KEGG   PATHWAY: agm00020
Entry
agm00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Agromyces badenianii
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
agm00020  Citrate cycle (TCA cycle)
agm00020

Module
agm_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:agm00020]
agm_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:agm00020]
agm_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:agm00020]
Other DBs
GO: 0006099
Organism
Agromyces badenianii [GN:agm]
Gene
DCE93_08405  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
DCE93_11080  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
DCE93_04535  kgd; multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit [KO:K01616] [EC:2.2.1.5 4.1.1.71 1.2.4.2 2.3.1.61]
DCE93_13425  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
DCE93_07195  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
DCE93_11155  succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
DCE93_11160  ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
DCE93_09990  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
DCE93_02480  succinate dehydrogenase [KO:K00239] [EC:1.3.5.1]
DCE93_09995  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
DCE93_09980  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
DCE93_09985  succinate dehydrogenase [KO:K00242]
DCE93_03860  aspA; aspartate ammonia-lyase [KO:K01679] [EC:4.2.1.2]
DCE93_12210  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
DCE93_10405  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
DCE93_06280  pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
DCE93_10155  phosphoenolpyruvate carboxykinase (GTP) [KO:K01596] [EC:4.1.1.32]
DCE93_07080  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
DCE93_07190  sucB; 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
agm00010  Glycolysis / Gluconeogenesis
agm00053  Ascorbate and aldarate metabolism
agm00061  Fatty acid biosynthesis
agm00062  Fatty acid elongation
agm00071  Fatty acid degradation
agm00190  Oxidative phosphorylation
agm00220  Arginine biosynthesis
agm00250  Alanine, aspartate and glutamate metabolism
agm00280  Valine, leucine and isoleucine degradation
agm00350  Tyrosine metabolism
agm00470  D-Amino acid metabolism
agm00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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