KEGG   PATHWAY: rpy00020
Entry
rpy00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Rhodococcus pyridinivorans SB3094
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
rpy00020  Citrate cycle (TCA cycle)
rpy00020

Module
rpy_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:rpy00020]
rpy_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:rpy00020]
rpy_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:rpy00020]
rpy_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:rpy00020]
rpy_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:rpy00020]
Other DBs
GO: 0006099
Organism
Rhodococcus pyridinivorans SB3094 [GN:rpy]
Gene
Y013_20600  citrate synthase [KO:K01647] [EC:2.3.3.1]
Y013_20640  gltA; type II citrate synthase [KO:K01647] [EC:2.3.3.1]
Y013_02720  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
Y013_23605  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
Y013_03200  isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
Y013_08055  isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
Y013_23100  kgd; alpha-ketoglutarate decarboxylase [KO:K01616] [EC:2.2.1.5 4.1.1.71 1.2.4.2 2.3.1.61]
Y013_13970  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
Y013_09850  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
Y013_12640  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Y013_11835  2-oxoglutarate ferredoxin oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
Y013_11830  2-oxoacid ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
Y013_21145  succinyl-CoA synthetase subunit alpha [KO:K01902] [EC:6.2.1.5]
Y013_21140  succinyl-CoA synthetase subunit beta [KO:K01903] [EC:6.2.1.5]
Y013_00860  acetyl-CoA hydrolase [KO:K18118] [EC:2.8.3.18]
Y013_05560  sdhA; succinate dehydrogenase [KO:K00239] [EC:1.3.5.1]
Y013_08020  succinate dehydrogenase [KO:K00239] [EC:1.3.5.1]
Y013_05555  fumarate reductase [KO:K00240] [EC:1.3.5.1]
Y013_08025  succinate dehydrogenase [KO:K00240] [EC:1.3.5.1]
Y013_08010  succinate dehydrogenase [KO:K00241]
Y013_08015  succinate dehydrogenase [KO:K00242]
Y013_22700  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
Y013_21900  aspartate ammonia-lyase [KO:K01679] [EC:4.2.1.2]
Y013_01225  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
Y013_03145  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
Y013_00905  pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
Y013_11615  phosphoenolpyruvate carboxykinase [KO:K01596] [EC:4.1.1.32]
Y013_06210  pyruvate dehydrogenase E1 [KO:K00163] [EC:1.2.4.1]
Y013_12635  diaminohydroxyphosphoribosylaminopyrimidine deaminase [KO:K00627] [EC:2.3.1.12]
Y013_06045  dihydrolipoamide acyltransferase [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
rpy00010  Glycolysis / Gluconeogenesis
rpy00053  Ascorbate and aldarate metabolism
rpy00061  Fatty acid biosynthesis
rpy00062  Fatty acid elongation
rpy00071  Fatty acid degradation
rpy00190  Oxidative phosphorylation
rpy00220  Arginine biosynthesis
rpy00250  Alanine, aspartate and glutamate metabolism
rpy00280  Valine, leucine and isoleucine degradation
rpy00350  Tyrosine metabolism
rpy00470  D-Amino acid metabolism
rpy00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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