KEGG   PATHWAY: lyb00020
Entry
lyb00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Lysinibacillus sp. B2A1
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
lyb00020  Citrate cycle (TCA cycle)
lyb00020

Module
lyb_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:lyb00020]
lyb_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:lyb00020]
lyb_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:lyb00020]
lyb_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:lyb00020]
lyb_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:lyb00020]
Other DBs
GO: 0006099
Organism
Lysinibacillus sp. B2A1 [GN:lyb]
Gene
C3943_10210  citrate synthase [KO:K01647] [EC:2.3.3.1]
C3943_16040  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
C3943_10215  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
C3943_16975  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
C3943_16970  dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
C3943_13755  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
C3943_26650  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
C3943_22930  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
C3943_05180  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
C3943_04710  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
C3943_06550  2-oxoacid:acceptor oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
C3943_06555  2-oxoacid ferredoxin oxidoreductase [KO:K00175] [EC:1.2.7.3 1.2.7.11]
C3943_06055  succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
C3943_06050  ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
C3943_24450  acetyl-CoA hydrolase [KO:K18118] [EC:2.8.3.18]
C3943_09120  acetyl-CoA hydrolase [KO:K18118] [EC:2.8.3.18]
C3943_02550  acetyl-CoA hydrolase [KO:K18118] [EC:2.8.3.18]
C3943_10660  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
C3943_10665  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
C3943_10655  succinate dehydrogenase [KO:K00241]
C3943_23285  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
C3943_19075  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
C3943_09560  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
C3943_19215  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
C3943_10220  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
C3943_26720  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
C3943_19995  pyc; pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
C3943_05290  pyc; pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
C3943_20475  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
C3943_05165  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
C3943_05170  alpha-ketoacid dehydrogenase subunit beta [KO:K00162] [EC:1.2.4.1]
C3943_26655  branched-chain alpha-keto acid dehydrogenase subunit E2 [KO:K00627] [EC:2.3.1.12]
C3943_05175  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
lyb00010  Glycolysis / Gluconeogenesis
lyb00061  Fatty acid biosynthesis
lyb00062  Fatty acid elongation
lyb00071  Fatty acid degradation
lyb00190  Oxidative phosphorylation
lyb00220  Arginine biosynthesis
lyb00250  Alanine, aspartate and glutamate metabolism
lyb00280  Valine, leucine and isoleucine degradation
lyb00350  Tyrosine metabolism
lyb00470  D-Amino acid metabolism
lyb00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

DBGET integrated database retrieval system