KEGG   PATHWAY: nov00020
Entry
nov00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Novosphingobium sp. P6W
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
nov00020  Citrate cycle (TCA cycle)
nov00020

Module
nov_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:nov00020]
nov_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:nov00020]
nov_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:nov00020]
nov_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:nov00020]
nov_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:nov00020]
nov_M00982  Methylcitrate cycle [PATH:nov00020]
Other DBs
GO: 0006099
Organism
Novosphingobium sp. P6W [GN:nov]
Gene
TQ38_000725  [KO:K01676] [EC:4.2.1.2]
TQ38_000905  [KO:K01903] [EC:6.2.1.5]
TQ38_005855  [KO:K00627] [EC:2.3.1.12]
TQ38_008345  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
TQ38_009535  [KO:K00162] [EC:1.2.4.1]
TQ38_009540  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
TQ38_009595  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
TQ38_009610  [KO:K00627] [EC:2.3.1.12]
TQ38_010400  [KO:K01610] [EC:4.1.1.49]
TQ38_010600  [KO:K00175] [EC:1.2.7.3 1.2.7.11]
TQ38_010605  [KO:K00174] [EC:1.2.7.3 1.2.7.11]
TQ38_010890  [KO:K00240] [EC:1.3.5.1]
TQ38_011620  [KO:K00031] [EC:1.1.1.42]
TQ38_011715  [KO:K00239] [EC:1.3.5.1]
TQ38_011720  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
TQ38_011725  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
TQ38_012815  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
TQ38_013345  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
TQ38_013350  [KO:K01902] [EC:6.2.1.5]
TQ38_013355  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
TQ38_013360  [KO:K00658] [EC:2.3.1.61]
TQ38_013365  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
TQ38_015730  acnA; aconitate hydratase AcnA [KO:K27802]
TQ38_017205  [KO:K00627] [EC:2.3.1.12]
TQ38_017775  [KO:K01682] [EC:4.2.1.3 4.2.1.99]
TQ38_019905  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
TQ38_019950  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
TQ38_024290  [KO:K18118] [EC:2.8.3.18]
TQ38_026865  [KO:K01659] [EC:2.3.3.5]
TQ38_026875  acnA; aconitate hydratase AcnA [KO:K27802]
TQ38_027785  [KO:K18118] [EC:2.8.3.18]
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
nov00010  Glycolysis / Gluconeogenesis
nov00053  Ascorbate and aldarate metabolism
nov00061  Fatty acid biosynthesis
nov00071  Fatty acid degradation
nov00190  Oxidative phosphorylation
nov00220  Arginine biosynthesis
nov00250  Alanine, aspartate and glutamate metabolism
nov00280  Valine, leucine and isoleucine degradation
nov00350  Tyrosine metabolism
nov00470  D-Amino acid metabolism
nov00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   

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