KEGG   PATHWAY: dmm00020
Entry
dmm00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Desulfonema magnum
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
dmm00020  Citrate cycle (TCA cycle)
dmm00020

Module
dmm_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:dmm00020]
dmm_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dmm00020]
dmm_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:dmm00020]
dmm_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dmm00020]
Other DBs
GO: 0006099
Organism
Desulfonema magnum [GN:dmm]
Gene
dnm_056360  gltA1; Citrate synthase [KO:K01647] [EC:2.3.3.1]
dnm_062050  gltA2; Citrate synthase [KO:K01647] [EC:2.3.3.1]
dnm_086830  acnA; Aconitate hydratase A [KO:K01681] [EC:4.2.1.3]
dnm_056460  icd; Isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
dnm_035370  sucB; Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
dnm_035380  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K01616] [EC:2.2.1.5 4.1.1.71 1.2.4.2 2.3.1.61]
dnm_035360  lpdA; Dihydrolipoyl dehydrogenase (E3 component of 2-oxoglutarate dehydrogenase complex) [KO:K00382] [EC:1.8.1.4]
dnm_064090  ipdA; Dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
dnm_032550  2-oxoglutarate synthase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
dnm_058640  korA1; 2-oxoglutarate synthase subunit KorA [KO:K00174] [EC:1.2.7.3 1.2.7.11]
dnm_069410  korA2; 2-oxoglutarate synthase subunit KorA [KO:K00174] [EC:1.2.7.3 1.2.7.11]
dnm_032540  2-oxoacid:ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
dnm_058650  korB1; 2-oxoglutarate synthase subunit KorB [KO:K00175] [EC:1.2.7.3 1.2.7.11]
dnm_069400  korB2; 2-oxoglutarate synthase subunit KorN [KO:K00175] [EC:1.2.7.3 1.2.7.11]
dnm_032530  2-oxoglutarate ferredoxin oxidoreductase subunit gamma [KO:K00177] [EC:1.2.7.3]
dnm_058660  korC; 2-oxoglutarate synthase subunit KorC [KO:K00177] [EC:1.2.7.3]
dnm_032560  4Fe-4S dicluster domain-containing protein [KO:K00176] [EC:1.2.7.3]
dnm_058630  4Fe-4S ferredoxin iron-sulfur binding domain protein [KO:K00176] [EC:1.2.7.3]
dnm_056670  sucD1; Succinate--CoA ligase [ADP-forming], subunit alpha [KO:K01902] [EC:6.2.1.5]
dnm_059050  sucD2; Succinate--CoA ligase [ADP-forming], subunit alpha [KO:K01902] [EC:6.2.1.5]
dnm_056660  sucC1; Succinate--CoA ligase [ADP-forming], subunit beta [KO:K01903] [EC:6.2.1.5]
dnm_059060  sucC2; Succinate--CoA ligase [ADP-forming], subunit beta [KO:K01903] [EC:6.2.1.5]
dnm_035860  sdhA1; Succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
dnm_042820  sdhA2; Succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00239] [EC:1.3.5.1]
dnm_035870  sdhB1; Succinate dehydrogenase and fumarate reductase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
dnm_042810  sdhB2; putative succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
dnm_035850  sdhC1; Succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
dnm_042840  sdhC2; Succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
dnm_078000  fumA; Fumarate hydratase, class I [KO:K01676] [EC:4.2.1.2]
dnm_099370  fumC; Fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
dnm_042790  mdh1; Malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
dnm_059240  mdh2; Malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
dnm_059070  Putative pyruvate carboxylase subunit B, PycB-like [KO:K01960] [EC:6.4.1.1]
dnm_061870  pckG; Phosphoenolpyruvate carboxykinase [KO:K01596] [EC:4.1.1.32]
dnm_022420  porA; Pyruvate synthase, subunit alpha [KO:K00169] [EC:1.2.7.1]
dnm_022440  porC; Pyruvate synthase subunit [KO:K00172] [EC:1.2.7.1]
dnm_042800  por1; Pyruvate:ferredoxin oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
dnm_078040  por2; Pyruvate:ferredoxin oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
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
dmm00010  Glycolysis / Gluconeogenesis
dmm00053  Ascorbate and aldarate metabolism
dmm00061  Fatty acid biosynthesis
dmm00071  Fatty acid degradation
dmm00190  Oxidative phosphorylation
dmm00220  Arginine biosynthesis
dmm00250  Alanine, aspartate and glutamate metabolism
dmm00280  Valine, leucine and isoleucine degradation
dmm00350  Tyrosine metabolism
dmm00470  D-Amino acid metabolism
dmm00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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