KEGG   PATHWAY: pdx00020
Entry
pdx00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Pseudonocardia dioxanivorans
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
pdx00020  Citrate cycle (TCA cycle)
pdx00020

Module
pdx_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:pdx00020]
pdx_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:pdx00020]
pdx_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:pdx00020]
pdx_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:pdx00020]
pdx_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:pdx00020]
Other DBs
GO: 0006099
Organism
Pseudonocardia dioxanivorans [GN:pdx]
Gene
Psed_0610  Citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
Psed_0613  citrate synthase I [KO:K01647] [EC:2.3.3.1]
Psed_6532  citrate synthase [KO:K01647] [EC:2.3.3.1]
Psed_3377  aconitate hydratase 1 [KO:K27802] [EC:4.2.1.3 4.2.1.99]
Psed_5312  isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
Psed_5115  2-oxoglutarate dehydrogenase, E1 subunit [KO:K01616] [EC:2.2.1.5 4.1.1.71 1.2.4.2 2.3.1.61]
Psed_3308  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Psed_4565  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Psed_5549  2-oxoacid:acceptor oxidoreductase, alpha subunit [KO:K00174] [EC:1.2.7.3 1.2.7.11]
Psed_5550  2-oxoglutarate synthase [KO:K00175] [EC:1.2.7.3 1.2.7.11]
Psed_5331  succinyl-CoA synthetase, alpha subunit [KO:K01902] [EC:6.2.1.5]
Psed_5332  Succinyl-CoA ligase (ADP-forming) subunit beta [KO:K01903] [EC:6.2.1.5]
Psed_4590  Succinate dehydrogenase (ubiquinone) [KO:K00239] [EC:1.3.5.1]
Psed_4593  succinate dehydrogenase or fumarate reductase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
Psed_4589  succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
Psed_4592  succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
Psed_4594  succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family [KO:K00241]
Psed_3979  hydro-lyase, Fe-S type, tartrate/fumarate subfamily, beta subunit [KO:K01676] [EC:4.2.1.2]
Psed_0958  Fumarate hydratase class II [KO:K01679] [EC:4.2.1.2]
Psed_2085  Malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
Psed_2875  Malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
Psed_4769  pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
Psed_6619  Phosphoenolpyruvate carboxykinase (GTP) [KO:K01596] [EC:4.1.1.32]
Psed_2141  2-oxo-acid dehydrogenase E1 subunit, homodimeric type [KO:K00163] [EC:1.2.4.1]
Psed_3930  Pyruvate dehydrogenase (acetyl-transferring) [KO:K00163] [EC:1.2.4.1]
Psed_3712  Dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
Psed_4566  2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase [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
pdx00010  Glycolysis / Gluconeogenesis
pdx00053  Ascorbate and aldarate metabolism
pdx00061  Fatty acid biosynthesis
pdx00071  Fatty acid degradation
pdx00190  Oxidative phosphorylation
pdx00220  Arginine biosynthesis
pdx00250  Alanine, aspartate and glutamate metabolism
pdx00280  Valine, leucine and isoleucine degradation
pdx00350  Tyrosine metabolism
pdx00470  D-Amino acid metabolism
pdx00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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