KEGG   PATHWAY: vpg00020
Entry
vpg00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Vibrio pelagius
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
vpg00020  Citrate cycle (TCA cycle)
vpg00020

Module
vpg_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:vpg00020]
vpg_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:vpg00020]
vpg_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:vpg00020]
vpg_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:vpg00020]
vpg_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:vpg00020]
Other DBs
GO: 0006099
Organism
Vibrio pelagius [GN:vpg]
Gene
LZI70_11075  citrate synthase [KO:K01647] [EC:2.3.3.1]
LZI70_09735  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
LZI70_01960  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
LZI70_11100  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
LZI70_11105  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
LZI70_09650  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
LZI70_11115  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
LZI70_11110  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
LZI70_11090  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
LZI70_11095  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
LZI70_11080  sdhC; succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
LZI70_11085  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
LZI70_05810  frdA; fumarate reductase (quinol) flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
LZI70_05815  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
LZI70_05820  frdC; fumarate reductase subunit FrdC [KO:K00246]
LZI70_05825  frdD; fumarate reductase subunit FrdD [KO:K00247]
LZI70_13150  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
LZI70_08000  class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
LZI70_05225  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
LZI70_06405  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
LZI70_09640  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
LZI70_09645  aceF; pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase [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
vpg00010  Glycolysis / Gluconeogenesis
vpg00053  Ascorbate and aldarate metabolism
vpg00061  Fatty acid biosynthesis
vpg00071  Fatty acid degradation
vpg00190  Oxidative phosphorylation
vpg00220  Arginine biosynthesis
vpg00250  Alanine, aspartate and glutamate metabolism
vpg00280  Valine, leucine and isoleucine degradation
vpg00350  Tyrosine metabolism
vpg00470  D-Amino acid metabolism
vpg00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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