KEGG   PATHWAY: agt00020
Entry
agt00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Agrobacterium sp. 33MFTa1.1
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
agt00020  Citrate cycle (TCA cycle)
agt00020

Module
agt_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:agt00020]
agt_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:agt00020]
agt_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:agt00020]
agt_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:agt00020]
Other DBs
GO: 0006099
Organism
Agrobacterium sp. 33MFTa1.1 [GN:agt]
Gene
EYD00_05175  gltA; citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
EYD00_11510  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
EYD00_14090  bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
EYD00_07665  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
EYD00_11260  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
EYD00_11255  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
EYD00_05260  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
EYD00_11240  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
EYD00_11265  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
EYD00_11270  ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
EYD00_00355  acetyl-CoA hydrolase/transferase family protein [KO:K18118] [EC:2.8.3.18]
EYD00_11295  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
EYD00_11290  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
EYD00_11305  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
EYD00_11300  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
EYD00_06160  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
EYD00_11275  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
EYD00_02310  mqo; malate dehydrogenase (quinone) [KO:K00116] [EC:1.1.5.4]
EYD00_11725  pyc; pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
EYD00_12435  phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
EYD00_05240  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
EYD00_05245  pyruvate dehydrogenase complex E1 component subunit beta [KO:K00162] [EC:1.2.4.1]
EYD00_05250  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
agt00010  Glycolysis / Gluconeogenesis
agt00053  Ascorbate and aldarate metabolism
agt00061  Fatty acid biosynthesis
agt00071  Fatty acid degradation
agt00190  Oxidative phosphorylation
agt00220  Arginine biosynthesis
agt00250  Alanine, aspartate and glutamate metabolism
agt00280  Valine, leucine and isoleucine degradation
agt00350  Tyrosine metabolism
agt00470  D-Amino acid metabolism
agt00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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