KEGG   PATHWAY: dyc00020
Entry
dyc00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Dyadobacter chenhuakuii
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
dyc00020  Citrate cycle (TCA cycle)
dyc00020

Module
dyc_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:dyc00020]
dyc_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dyc00020]
dyc_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:dyc00020]
dyc_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dyc00020]
Other DBs
GO: 0006099
Organism
Dyadobacter chenhuakuii [GN:dyc]
Gene
NFI80_05825  citrate synthase [KO:K01647] [EC:2.3.3.1]
NFI80_04880  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
NFI80_04875  bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
NFI80_18870  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
NFI80_24890  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
NFI80_05355  2-oxo acid dehydrogenase subunit E2 [KO:K00658] [EC:2.3.1.61]
NFI80_24895  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
NFI80_17550  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
NFI80_22910  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
NFI80_23775  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
NFI80_17655  fumarate reductase/succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
NFI80_17650  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
NFI80_17660  succinate dehydrogenase cytochrome b subunit [KO:K00241]
NFI80_23365  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
NFI80_14865  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
NFI80_14495  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
NFI80_18040  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
NFI80_19765  pyruvate dehydrogenase complex E1 component subunit beta [KO:K00162] [EC:1.2.4.1]
NFI80_10860  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
dyc00010  Glycolysis / Gluconeogenesis
dyc00053  Ascorbate and aldarate metabolism
dyc00061  Fatty acid biosynthesis
dyc00071  Fatty acid degradation
dyc00190  Oxidative phosphorylation
dyc00220  Arginine biosynthesis
dyc00250  Alanine, aspartate and glutamate metabolism
dyc00280  Valine, leucine and isoleucine degradation
dyc00350  Tyrosine metabolism
dyc00470  D-Amino acid metabolism
dyc00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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