KEGG   PATHWAY: ssem00020
Entry
ssem00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Shewanella sedimentimangrovi
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
ssem00020  Citrate cycle (TCA cycle)
ssem00020

Module
ssem_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:ssem00020]
ssem_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:ssem00020]
ssem_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:ssem00020]
ssem_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:ssem00020]
ssem_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:ssem00020]
Other DBs
GO: 0006099
Organism
Shewanella sedimentimangrovi [GN:ssem]
Gene
JYB85_07155  citrate synthase [KO:K01647] [EC:2.3.3.1]
JYB85_16820  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
JYB85_10205  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
JYB85_05280  isocitrate dehydrogenase [KO:K00030] [EC:1.1.1.41]
JYB85_07180  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
JYB85_07185  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
JYB85_16845  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
JYB85_15830  2-oxoacid:acceptor oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
JYB85_15825  2-oxoacid:ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
JYB85_07195  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
JYB85_07190  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
JYB85_07170  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
JYB85_07175  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
JYB85_07160  sdhC; succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
JYB85_07165  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
JYB85_01965  fumarate reductase flavoprotein subunit [KO:K00233] [EC:1.3.5.1 7.1.1.12]
JYB85_01970  fumarate reductase iron-sulfur subunit [KO:K25995] [EC:1.3.5.1 7.1.1.12]
JYB85_01960  fumarate reductase cytochrome b subunit [KO:K25996]
JYB85_09450  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
JYB85_03895  class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
JYB85_15025  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
JYB85_00790  phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
JYB85_16855  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
JYB85_16850  aceF; pyruvate dehydrogenase complex 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
ssem00010  Glycolysis / Gluconeogenesis
ssem00053  Ascorbate and aldarate metabolism
ssem00061  Fatty acid biosynthesis
ssem00071  Fatty acid degradation
ssem00190  Oxidative phosphorylation
ssem00220  Arginine biosynthesis
ssem00250  Alanine, aspartate and glutamate metabolism
ssem00280  Valine, leucine and isoleucine degradation
ssem00350  Tyrosine metabolism
ssem00470  D-Amino acid metabolism
ssem00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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