KEGG   PATHWAY: smd00020
Entry
smd00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Sinorhizobium medicae
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
smd00020  Citrate cycle (TCA cycle)
smd00020

Module
smd_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:smd00020]
smd_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:smd00020]
smd_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:smd00020]
smd_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:smd00020]
smd_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:smd00020]
Other DBs
GO: 0006099
Organism
Sinorhizobium medicae [GN:smd]
Gene
Smed_1144  citrate synthase I [KO:K01647] [EC:2.3.3.1]
Smed_0365  aconitate hydratase domain protein [KO:K01681] [EC:4.2.1.3]
Smed_3083  aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
Smed_1519  isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
Smed_2941  2-oxoglutarate dehydrogenase, E1 subunit [KO:K00164] [EC:1.2.4.2]
Smed_4111  Dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
Smed_2940  2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
Smed_2936  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Smed_1081  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Smed_2829  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Smed_2942  succinyl-CoA synthetase, alpha subunit [KO:K01902] [EC:6.2.1.5]
Smed_2943  succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
Smed_2957  succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
Smed_2956  succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
Smed_2959  Succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
Smed_2958  Succinate dehydrogenase hydrophobic membrane anchor [KO:K00242]
Smed_1576  fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
Smed_2944  malate dehydrogenase, NAD-dependent [KO:K00024] [EC:1.1.1.37]
Smed_3139  pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
Smed_3253  Phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
Smed_1076  dehydrogenase E1 component [KO:K00161] [EC:1.2.4.1]
Smed_1077  Transketolase central region [KO:K00162] [EC:1.2.4.1]
Smed_1078  pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase [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
smd00010  Glycolysis / Gluconeogenesis
smd00053  Ascorbate and aldarate metabolism
smd00061  Fatty acid biosynthesis
smd00071  Fatty acid degradation
smd00190  Oxidative phosphorylation
smd00220  Arginine biosynthesis
smd00250  Alanine, aspartate and glutamate metabolism
smd00280  Valine, leucine and isoleucine degradation
smd00350  Tyrosine metabolism
smd00470  D-Amino acid metabolism
smd00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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