KEGG   PATHWAY: dpub00020
Entry
dpub00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Dryobates pubescens (Downy woodpecker)
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
dpub00020  Citrate cycle (TCA cycle)
dpub00020

Module
dpub_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:dpub00020]
dpub_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dpub00020]
Other DBs
GO: 0006099
Organism
Dryobates pubescens (Downy woodpecker) [GN:dpub]
Gene
104309581  ACLY; ATP-citrate synthase [KO:K01648] [EC:2.3.3.8]
104300059  ACO1; cytoplasmic aconitate hydratase [KO:K01681] [EC:4.2.1.3]
104302081  ACO2; aconitate hydratase, mitochondrial [KO:K01681] [EC:4.2.1.3]
104297375  IDH2; isocitrate dehydrogenase [NADP], mitochondrial [KO:K00031] [EC:1.1.1.42]
104298934  IDH1; isocitrate dehydrogenase [NADP] cytoplasmic [KO:K00031] [EC:1.1.1.42]
104297642  IDH3A; isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial [KO:K00030] [EC:1.1.1.41]
104308817  IDH3B; isocitrate dehydrogenase [NAD] subunit beta, mitochondrial [KO:K00030] [EC:1.1.1.41]
104305933  OGDH; 2-oxoglutarate dehydrogenase, mitochondrial isoform X1 [KO:K00164] [EC:1.2.4.2]
104301342  OGDHL; 2-oxoglutarate dehydrogenase-like, mitochondrial isoform X1 [KO:K00164] [EC:1.2.4.2]
104308232  DLST; dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial [KO:K00658] [EC:2.3.1.61]
104308930  DLD; dihydrolipoyl dehydrogenase, mitochondrial isoform X1 [KO:K00382] [EC:1.8.1.4]
104296952  RPIA; ribose-5-phosphate isomerase [KO:K01899] [EC:6.2.1.4 6.2.1.5]
104302281  SUCLG2; succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial [KO:K01900] [EC:6.2.1.4 6.2.1.5]
104305415  SUCLA2; succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial [KO:K01900] [EC:6.2.1.4 6.2.1.5]
104299420  SDHA; succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial [KO:K00234] [EC:1.3.5.1]
104308600  SDHB; succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial [KO:K00235] [EC:1.3.5.1]
104302665  SDHD; succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial [KO:K00237]
104299423  FH; fumarate hydratase, mitochondrial [KO:K01679] [EC:4.2.1.2]
104301453  MDH1; malate dehydrogenase, cytoplasmic [KO:K00025] [EC:1.1.1.37]
104301793  MDH2; malate dehydrogenase, mitochondrial [KO:K00026] [EC:1.1.1.37]
104302647  PCK1; phosphoenolpyruvate carboxykinase, cytosolic [GTP] [KO:K01596] [EC:4.1.1.32]
104300478  PDHA1; pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial [KO:K00161] [EC:1.2.4.1]
104305137  PDHB; pyruvate dehydrogenase E1 component subunit beta, mitochondrial [KO:K00162] [EC:1.2.4.1]
104300093  DLAT; dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial [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
dpub00010  Glycolysis / Gluconeogenesis
dpub00053  Ascorbate and aldarate metabolism
dpub00061  Fatty acid biosynthesis
dpub00062  Fatty acid elongation
dpub00071  Fatty acid degradation
dpub00190  Oxidative phosphorylation
dpub00220  Arginine biosynthesis
dpub00250  Alanine, aspartate and glutamate metabolism
dpub00280  Valine, leucine and isoleucine degradation
dpub00350  Tyrosine metabolism
dpub00470  D-Amino acid metabolism
dpub00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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