KEGG   PATHWAY: pnt00020
Entry
pnt00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Pseudomonas 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
pnt00020  Citrate cycle (TCA cycle)
pnt00020

Module
pnt_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:pnt00020]
pnt_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:pnt00020]
pnt_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:pnt00020]
pnt_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:pnt00020]
pnt_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:pnt00020]
Other DBs
GO: 0006099
Organism
Pseudomonas nitroreducens [GN:pnt]
Gene
G5B91_13485  gltA; citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
G5B91_20295  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
G5B91_11965  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
G5B91_18275  icd; NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
G5B91_18280  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
G5B91_13510  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
G5B91_13515  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
G5B91_12815  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
G5B91_13520  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
G5B91_16150  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
G5B91_13530  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
G5B91_34345  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
G5B91_13525  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
G5B91_00540  acetyl-CoA hydrolase/transferase family protein [KO:K18118] [EC:2.8.3.18]
G5B91_13500  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
G5B91_13505  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
G5B91_13490  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
G5B91_13495  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
G5B91_26870  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
G5B91_05800  class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
G5B91_09920  class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
G5B91_15205  mqo; malate dehydrogenase (quinone) [KO:K00116] [EC:1.1.5.4]
G5B91_26715  mqo; malate dehydrogenase (quinone) [KO:K00116] [EC:1.1.5.4]
G5B91_31935  acetyl-CoA carboxylase biotin carboxylase subunit [KO:K01959] [EC:6.4.1.1]
G5B91_31930  oadA; sodium-extruding oxaloacetate decarboxylase subunit alpha [KO:K01960] [EC:6.4.1.1]
G5B91_30645  phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
G5B91_20180  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
G5B91_29765  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
G5B91_20185  aceF; dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
G5B91_29770  aceF; 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
pnt00010  Glycolysis / Gluconeogenesis
pnt00053  Ascorbate and aldarate metabolism
pnt00061  Fatty acid biosynthesis
pnt00071  Fatty acid degradation
pnt00190  Oxidative phosphorylation
pnt00220  Arginine biosynthesis
pnt00250  Alanine, aspartate and glutamate metabolism
pnt00280  Valine, leucine and isoleucine degradation
pnt00350  Tyrosine metabolism
pnt00470  D-Amino acid metabolism
pnt00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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