KEGG   PATHWAY: sfd00020
Entry
sfd00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Sinorhizobium fredii USDA 257
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
sfd00020  Citrate cycle (TCA cycle)
sfd00020

Module
sfd_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:sfd00020]
sfd_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:sfd00020]
sfd_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:sfd00020]
sfd_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:sfd00020]
sfd_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:sfd00020]
Other DBs
GO: 0006099
Organism
Sinorhizobium fredii USDA 257 [GN:sfd]
Gene
USDA257_c15620  putative citrate synthase [KO:K01647] [EC:2.3.3.1]
USDA257_c35480  gltA; citrate synthase GltA [KO:K01647] [EC:2.3.3.1]
USDA257_c26570  acnA1; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
USDA257_c57520  acnA2; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
USDA257_c40680  icd; isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
USDA257_c55770  sucA; 2-oxoglutarate dehydrogenase E1 componentSucA [KO:K00164] [EC:1.2.4.2]
USDA257_c31430  sucB1; dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
USDA257_c55760  sucB2; dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
USDA257_c18870  lpdA1; dihydrolipoyl dehydrogenase LpdA [KO:K00382] [EC:1.8.1.4]
USDA257_c34860  lpdA2; dihydrolipoyl dehydrogenase LpdA [KO:K00382] [EC:1.8.1.4]
USDA257_c31420  lpd3; dihydrolipoyl dehydrogenase 3 [KO:K00382] [EC:1.8.1.4]
USDA257_c54080  lpdV; dihydrolipoyl dehydrogenase LpdV [KO:K00382] [EC:1.8.1.4]
USDA257_c55720  lpd; dihydrolipoyl dehydrogenase Lpd [KO:K00382] [EC:1.8.1.4]
USDA257_c55780  sucD; succinyl-CoA ligase [ADP-forming] subunit alpha [KO:K01902] [EC:6.2.1.5]
USDA257_c55790  sucC; succinyl-CoA ligase [ADP-forming] subunit beta [KO:K01903] [EC:6.2.1.5]
USDA257_c55850  sdhA; succinate dehydrogenase flavoprotein subunit SdhA [KO:K00239] [EC:1.3.5.1]
USDA257_c55840  sdhB; succinate dehydrogenase iron-sulfur subunit SdhB [KO:K00240] [EC:1.3.5.1]
USDA257_c55870  putative succinate dehydrogenase membrane anchor subunit [KO:K00241]
USDA257_c55860  putative succinate dehydrogenase hydrophobic membrane anchor protein [KO:K00242]
USDA257_c41330  fumC; fumarate hydratase class II [KO:K01679] [EC:4.2.1.2]
USDA257_c55800  mdh2; malate dehydrogenase Mdh [KO:K00024] [EC:1.1.1.37]
USDA257_c57930  pyc; pyruvate carboxylase Pyc [KO:K01958] [EC:6.4.1.1]
USDA257_c59080  pckA; phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
USDA257_c19150  pdhA1; pyruvate dehydrogenase E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
USDA257_c34810  pdhA2; pyruvate dehydrogenase E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
USDA257_c34820  pdhB; pyruvate dehydrogenase E1 component subunit beta [KO:K00162] [EC:1.2.4.1]
USDA257_c18880  pdhC1; dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex [KO:K00627] [EC:2.3.1.12]
USDA257_c17940  acoC1; dihydrolipoyllysine-residue acetyltransferase component of acetoin cleaving system [KO:K00627] [EC:2.3.1.12]
USDA257_c18040  acoC2; dihydrolipoyllysine-residue acetyltransferase component of acetoin cleaving system [KO:K00627] [EC:2.3.1.12]
USDA257_c18140  acoC3; dihydrolipoyllysine-residue acetyltransferase component of acetoin cleaving system [KO:K00627] [EC:2.3.1.12]
USDA257_c34830  pdhC2; dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex [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
sfd00010  Glycolysis / Gluconeogenesis
sfd00053  Ascorbate and aldarate metabolism
sfd00061  Fatty acid biosynthesis
sfd00071  Fatty acid degradation
sfd00190  Oxidative phosphorylation
sfd00220  Arginine biosynthesis
sfd00250  Alanine, aspartate and glutamate metabolism
sfd00280  Valine, leucine and isoleucine degradation
sfd00350  Tyrosine metabolism
sfd00470  D-Amino acid metabolism
sfd00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   

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