC:6.2.1.5]
Dfer_2736  succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
Dfer_2213  succinate CoA transferase [KO:K18118] [EC:2.8.3.18]
Dfer_3970  succinate dehydrogenase or fumarate reductase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
Dfer_3971  succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
Dfer_3969  succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family [KO:K00241]
Dfer_2816  fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
Dfer_4459  malate dehydrogenase, NAD-dependent [KO:K00024] [EC:1.1.1.37]
Dfer_4539  malate/quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
Dfer_3887  pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit [KO:K00161] [EC:1.2.4.1]
Dfer_3509  Transketolase central region [KO:K00162] [EC:1.2.4.1]
Dfer_5625  pyruvate dehydrogenase complex dihydrolipoamide 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
dfe00010  Glycolysis / Gluconeogenesis
dfe00053  Ascorbate and aldarate metabolism
dfe00061  Fatty acid biosynthesis
dfe00071  Fatty acid degradation
dfe00190  Oxidative phosphorylation
dfe00220  Arginine biosynthesis
dfe00250  Alanine, aspartate and glutamate metabolism
dfe00280  Valine, leucine and isoleucine degradation
dfe00350  Tyrosine metabolism
dfe00470  D-Amino acid metabolism
dfe00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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