KEGG   PATHWAY: pgv00020
Entry
pgv00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Polymorphum gilvum
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
pgv00020  Citrate cycle (TCA cycle)
pgv00020

Module
pgv_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:pgv00020]
pgv_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:pgv00020]
pgv_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:pgv00020]
pgv_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:pgv00020]
pgv_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:pgv00020]
Other DBs
GO: 0006099
Organism
Polymorphum gilvum [GN:pgv]
Gene
SL003B_2471  Citrate synthase [KO:K01647] [EC:2.3.3.1]
SL003B_2107  gltA; Citrate synthase, chromosomal [KO:K01647] [EC:2.3.3.1]
SL003B_0255  Aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
SL003B_1563  Isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
SL003B_1566  Isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
SL003B_0542  Probable 3-isopropylmalate dehydrogenase oxidoreductase protein [KO:K00030] [EC:1.1.1.41]
SL003B_4231  sucA; Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component [KO:K00164] [EC:1.2.4.2]
SL003B_4230  sucB; 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
SL003B_4229  Dihydrolipoamide dehydrogenase protein [KO:K00382] [EC:1.8.1.4]
SL003B_2318  Dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
SL003B_4232  Succinyl-CoA ligase [ADP-forming] subunit alpha [KO:K01902] [EC:6.2.1.5]
SL003B_4233  sucC; ATP-dependent carboxylate-amine ligase-like, ATP-grasp:Succinyl-CoA synthetase, beta subunit:ATP-citrate lyase/succinyl-CoA l [KO:K01903] [EC:6.2.1.5]
SL003B_0185  sdhA; Succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
SL003B_0184  sdhB; Succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
SL003B_0187  Succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
SL003B_0186  Succinate dehydrogenase, hydrophobic membrane anchor protein, putative [KO:K00242]
SL003B_2806  fumB; Fumarate hydratase I, N-terminal region or alpha subunit domain protein [KO:K01676] [EC:4.2.1.2]
SL003B_0982  putative Fumarate hydratase [KO:K01679] [EC:4.2.1.2]
SL003B_4234  mdh; Malate dehydrogenase 1 [KO:K00024] [EC:1.1.1.37]
SL003B_0402  Probable pyruvate carboxylase protein [KO:K01958] [EC:6.4.1.1]
SL003B_4208  Phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
SL003B_4089  Pyruvate dehydrogenase (Acetyl-transferring) [KO:K00163] [EC:1.2.4.1]
SL003B_2321  Pyruvate dehydrogenase (Acetyl-transferring) E1 component, alpha subunit [KO:K00161] [EC:1.2.4.1]
SL003B_2320  Biotin/lipoyl attachment:2-oxo acid dehydrogenase, acyltransferase component, lipoyl-binding:Transketolase, central region:Tr [KO:K00162] [EC:1.2.4.1]
SL003B_2319  pdhB; Dihydrolipoamide acetyltransferase protein [KO:K00627] [EC:2.3.1.12]
SL003B_1093  Probable pyruvate dehydrogenase, E2 component, dihydrolipoamide acetyltransferase [KO:K00627] [EC:2.3.1.12]
SL003B_1038  2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase [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
pgv00010  Glycolysis / Gluconeogenesis
pgv00053  Ascorbate and aldarate metabolism
pgv00061  Fatty acid biosynthesis
pgv00071  Fatty acid degradation
pgv00190  Oxidative phosphorylation
pgv00220  Arginine biosynthesis
pgv00250  Alanine, aspartate and glutamate metabolism
pgv00280  Valine, leucine and isoleucine degradation
pgv00350  Tyrosine metabolism
pgv00470  D-Amino acid metabolism
pgv00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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