KEGG   PATHWAY: xnm00020
Entry
xnm00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Xenorhabdus nematophila AN6/1
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
xnm00020  Citrate cycle (TCA cycle)
xnm00020

Module
xnm_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:xnm00020]
xnm_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:xnm00020]
xnm_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:xnm00020]
xnm_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:xnm00020]
xnm_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:xnm00020]
Other DBs
GO: 0006099
Organism
Xenorhabdus nematophila AN6/1 [GN:xnm]
Gene
XNC2_1365  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
XNC2_2322  acnA; aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
XNC2_1073  acnB; bifunctional: aconitate hydratase 2; 2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
XNC2_2601  icd; e14 prophage; isocitrate dehydrogenase, specific for NADP+ [KO:K00031] [EC:1.1.1.42]
XNC2_1370  sucA; 2-oxoglutarate decarboxylase, component of the 2-oxoglutarate dehydrogenase complex, thiamin-binding [KO:K00164] [EC:1.2.4.2]
XNC2_1371  sucB; dihydrolipoyltranssuccinate transferase, component of the 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
XNC2_1065  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]
XNC2_1373  sucD; succinyl-CoA synthetase, alpha subunit, NAD(P)-binding [KO:K01902] [EC:6.2.1.5]
XNC2_1372  sucC; succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
XNC2_1368  sdhA; succinate dehydrogenase, catalytic and NAD/flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
XNC2_1369  sdhB; succinate dehydrogenase, Fe-S protein [KO:K00240] [EC:1.3.5.1]
XNC2_1366  sdhC; succinate dehydrogenase, hydrophobic subunit, cytochrome b556 with SdhD [KO:K00241]
XNC2_1367  sdhD; succinate dehydrogenase, hydrophobic subunit, cytochrome b556 with SdhC [KO:K00242]
XNC2_0624  frdA; fumarate reductase, anaerobic, catalytic and NAD/flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
XNC2_0623  frdB; fumarate reductase, anaerobic, Fe-S subunit [KO:K00245] [EC:1.3.5.1]
XNC2_0622  frdC; fumarate reductase, anaerobic, membrane anchor polypeptide [KO:K00246]
XNC2_0621  frdD; fumarate reductase, anaerobic, membrane anchor polypeptide [KO:K00247]
XNC2_2232  fumC; fumarase C (fumarate hydratase Class II) [KO:K01679] [EC:4.2.1.2]
XNC2_0474  mdh; malate dehydrogenase, NAD(P)-binding [KO:K00024] [EC:1.1.1.37]
XNC2_4438  pck; phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
XNC2_1063  aceE; pyruvate dehydrogenase, decarboxylase subunit, thiamin-binding [KO:K00163] [EC:1.2.4.1]
XNC2_1064  aceF; pyruvate dehydrogenase, dihydrolipoyltransacetylase subunit [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
xnm00010  Glycolysis / Gluconeogenesis
xnm00053  Ascorbate and aldarate metabolism
xnm00061  Fatty acid biosynthesis
xnm00071  Fatty acid degradation
xnm00190  Oxidative phosphorylation
xnm00220  Arginine biosynthesis
xnm00250  Alanine, aspartate and glutamate metabolism
xnm00280  Valine, leucine and isoleucine degradation
xnm00350  Tyrosine metabolism
xnm00470  D-Amino acid metabolism
xnm00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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