KEGG   PATHWAY: nik00020
Entry
nik00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Nitrincola iocasae
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
nik00020  Citrate cycle (TCA cycle)
nik00020

Module
nik_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:nik00020]
nik_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:nik00020]
nik_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:nik00020]
nik_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:nik00020]
nik_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:nik00020]
Other DBs
GO: 0006099
Organism
Nitrincola iocasae [GN:nik]
Gene
F5I99_06640  gltA; citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
F5I99_09185  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
F5I99_10895  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
F5I99_10050  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
F5I99_06665  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
F5I99_06670  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
F5I99_06675  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
F5I99_07805  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
F5I99_06685  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
F5I99_06680  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
F5I99_06655  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
F5I99_06660  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
F5I99_06645  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
F5I99_06650  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
F5I99_13610  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
F5I99_14770  class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
F5I99_14370  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
F5I99_11400  mqo; malate dehydrogenase (quinone) [KO:K00116] [EC:1.1.5.4]
F5I99_00945  phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
F5I99_03900  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
F5I99_03905  aceF; dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
F5I99_05330  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
nik00010  Glycolysis / Gluconeogenesis
nik00053  Ascorbate and aldarate metabolism
nik00061  Fatty acid biosynthesis
nik00071  Fatty acid degradation
nik00190  Oxidative phosphorylation
nik00220  Arginine biosynthesis
nik00250  Alanine, aspartate and glutamate metabolism
nik00280  Valine, leucine and isoleucine degradation
nik00350  Tyrosine metabolism
nik00470  D-Amino acid metabolism
nik00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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