KEGG   PATHWAY: sbk00020
Entry
sbk00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Shewanella benthica
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
sbk00020  Citrate cycle (TCA cycle)
sbk00020

Module
sbk_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:sbk00020]
sbk_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:sbk00020]
sbk_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:sbk00020]
sbk_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:sbk00020]
sbk_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:sbk00020]
Other DBs
GO: 0006099
Organism
Shewanella benthica [GN:sbk]
Gene
SHEWBE_3179  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
SHEWBE_0920  acnB; aconitate hydratase 2 [KO:K01682] [EC:4.2.1.3 4.2.1.99]
SHEWBE_2370  idh; isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
SHEWBE_1843  leuB; 3-isopropylmalate dehydrogenase [KO:K00030] [EC:1.1.1.41]
SHEWBE_3172  sucA; 2-oxoglutarate decarboxylase, thiamin-requiring [KO:K00164] [EC:1.2.4.2]
SHEWBE_3171  sucB; dihydrolipoamide succinyltransferase, E2 component of 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
SHEWBE_0912  lpd; Dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
SHEWBE_3169  sucD; succinyl-CoA synthetase alpha chain [KO:K01902] [EC:6.2.1.5]
SHEWBE_3170  sucC; succinyl-CoA synthetase beta chain [KO:K01903] [EC:6.2.1.5]
SHEWBE_3174  sdhA; succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
SHEWBE_3173  sdhB; succinate dehydrogenase, iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
SHEWBE_3176  sdhC; succinate dehydrogenase, membrane subunit, binds cytochrome b556 [KO:K00241]
SHEWBE_3175  sdhD; succinate dehydrogenase, membrane subunit, binds cytochrome b556 [KO:K00242]
SHEWBE_4504  frdA; Fumarate reductase flavoprotein subunit [KO:K00233] [EC:1.3.5.1 7.1.1.12]
SHEWBE_4503  frdB; Fumarate reductase iron-sulfur subunit [KO:K25995] [EC:1.3.5.1 7.1.1.12]
SHEWBE_4506  frdC; Fumarate reductase cytochrome b subunit [KO:K25996]
SHEWBE_4505  frdC; Fumarate reductase cytochrome b subunit [KO:K25996]
SHEWBE_1282  fccA; Fumarate reductase flavoprotein subunit [KO:K26318] [EC:1.3.2.4]
SHEWBE_2839  Fumarate hydratase class I [KO:K01676] [EC:4.2.1.2]
SHEWBE_1055  fumC; Fumarate hydratase class II 1 [KO:K01679] [EC:4.2.1.2]
SHEWBE_4231  mdh; malate dehydrogenase, NAD(P)-binding [KO:K00024] [EC:1.1.1.37]
SHEWBE_0381  pck; phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
SHEWBE_0910  aceE; pyruvate dehydrogenase, decarboxylase component E1, thiamin-binding [KO:K00163] [EC:1.2.4.1]
SHEWBE_0911  aceF; pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 [KO:K00627] [EC:2.3.1.12]
SHEWBE_3745  nifJ; Pyruvate-flavodoxin oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
SHEWBE_4177  putative Pyruvate dehydrogenase (NADP(+)) [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
sbk00010  Glycolysis / Gluconeogenesis
sbk00053  Ascorbate and aldarate metabolism
sbk00061  Fatty acid biosynthesis
sbk00071  Fatty acid degradation
sbk00190  Oxidative phosphorylation
sbk00220  Arginine biosynthesis
sbk00250  Alanine, aspartate and glutamate metabolism
sbk00280  Valine, leucine and isoleucine degradation
sbk00350  Tyrosine metabolism
sbk00470  D-Amino acid metabolism
sbk00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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