KEGG   PATHWAY: rde00020
Entry
rde00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Roseobacter denitrificans
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
rde00020  Citrate cycle (TCA cycle)
rde00020

Module
rde_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:rde00020]
rde_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:rde00020]
rde_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:rde00020]
rde_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:rde00020]
rde_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:rde00020]
Other DBs
GO: 0006099
Organism
Roseobacter denitrificans [GN:rde]
Gene
RD1_3219  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
RD1_2555  acnA; aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
RD1_2204  icd; isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
RD1_2704  icd; isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
RD1_1609  sucA; alpha-ketoglutarate dehydrogenase [KO:K00164] [EC:1.2.4.2]
RD1_1608  sucB; dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
RD1_1603  lpdA; dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
RD1_2995  lpdA; dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
RD1_3670  pyridine nucleotide-disulfide oxidoreductase, putative [KO:K00382] [EC:1.8.1.4]
RD1_1611  sucD; succinyl-CoA synthase, alpha subunit [KO:K01902] [EC:6.2.1.5]
RD1_1615  sucC; succinyl-CoA synthase, beta subunit [KO:K01903] [EC:6.2.1.5]
RD1_1628  sdhA; succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
RD1_1630  sdhB; succinate dehydrogenase, iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
RD1_1626  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
RD1_1627  sdhD; suc [KO:K00242]
RD1_2273  fumC; fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
RD1_1617  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
RD1_3376  pyc; pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
RD1_1376  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
RD1_3011  pdhA; pyruvate dehydrogenase complex, E1 component, alpha subunit [KO:K00161] [EC:1.2.4.1]
RD1_3013  pdhB; pyruvate dehydrogenase complex, E1 component, beta subunit [KO:K00162] [EC:1.2.4.1]
RD1_3014  pdhC; pyruvate dehydrogenase complex dihydrolipoamide 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
rde00010  Glycolysis / Gluconeogenesis
rde00053  Ascorbate and aldarate metabolism
rde00061  Fatty acid biosynthesis
rde00071  Fatty acid degradation
rde00190  Oxidative phosphorylation
rde00220  Arginine biosynthesis
rde00250  Alanine, aspartate and glutamate metabolism
rde00280  Valine, leucine and isoleucine degradation
rde00350  Tyrosine metabolism
rde00470  D-Amino acid metabolism
rde00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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