KEGG   PATHWAY: dpy00020
Entry
dpy00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Diaphorobacter nitroreducens
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
dpy00020  Citrate cycle (TCA cycle)
dpy00020

Module
dpy_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:dpy00020]
dpy_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:dpy00020]
dpy_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dpy00020]
dpy_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:dpy00020]
dpy_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dpy00020]
Other DBs
GO: 0006099
Organism
Diaphorobacter nitroreducens [GN:dpy]
Gene
BA022_02245  citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
BA022_02830  2-methylcitrate synthase [KO:K01659] [EC:2.3.3.5]
BA022_09475  acnA; aconitate hydratase [KO:K27802] [EC:4.2.1.3 4.2.1.99]
BA022_02300  bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
BA022_06235  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
BA022_06250  isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
BA022_04035  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
BA022_04040  dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
BA022_04045  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
BA022_05795  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
BA022_05955  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
BA022_15430  succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
BA022_15425  succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
BA022_14590  acetyl-CoA hydrolase [KO:K18118] [EC:2.8.3.18]
BA022_02260  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
BA022_02255  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
BA022_02270  succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
BA022_02265  succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
BA022_09925  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
BA022_09920  fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
BA022_02280  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
BA022_14445  phosphoenolpyruvate carboxykinase [KO:K01596] [EC:4.1.1.32]
BA022_02735  pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
BA022_05805  pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
BA022_05800  dihydrolipoyllysine-residue 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
dpy00010  Glycolysis / Gluconeogenesis
dpy00053  Ascorbate and aldarate metabolism
dpy00061  Fatty acid biosynthesis
dpy00062  Fatty acid elongation
dpy00071  Fatty acid degradation
dpy00190  Oxidative phosphorylation
dpy00220  Arginine biosynthesis
dpy00250  Alanine, aspartate and glutamate metabolism
dpy00280  Valine, leucine and isoleucine degradation
dpy00350  Tyrosine metabolism
dpy00470  D-Amino acid metabolism
dpy00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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