KEGG   PATHWAY: smi00020
Entry
smi00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Sinorhizobium meliloti Rm41
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
smi00020  Citrate cycle (TCA cycle)
smi00020

Module
smi_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:smi00020]
smi_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:smi00020]
smi_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:smi00020]
smi_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:smi00020]
smi_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:smi00020]
Other DBs
GO: 0006099
Organism
Sinorhizobium meliloti Rm41 [GN:smi]
Gene
BN406_01240  gltA; type II citrate synthase [KO:K01647] [EC:2.3.3.1]
BN406_03030  acnA; Aconitate hydratase [KO:K01681] [EC:4.2.1.3]
BN406_01525  icd; Isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
BN406_02909  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
BN406_02908  sucB; Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
BN406_05114  dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
BN406_02792  lpdV; Dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
BN406_02904  LPD2; Dihydrolipoyl dehydrogenase 2, mitochondrial [KO:K00382] [EC:1.8.1.4]
BN406_01183  lpdA; Dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
BN406_06654  lpdA; Dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
BN406_02910  sucD; Succinyl-CoA ligase [ADP-forming] subunit alpha [KO:K01902] [EC:6.2.1.5]
BN406_02911  sucC; succinyl-CoA synthetase subunit beta [KO:K01903] [EC:6.2.1.5]
BN406_02926  sdhA; Succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
BN406_02925  sdhB; Succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
BN406_02928  sdhC; succinate dehydrogenase cytochrome B-556 subunit transmembrane protein [KO:K00241]
BN406_02927  sdhD; succinate dehydrogenase membrane anchor subunit protein [KO:K00242]
BN406_01593  fumC; Fumarate hydratase class II [KO:K01679] [EC:4.2.1.2]
BN406_02912  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
BN406_03077  pyc; Pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
BN406_03179  pckA; phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
BN406_01178  pdhA; Pyruvate dehydrogenase E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
BN406_01179  pdhB; Pyruvate dehydrogenase E1 component subunit beta [KO:K00162] [EC:1.2.4.1]
BN406_01180  pdhC; Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex [KO:K00627] [EC:2.3.1.12]
BN406_06766  acoC1; Dihydrolipoyllysine-residue acetyltransferase component of acetoin cleaving system [KO:K00627] [EC:2.3.1.12]
BN406_06774  acoC3; Dihydrolipoyllysine-residue acetyltransferase component of acetoin cleaving system [KO:K00627] [EC:2.3.1.12]
BN406_06653  pdhC; 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
smi00010  Glycolysis / Gluconeogenesis
smi00053  Ascorbate and aldarate metabolism
smi00061  Fatty acid biosynthesis
smi00071  Fatty acid degradation
smi00190  Oxidative phosphorylation
smi00220  Arginine biosynthesis
smi00250  Alanine, aspartate and glutamate metabolism
smi00280  Valine, leucine and isoleucine degradation
smi00350  Tyrosine metabolism
smi00470  D-Amino acid metabolism
smi00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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