KEGG   PATHWAY: lgy00020
Entry
lgy00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Lysinibacillus varians
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
lgy00020  Citrate cycle (TCA cycle)
lgy00020

Module
lgy_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:lgy00020]
lgy_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:lgy00020]
lgy_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:lgy00020]
lgy_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:lgy00020]
lgy_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:lgy00020]
Other DBs
GO: 0006099
Organism
Lysinibacillus varians [GN:lgy]
Gene
T479_17520  citrate synthase [KO:K01647] [EC:2.3.3.1]
T479_10345  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
T479_17515  isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
T479_11335  2-oxoglutarate dehydrogenase E1 [KO:K00164] [EC:1.2.4.2]
T479_11330  dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
T479_03765  acetoin dehydrogenase [KO:K00382] [EC:1.8.1.4]
T479_04170  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
T479_14160  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
T479_05500  2-oxoglutarate ferredoxin oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
T479_05505  2-oxoacid ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
T479_04975  succinyl-CoA synthetase subsunit alpha [KO:K01902] [EC:6.2.1.5]
T479_04970  sucC; malate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
T479_01920  acetyl-CoA hydrolase [KO:K18118] [EC:2.8.3.18]
T479_21535  acetyl-CoA hydrolase [KO:K18118] [EC:2.8.3.18]
T479_17145  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
T479_17140  succinate dehydrogenase [KO:K00240] [EC:1.3.5.1]
T479_17150  succinate dehydrogenase cytochrome B558 [KO:K00241]
T479_02990  hypothetical protein [KO:K00242]
T479_20455  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
T479_09650  fumC; fumarate hydratase [KO:K01679] [EC:4.2.1.2]
T479_08305  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
T479_17510  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
T479_08015  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
T479_04290  pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
T479_17995  phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
T479_04155  pyruvate dehydrogenase E1 subunit alpha [KO:K00161] [EC:1.2.4.1]
T479_04160  2-oxoisovalerate dehydrogenase subunit beta [KO:K00162] [EC:1.2.4.1]
T479_04165  branched-chain alpha-keto 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
lgy00010  Glycolysis / Gluconeogenesis
lgy00053  Ascorbate and aldarate metabolism
lgy00061  Fatty acid biosynthesis
lgy00062  Fatty acid elongation
lgy00071  Fatty acid degradation
lgy00190  Oxidative phosphorylation
lgy00220  Arginine biosynthesis
lgy00250  Alanine, aspartate and glutamate metabolism
lgy00280  Valine, leucine and isoleucine degradation
lgy00350  Tyrosine metabolism
lgy00470  D-Amino acid metabolism
lgy00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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