KEGG   PATHWAY: dey00020
Entry
dey00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Dechloromonas sp. HYN0024
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
dey00020  Citrate cycle (TCA cycle)
dey00020

Module
dey_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:dey00020]
dey_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:dey00020]
dey_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dey00020]
dey_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:dey00020]
dey_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dey00020]
Other DBs
GO: 0006099
Organism
Dechloromonas sp. HYN0024 [GN:dey]
Gene
HYN24_05690  gltA; citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
HYN24_09595  gltA; citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
HYN24_09745  bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
HYN24_04420  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
HYN24_09590  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
HYN24_09585  2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
HYN24_01945  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
HYN24_09580  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
HYN24_12245  succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
HYN24_12250  ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
HYN24_09610  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
HYN24_09605  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
HYN24_09620  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
HYN24_09615  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
HYN24_09280  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
HYN24_10035  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
HYN24_09630  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
HYN24_03130  phosphoenolpyruvate carboxykinase (GTP) [KO:K01596] [EC:4.1.1.32]
HYN24_01955  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
HYN24_01950  aceF; dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
HYN24_06180  nifJ; pyruvate:ferredoxin (flavodoxin) oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
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
dey00010  Glycolysis / Gluconeogenesis
dey00053  Ascorbate and aldarate metabolism
dey00061  Fatty acid biosynthesis
dey00071  Fatty acid degradation
dey00190  Oxidative phosphorylation
dey00220  Arginine biosynthesis
dey00250  Alanine, aspartate and glutamate metabolism
dey00280  Valine, leucine and isoleucine degradation
dey00350  Tyrosine metabolism
dey00470  D-Amino acid metabolism
dey00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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