KEGG   PATHWAY: lys00020
Entry
lys00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Lysinibacillus sp. YS11
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
lys00020  Citrate cycle (TCA cycle)
lys00020

Module
lys_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:lys00020]
lys_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:lys00020]
lys_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:lys00020]
lys_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:lys00020]
lys_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:lys00020]
Other DBs
GO: 0006099
Organism
Lysinibacillus sp. YS11 [GN:lys]
Gene
LBYS11_16975  citrate synthase [KO:K01647] [EC:2.3.3.1]
LBYS11_12015  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
LBYS11_16970  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
LBYS11_10820  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
LBYS11_10825  dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
LBYS11_03710  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
LBYS11_04115  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
LBYS11_14130  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
LBYS11_05450  2-oxoacid:acceptor oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
LBYS11_05455  2-oxoacid ferredoxin oxidoreductase [KO:K00175] [EC:1.2.7.3 1.2.7.11]
LBYS11_04920  succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
LBYS11_04915  ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
LBYS11_20735  acetyl-CoA hydrolase [KO:K18118] [EC:2.8.3.18]
LBYS11_01975  acetyl-CoA hydrolase [KO:K18118] [EC:2.8.3.18]
LBYS11_16600  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
LBYS11_16595  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
LBYS11_16605  succinate dehydrogenase [KO:K00241]
LBYS11_19690  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
LBYS11_08880  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
LBYS11_07530  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
LBYS11_16965  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
LBYS11_08835  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
LBYS11_22685  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
LBYS11_04240  pyc; pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
LBYS11_17480  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
LBYS11_04100  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
LBYS11_04105  alpha-ketoacid dehydrogenase subunit beta [KO:K00162] [EC:1.2.4.1]
LBYS11_04110  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
lys00010  Glycolysis / Gluconeogenesis
lys00053  Ascorbate and aldarate metabolism
lys00061  Fatty acid biosynthesis
lys00062  Fatty acid elongation
lys00071  Fatty acid degradation
lys00190  Oxidative phosphorylation
lys00220  Arginine biosynthesis
lys00250  Alanine, aspartate and glutamate metabolism
lys00280  Valine, leucine and isoleucine degradation
lys00350  Tyrosine metabolism
lys00470  D-Amino acid metabolism
lys00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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