KEGG   PATHWAY: vim00020
Entry
vim00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Virgibacillus sp. MSP4-1
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
vim00020  Citrate cycle (TCA cycle)
vim00020

Module
vim_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:vim00020]
vim_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:vim00020]
vim_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:vim00020]
vim_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:vim00020]
vim_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:vim00020]
Other DBs
GO: 0006099
Organism
Virgibacillus sp. MSP4-1 [GN:vim]
Gene
GWK91_08540  citZ; citrate synthase [KO:K01647] [EC:2.3.3.1]
GWK91_05035  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
GWK91_15545  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
GWK91_08535  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
GWK91_00570  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
GWK91_00575  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
GWK91_06875  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
GWK91_03755  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
GWK91_04865  2-oxoacid:acceptor oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
GWK91_04870  2-oxoacid:ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
GWK91_04420  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
GWK91_04415  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
GWK91_05325  acetyl-CoA hydrolase/transferase family protein [KO:K18118] [EC:2.8.3.18]
GWK91_08300  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
GWK91_02800  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
GWK91_08295  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
GWK91_08305  succinate dehydrogenase [KO:K00241]
GWK91_00835  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
GWK91_08530  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
GWK91_12595  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
GWK91_03860  pyc; pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
GWK91_09080  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
GWK91_03740  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
GWK91_03745  alpha-ketoacid dehydrogenase subunit beta [KO:K00162] [EC:1.2.4.1]
GWK91_03750  2-oxo acid dehydrogenase subunit E2 [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
vim00010  Glycolysis / Gluconeogenesis
vim00053  Ascorbate and aldarate metabolism
vim00061  Fatty acid biosynthesis
vim00071  Fatty acid degradation
vim00190  Oxidative phosphorylation
vim00220  Arginine biosynthesis
vim00250  Alanine, aspartate and glutamate metabolism
vim00280  Valine, leucine and isoleucine degradation
vim00350  Tyrosine metabolism
vim00470  D-Amino acid metabolism
vim00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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