KEGG   PATHWAY: pnp00020
Entry
pnp00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Paenibacillus naphthalenovorans
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
pnp00020  Citrate cycle (TCA cycle)
pnp00020

Module
pnp_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:pnp00020]
pnp_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:pnp00020]
pnp_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:pnp00020]
pnp_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:pnp00020]
pnp_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:pnp00020]
Other DBs
GO: 0006099
Organism
Paenibacillus naphthalenovorans [GN:pnp]
Gene
IJ22_24820  citrate synthase [KO:K01647] [EC:2.3.3.1]
IJ22_04800  citrate synthase [KO:K01647] [EC:2.3.3.1]
IJ22_39030  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
IJ22_04810  isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
IJ22_24000  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
IJ22_26490  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
IJ22_27040  acetoin dehydrogenase [KO:K00382] [EC:1.8.1.4]
IJ22_27650  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
IJ22_36220  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
IJ22_13410  subunit alpha of 2-oxoglutarate ferredoxin oxidoreductase [KO:K00174] [EC:1.2.7.3 1.2.7.11]
IJ22_13420  2-oxoacid ferredoxin oxidoreductase [KO:K00175] [EC:1.2.7.3 1.2.7.11]
IJ22_12450  subunit alpha of succinyl-CoA synthetase [KO:K01902] [EC:6.2.1.5]
IJ22_12440  subunit beta of succinyl-CoA synthetase [KO:K01903] [EC:6.2.1.5]
IJ22_39920  succinyl-CoA:coenzyme A transferase [KO:K18118] [EC:2.8.3.18]
IJ22_30800  succinate dehydrogenase [KO:K00239] [EC:1.3.5.1]
IJ22_30790  succinate dehydrogenase [KO:K00240] [EC:1.3.5.1]
IJ22_30810  succinate dehydrogenase cytochrome B558 [KO:K00241]
IJ22_04870  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
IJ22_00490  subunit alpha of L(+)-tartrate dehydratase [KO:K01677] [EC:4.2.1.2]
IJ22_00500  class I anaerobic fumarate hydratase [KO:K01678] [EC:4.2.1.2]
IJ22_20050  fumarate hydratase [KO:K01679] [EC:4.2.1.2]
IJ22_04820  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
IJ22_46840  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
IJ22_32930  phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
IJ22_27680  pyruvate dehydrogenase [KO:K00161] [EC:1.2.4.1]
IJ22_27670  2-oxoisovalerate dehydrogenase [KO:K00162] [EC:1.2.4.1]
IJ22_26480  subunit E2 of branched-chain alpha-keto acid dehydrogenase [KO:K00627] [EC:2.3.1.12]
IJ22_27050  subunit E2 of branched-chain alpha-keto acid dehydrogenase [KO:K00627] [EC:2.3.1.12]
IJ22_27660  dienelactone hydrolase [KO:K00627] [EC:2.3.1.12]
IJ22_16590  pyruvate synthase [KO:K00169] [EC:1.2.7.1]
IJ22_16600  ferredoxin [KO:K00172] [EC:1.2.7.1]
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
pnp00010  Glycolysis / Gluconeogenesis
pnp00053  Ascorbate and aldarate metabolism
pnp00061  Fatty acid biosynthesis
pnp00071  Fatty acid degradation
pnp00190  Oxidative phosphorylation
pnp00220  Arginine biosynthesis
pnp00250  Alanine, aspartate and glutamate metabolism
pnp00280  Valine, leucine and isoleucine degradation
pnp00350  Tyrosine metabolism
pnp00470  D-Amino acid metabolism
pnp00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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