KEGG   PATHWAY: snem00020
Entry
snem00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Serratia nematodiphila
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
snem00020  Citrate cycle (TCA cycle)
snem00020

Module
snem_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:snem00020]
snem_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:snem00020]
snem_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:snem00020]
snem_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:snem00020]
snem_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:snem00020]
Other DBs
GO: 0006099
Organism
Serratia nematodiphila [GN:snem]
Gene
NLX84_06095  citrate synthase [KO:K01647] [EC:2.3.3.1]
NLX84_13420  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
NLX84_20885  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
NLX84_10360  icd; NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
NLX84_06120  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
NLX84_06125  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
NLX84_20890  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
NLX84_24205  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
NLX84_06135  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
NLX84_06130  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
NLX84_06110  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
NLX84_06115  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
NLX84_06100  sdhC; succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
NLX84_06105  sdhD; succinate dehydrogenase membrane anchor subunit [KO:K00242]
NLX84_01580  frdA; fumarate reductase (quinol) flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
NLX84_01575  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
NLX84_01570  frdC; fumarate reductase subunit FrdC [KO:K00246]
NLX84_01565  frdD; fumarate reductase subunit FrdD [KO:K00247]
NLX84_20950  fumA; class I fumarate hydratase FumA [KO:K01676] [EC:4.2.1.2]
NLX84_01855  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
NLX84_22425  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
NLX84_07585  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
NLX84_23455  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
NLX84_10640  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
NLX84_20900  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
NLX84_20895  aceF; pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
NLX84_13110  nifJ; pyruvate:ferredoxin (flavodoxin) oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
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
snem00010  Glycolysis / Gluconeogenesis
snem00053  Ascorbate and aldarate metabolism
snem00061  Fatty acid biosynthesis
snem00071  Fatty acid degradation
snem00190  Oxidative phosphorylation
snem00220  Arginine biosynthesis
snem00250  Alanine, aspartate and glutamate metabolism
snem00280  Valine, leucine and isoleucine degradation
snem00350  Tyrosine metabolism
snem00470  D-Amino acid metabolism
snem00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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