KEGG   PATHWAY: sil00020
Entry
sil00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Ruegeria pomeroyi
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
sil00020  Citrate cycle (TCA cycle)
sil00020

Module
sil_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:sil00020]
sil_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:sil00020]
sil_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:sil00020]
sil_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:sil00020]
sil_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:sil00020]
Other DBs
GO: 0006099
Organism
Ruegeria pomeroyi [GN:sil]
Gene
SPO2157  gltA; citrate synthase I [KO:K01647] [EC:2.3.3.1]
SPO2312  acnA; aconitate hydratase 1 [KO:K27802] [EC:4.2.1.3 4.2.1.99]
SPOA0315  icd; isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
SPO0344  sucA; 2-oxoglutarate dehydrogenase, E1 component [KO:K00164] [EC:1.2.4.2]
SPO0343  sucB; 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
SPO2222  pyruvate dehydrogenase complex, E3 component, lipoamide dehydrogenase, putative [KO:K00382] [EC:1.8.1.4]
SPO0340  lpdA; 2-oxoglutarate dehydrogenase, E3 component, dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
SPO0346  sucD; succinyl-CoA synthase, alpha subunit [KO:K01902] [EC:6.2.1.5]
SPO0347  succinyl-CoA synthase, beta subunit [KO:K01903] [EC:6.2.1.5]
SPO0360  sdhA; succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
SPO0361  sdhB; succinate dehydrogenase, iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
SPO0358  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
SPO0359  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
SPO1498  fumarate hydratase, class I, putative [KO:K01676] [EC:4.2.1.2]
SPO1905  fumC; fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
SPO0349  mdh; malate dehydrogenase, NAD-dependent [KO:K00024] [EC:1.1.1.37]
SPO1171  pyc; pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
SPO0709  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
SPOA0319  transketolase, putative [KO:K00163] [EC:1.2.4.1]
SPO2240  pdhA; pyruvate dehydrogenase complex, E1 component, alpha subunit [KO:K00161] [EC:1.2.4.1]
SPO2241  pdhB; pyruvate dehydrogenase complex, E1 component, beta subunit [KO:K00162] [EC:1.2.4.1]
SPO3790  acoC; acetoin dehydrogenase complex, E2 component, dihydrolipoamide acetyltransferase [KO:K00627] [EC:2.3.1.12]
SPO2242  pdhC; pyruvate dehydrogenase complex, E2 component, dihydrolipoamide 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
sil00010  Glycolysis / Gluconeogenesis
sil00053  Ascorbate and aldarate metabolism
sil00061  Fatty acid biosynthesis
sil00071  Fatty acid degradation
sil00190  Oxidative phosphorylation
sil00220  Arginine biosynthesis
sil00250  Alanine, aspartate and glutamate metabolism
sil00280  Valine, leucine and isoleucine degradation
sil00350  Tyrosine metabolism
sil00470  D-Amino acid metabolism
sil00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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