KEGG   PATHWAY: xbo00020
Entry
xbo00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Xenorhabdus bovienii SS-2004
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
xbo00020  Citrate cycle (TCA cycle)
xbo00020

Module
xbo_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:xbo00020]
xbo_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:xbo00020]
xbo_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:xbo00020]
xbo_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:xbo00020]
xbo_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:xbo00020]
xbo_M00982  Methylcitrate cycle [PATH:xbo00020]
Other DBs
GO: 0006099
Organism
Xenorhabdus bovienii SS-2004 [GN:xbo]
Gene
XBJ1_0071  pck; phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
XBJ1_0349  mdh; malate dehydrogenase, NAD(P)-binding [KO:K00024] [EC:1.1.1.37]
XBJ1_0534  frdD; fumarate reductase, anaerobic, membrane anchor polypeptide [KO:K00247]
XBJ1_0535  frdC; fumarate reductase, anaerobic, membrane anchor polypeptide [KO:K00246]
XBJ1_0536  frdB; fumarate reductase, anaerobic, Fe-S subunit [KO:K00245] [EC:1.3.5.1]
XBJ1_0537  frdA; fumarate reductase, anaerobic, catalytic and NAD/flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
XBJ1_1054  sucD; succinyl-CoA synthetase, alpha subunit, NAD(P)-binding [KO:K01902] [EC:6.2.1.5]
XBJ1_1055  sucC; succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
XBJ1_1056  sucB; dihydrolipoyltranssuccinate transferase, component of the 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
XBJ1_1057  sucA; 2-oxoglutarate decarboxylase, component of the 2-oxoglutarate dehydrogenase complex, thiamin-binding [KO:K00164] [EC:1.2.4.2]
XBJ1_1058  sdhB; succinate dehydrogenase, Fe-S protein [KO:K00240] [EC:1.3.5.1]
XBJ1_1059  sdhA; succinate dehydrogenase, catalytic and NAD/flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
XBJ1_1060  sdhD; succinate dehydrogenase, hydrophobic subunit, cytochrome b556 with SdhC [KO:K00242]
XBJ1_1061  sdhC; succinate dehydrogenase, hydrophobic subunit, cytochrome b556 with SdhD [KO:K00241]
XBJ1_1062  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
XBJ1_1345  prpC; methylcitrate synthase (citrate synthase 2) [KO:K01659] [EC:2.3.3.5]
XBJ1_2292  acnA; aconitate hydratase 1 [KO:K27802]
XBJ1_2316  fumC; fumarase C (fumarate hydratase Class II) [KO:K01679] [EC:4.2.1.2]
XBJ1_2828  icd; e14 prophage; isocitrate dehydrogenase, specific for NADP+ [KO:K00031] [EC:1.1.1.42]
XBJ1_3452  acnB; bifunctional: aconitate hydratase 2; 2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
XBJ1_3453  lpd; dihydrolipoamide dehydrogenase, FAD/NAD(P)-binding, component of the 2-oxoglutarate dehydrogenase and the pyruvate dehydrogenase complexes [KO:K00382] [EC:1.8.1.4]
XBJ1_3454  aceF; pyruvate dehydrogenase, dihydrolipoyltransacetylase subunit [KO:K00627] [EC:2.3.1.12]
XBJ1_3455  aceE; pyruvate dehydrogenase, decarboxylase subunit, thiamin-binding [KO:K00163] [EC:1.2.4.1]
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
xbo00010  Glycolysis / Gluconeogenesis
xbo00053  Ascorbate and aldarate metabolism
xbo00061  Fatty acid biosynthesis
xbo00071  Fatty acid degradation
xbo00190  Oxidative phosphorylation
xbo00220  Arginine biosynthesis
xbo00250  Alanine, aspartate and glutamate metabolism
xbo00280  Valine, leucine and isoleucine degradation
xbo00350  Tyrosine metabolism
xbo00470  D-Amino acid metabolism
xbo00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   

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