KEGG   PATHWAY: ndn00020
Entry
ndn00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Neisseria dentiae
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
ndn00020  Citrate cycle (TCA cycle)
ndn00020

Module
ndn_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:ndn00020]
ndn_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:ndn00020]
ndn_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:ndn00020]
ndn_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:ndn00020]
Other DBs
GO: 0006099
Organism
Neisseria dentiae [GN:ndn]
Gene
H3L92_05820  gltA; citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
H3L92_02350  prpC; 2-methylcitrate synthase [KO:K01659] [EC:2.3.3.5]
H3L92_10320  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
H3L92_04210  icd; NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
H3L92_05815  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
H3L92_05810  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
H3L92_07505  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
H3L92_02095  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
H3L92_05800  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
H3L92_06810  acetyl-CoA hydrolase/transferase family protein [KO:K18118] [EC:2.8.3.18]
H3L92_05835  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
H3L92_05830  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
H3L92_05845  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
H3L92_05840  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
H3L92_04450  frdA; fumarate reductase (quinol) flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
H3L92_04455  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
H3L92_04460  fumarate reductase subunit C [KO:K00246]
H3L92_04465  fumarate reductase subunit D [KO:K00247]
H3L92_09240  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
H3L92_09245  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
H3L92_05850  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
H3L92_07515  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
H3L92_07510  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
ndn00010  Glycolysis / Gluconeogenesis
ndn00061  Fatty acid biosynthesis
ndn00071  Fatty acid degradation
ndn00190  Oxidative phosphorylation
ndn00220  Arginine biosynthesis
ndn00250  Alanine, aspartate and glutamate metabolism
ndn00280  Valine, leucine and isoleucine degradation
ndn00350  Tyrosine metabolism
ndn00470  D-Amino acid metabolism
ndn00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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