KEGG   PATHWAY: pjd00020
Entry
pjd00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Paenibacillus sp. JDR-2
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
pjd00020  Citrate cycle (TCA cycle)
pjd00020

Module
pjd_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:pjd00020]
pjd_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:pjd00020]
pjd_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:pjd00020]
pjd_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:pjd00020]
Other DBs
GO: 0006099
Organism
Paenibacillus sp. JDR-2 [GN:pjd]
Gene
Pjdr2_4473  2-methylcitrate synthase/citrate synthase II [KO:K01647] [EC:2.3.3.1]
Pjdr2_2034  aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
Pjdr2_0811  aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
Pjdr2_4472  isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
Pjdr2_4724  2-oxoglutarate dehydrogenase, E1 subunit [KO:K00164] [EC:1.2.4.2]
Pjdr2_4725  2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
Pjdr2_2320  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Pjdr2_2653  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Pjdr2_1144  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Pjdr2_3373  pyruvate flavodoxin/ferredoxin oxidoreductase domain protein [KO:K00174] [EC:1.2.7.3 1.2.7.11]
Pjdr2_3372  pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit [KO:K00175] [EC:1.2.7.3 1.2.7.11]
Pjdr2_3467  succinyl-CoA synthetase, alpha subunit [KO:K01902] [EC:6.2.1.5]
Pjdr2_3468  succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
Pjdr2_4809  succinate dehydrogenase or fumarate reductase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
Pjdr2_4808  succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
Pjdr2_4810  succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family [KO:K00241]
Pjdr2_0765  fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
Pjdr2_4471  malate dehydrogenase, NAD-dependent [KO:K00024] [EC:1.1.1.37]
Pjdr2_6163  malate/quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
Pjdr2_2650  pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit [KO:K00161] [EC:1.2.4.1]
Pjdr2_2651  Transketolase central region [KO:K00162] [EC:1.2.4.1]
Pjdr2_2652  catalytic domain of components of various dehydrogenase complexes [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
pjd00010  Glycolysis / Gluconeogenesis
pjd00053  Ascorbate and aldarate metabolism
pjd00061  Fatty acid biosynthesis
pjd00071  Fatty acid degradation
pjd00190  Oxidative phosphorylation
pjd00220  Arginine biosynthesis
pjd00250  Alanine, aspartate and glutamate metabolism
pjd00280  Valine, leucine and isoleucine degradation
pjd00350  Tyrosine metabolism
pjd00470  D-Amino acid metabolism
pjd00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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