KEGG   PATHWAY: syb00020
Entry
syb00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Sphingobium sp. YBL2
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
syb00020  Citrate cycle (TCA cycle)
syb00020

Module
syb_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:syb00020]
syb_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:syb00020]
syb_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:syb00020]
syb_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:syb00020]
syb_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:syb00020]
Other DBs
GO: 0006099
Organism
Sphingobium sp. YBL2 [GN:syb]
Gene
TZ53_14080  citrate synthase [KO:K01647] [EC:2.3.3.1]
TZ53_15170  gltA; type II citrate synthase [KO:K01647] [EC:2.3.3.1]
TZ53_20350  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
TZ53_14925  isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
TZ53_14860  sucA; 2-oxoglutarate dehydrogenase [KO:K00164] [EC:1.2.4.2]
TZ53_14865  dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
TZ53_14875  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
TZ53_19885  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
TZ53_14855  succinate--CoA ligase [KO:K01902] [EC:6.2.1.5]
TZ53_21280  sucC; succinyl-CoA synthetase subunit beta [KO:K01903] [EC:6.2.1.5]
TZ53_10880  acetyl-CoA hydrolase [KO:K18118] [EC:2.8.3.18]
TZ53_22115  fumarate reductase [KO:K00239] [EC:1.3.5.1]
TZ53_14835  succinate dehydrogenase [KO:K00240] [EC:1.3.5.1]
TZ53_22125  succinate dehydrogenase [KO:K00241]
TZ53_22120  succinate dehydrogenase [KO:K00242]
TZ53_02995  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
TZ53_15495  fumarate hydratase [KO:K01679] [EC:4.2.1.2]
TZ53_14850  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
TZ53_23990  phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
TZ53_21910  phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
TZ53_00425  transketolase [KO:K00163] [EC:1.2.4.1]
TZ53_16800  pyruvate dehydrogenase [KO:K00161] [EC:1.2.4.1]
TZ53_16805  pyruvate dehydrogenase [KO:K00162] [EC:1.2.4.1]
TZ53_00420  branched-chain alpha-keto acid dehydrogenase subunit E2 [KO:K00627] [EC:2.3.1.12]
TZ53_19895  branched-chain alpha-keto acid dehydrogenase subunit E2 [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
syb00010  Glycolysis / Gluconeogenesis
syb00053  Ascorbate and aldarate metabolism
syb00061  Fatty acid biosynthesis
syb00071  Fatty acid degradation
syb00190  Oxidative phosphorylation
syb00220  Arginine biosynthesis
syb00250  Alanine, aspartate and glutamate metabolism
syb00280  Valine, leucine and isoleucine degradation
syb00350  Tyrosine metabolism
syb00470  D-Amino acid metabolism
syb00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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