KEGG   PATHWAY: spyg00020
Entry
spyg00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Sphingobium sp. YG1
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
spyg00020  Citrate cycle (TCA cycle)
spyg00020

Module
spyg_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:spyg00020]
spyg_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:spyg00020]
spyg_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:spyg00020]
spyg_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:spyg00020]
spyg_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:spyg00020]
Other DBs
GO: 0006099
Organism
Sphingobium sp. YG1 [GN:spyg]
Gene
YGS_C1P1206  citrate synthase [KO:K01647] [EC:2.3.3.1]
YGS_C1P1486  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
YGS_C1P1487  aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
YGS_C1P1596  isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
YGS_C1P0319  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
YGS_C1P0320  dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
YGS_C1P0942  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
YGS_C1P0322  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
YGS_C1P0318  succinyl-CoA synthetase alpha subunit [KO:K01902] [EC:6.2.1.5]
YGS_C1P1617  succinyl-CoA synthetase beta subunit [KO:K01903] [EC:6.2.1.5]
YGS_C1P2197  succinyl-CoA:acetate CoA-transferase [KO:K18118] [EC:2.8.3.18]
YGS_C1P1870  succinate dehydrogenase/fumarate reductase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
YGS_C1P0313  succinate dehydrogenase/fumarate reductase, iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
YGS_C1P1872  succinate dehydrogenase/fumarate reductase, cytochrome b subunit [KO:K00241]
YGS_C1P1871  succinate dehydrogenase/fumarate reductase, membrane anchor subunit [KO:K00242]
YGS_C1P2414  fumarate hydratase, class I [KO:K01676] [EC:4.2.1.2]
YGS_C1P3021  fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
YGS_C1P0316  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
YGS_C1P0854  malate dehydrogenase (quinone) [KO:K00116] [EC:1.1.5.4]
YGS_C1P0049  phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
YGS_C1P0586  pyruvate dehydrogenase E1 component alpha subunit [KO:K00161] [EC:1.2.4.1]
YGS_C1P0587  pyruvate dehydrogenase E1 component beta subunit [KO:K00162] [EC:1.2.4.1]
YGS_C1P0940  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
spyg00010  Glycolysis / Gluconeogenesis
spyg00053  Ascorbate and aldarate metabolism
spyg00061  Fatty acid biosynthesis
spyg00062  Fatty acid elongation
spyg00071  Fatty acid degradation
spyg00190  Oxidative phosphorylation
spyg00220  Arginine biosynthesis
spyg00250  Alanine, aspartate and glutamate metabolism
spyg00280  Valine, leucine and isoleucine degradation
spyg00350  Tyrosine metabolism
spyg00470  D-Amino acid metabolism
spyg00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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