KEGG   PATHWAY: vik00020
Entry
vik00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Virgibacillus sp. NKC19-16
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
vik00020  Citrate cycle (TCA cycle)
vik00020

Module
vik_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:vik00020]
vik_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:vik00020]
vik_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:vik00020]
vik_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:vik00020]
vik_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:vik00020]
Other DBs
GO: 0006099
Organism
Virgibacillus sp. NKC19-16 [GN:vik]
Gene
KFZ58_11490  citZ; citrate synthase [KO:K01647] [EC:2.3.3.1]
KFZ58_07870  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
KFZ58_09300  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
KFZ58_11485  icd; NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
KFZ58_06520  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
KFZ58_06525  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
KFZ58_08115  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
KFZ58_10090  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
KFZ58_08770  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
KFZ58_08765  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
KFZ58_11250  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
KFZ58_11245  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
KFZ58_11255  succinate dehydrogenase cytochrome b558 subunit [KO:K00241]
KFZ58_06700  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
KFZ58_11480  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
KFZ58_18660  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
KFZ58_15290  mqo; malate dehydrogenase (quinone) [KO:K00116] [EC:1.1.5.4]
KFZ58_08205  pyc; pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
KFZ58_11925  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
KFZ58_08100  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
KFZ58_14165  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
KFZ58_08105  alpha-ketoacid dehydrogenase subunit beta [KO:K00162] [EC:1.2.4.1]
KFZ58_14160  alpha-ketoacid dehydrogenase subunit beta [KO:K00162] [EC:1.2.4.1]
KFZ58_08110  2-oxo acid dehydrogenase subunit E2 [KO:K00627] [EC:2.3.1.12]
KFZ58_14155  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
vik00010  Glycolysis / Gluconeogenesis
vik00053  Ascorbate and aldarate metabolism
vik00061  Fatty acid biosynthesis
vik00071  Fatty acid degradation
vik00190  Oxidative phosphorylation
vik00220  Arginine biosynthesis
vik00250  Alanine, aspartate and glutamate metabolism
vik00280  Valine, leucine and isoleucine degradation
vik00350  Tyrosine metabolism
vik00470  D-Amino acid metabolism
vik00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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