KEGG   PATHWAY: mvar00020
Entry
mvar00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Massilia varians
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
mvar00020  Citrate cycle (TCA cycle)
mvar00020

Module
mvar_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:mvar00020]
mvar_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:mvar00020]
mvar_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:mvar00020]
mvar_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:mvar00020]
mvar_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:mvar00020]
Other DBs
GO: 0006099
Organism
Massilia varians [GN:mvar]
Gene
MasN3_37890  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
MasN3_37990  citB; aconitate hydratase [KO:K01681] [EC:4.2.1.3]
MasN3_17410  icd2; isocitrate dehydrogenase, NADP-dependent [KO:K00031] [EC:1.1.1.42]
MasN3_17430  icd; isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
MasN3_37530  sucA; 2-oxoglutarate dehydrogenase subunit E1 [KO:K00164] [EC:1.2.4.2]
MasN3_37520  sucB; dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
MasN3_00740  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
MasN3_27230  odhL_1; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
MasN3_28420  lpdV; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
MasN3_37500  odhL_2; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
MasN3_42440  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
MasN3_47110  sucD; succinate--CoA ligase [ADP-forming] subunit alpha [KO:K01902] [EC:6.2.1.5]
MasN3_47120  sucC; succinate--CoA ligase [ADP-forming] subunit beta [KO:K01903] [EC:6.2.1.5]
MasN3_05730  acetyl-CoA hydrolase [KO:K18118] [EC:2.8.3.18]
MasN3_37920  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
MasN3_37910  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
MasN3_37940  sdhC; succinate dehydrogenase cytochrome b-556 subunit [KO:K00241]
MasN3_37930  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
MasN3_14280  fumarate hydratase class I [KO:K01676] [EC:4.2.1.2]
MasN3_15490  fumC; fumarate hydratase class II [KO:K01679] [EC:4.2.1.2]
MasN3_37960  mdH; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
MasN3_07320  hypothetical protein [KO:K00116] [EC:1.1.5.4]
MasN3_00460  pckG; phosphoenolpyruvate carboxykinase [GTP] [KO:K01596] [EC:4.1.1.32]
MasN3_42460  aceE; pyruvate dehydrogenase E1 component [KO:K00163] [EC:1.2.4.1]
MasN3_42450  pdhB; acetyltransferase component of pyruvate dehydrogenase complex [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
mvar00010  Glycolysis / Gluconeogenesis
mvar00053  Ascorbate and aldarate metabolism
mvar00061  Fatty acid biosynthesis
mvar00071  Fatty acid degradation
mvar00190  Oxidative phosphorylation
mvar00220  Arginine biosynthesis
mvar00250  Alanine, aspartate and glutamate metabolism
mvar00280  Valine, leucine and isoleucine degradation
mvar00350  Tyrosine metabolism
mvar00470  D-Amino acid metabolism
mvar00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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