KEGG   PATHWAY: syi00020
Entry
syi00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Sediminicola sp. YIK13
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
syi00020  Citrate cycle (TCA cycle)
syi00020

Module
syi_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:syi00020]
syi_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:syi00020]
syi_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:syi00020]
syi_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:syi00020]
syi_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:syi00020]
Other DBs
GO: 0006099
Organism
Sediminicola sp. YIK13 [GN:syi]
Gene
SB49_08645  gltA; type II citrate synthase [KO:K01647] [EC:2.3.3.1]
SB49_01425  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
SB49_05510  isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
SB49_14465  2-oxoglutarate dehydrogenase [KO:K00164] [EC:1.2.4.2]
SB49_14470  2-oxoglutarate dehydrogenase [KO:K00658] [EC:2.3.1.61]
SB49_01185  diapophytoene dehydrogenase [KO:K00658] [EC:2.3.1.61]
SB49_01850  hypothetical protein [KO:K00382] [EC:1.8.1.4]
SB49_03345  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
SB49_04485  succinate--CoA ligase [KO:K01902] [EC:6.2.1.5]
SB49_07135  sucC; succinyl-CoA synthetase subunit beta [KO:K01903] [EC:6.2.1.5]
SB49_11630  sdhA; succinate dehydrogenase [KO:K00239] [EC:1.3.5.1]
SB49_11635  fumarate reductase [KO:K00240] [EC:1.3.5.1]
SB49_11625  succinate dehydrogenase [KO:K00241]
SB49_04945  fumC; fumarate hydratase [KO:K01679] [EC:4.2.1.2]
SB49_07815  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
SB49_09475  biotin carboxylase [KO:K01959] [EC:6.4.1.1]
SB49_13770  phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
SB49_09035  pyruvate dehydrogenase [KO:K00161] [EC:1.2.4.1]
SB49_15150  pyruvate dehydrogenase [KO:K00162] [EC:1.2.4.1]
SB49_09030  pyruvate dehydrogenase [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
syi00010  Glycolysis / Gluconeogenesis
syi00053  Ascorbate and aldarate metabolism
syi00061  Fatty acid biosynthesis
syi00071  Fatty acid degradation
syi00190  Oxidative phosphorylation
syi00220  Arginine biosynthesis
syi00250  Alanine, aspartate and glutamate metabolism
syi00280  Valine, leucine and isoleucine degradation
syi00350  Tyrosine metabolism
syi00470  D-Amino acid metabolism
syi00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

DBGET integrated database retrieval system