KEGG   PATHWAY: mgry00020
Entry
mgry00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Magnetospirillum gryphiswaldense MSR-1
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
mgry00020  Citrate cycle (TCA cycle)
mgry00020

Module
mgry_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:mgry00020]
mgry_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:mgry00020]
mgry_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:mgry00020]
mgry_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:mgry00020]
mgry_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:mgry00020]
Other DBs
GO: 0006099
Organism
Magnetospirillum gryphiswaldense MSR-1 [GN:mgry]
Gene
MSR1_09220  gltA; Citrate synthase [KO:K01647] [EC:2.3.3.1]
MSR1_29060  acnB; Aconitate hydratase 2 [KO:K01682] [EC:4.2.1.3 4.2.1.99]
MSR1_23020  icd; Isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
MSR1_27360  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
MSR1_27350  sucB; Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
MSR1_27340  lpd3; Dihydrolipoyl dehydrogenase 3 [KO:K00382] [EC:1.8.1.4]
MSR1_12880  lpd; Dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
MSR1_27370  sucD; Succinyl-CoA ligase [ADP-forming] subunit alpha [KO:K01902] [EC:6.2.1.5]
MSR1_27380  sucC; Succinyl-CoA ligase [ADP-forming] subunit beta [KO:K01903] [EC:6.2.1.5]
MSR1_22120  sdhA; Succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
MSR1_22110  sdhB; Succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
MSR1_22140  sdhC; Succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
MSR1_22130  Succinate dehydrogenase/Fumarate reductase transmembrane subunit [KO:K00242]
MSR1_07890  fumA; Fumarate hydratase class I, aerobic [KO:K01676] [EC:4.2.1.2]
MSR1_27390  mdh; Malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
MSR1_05450  pckG; Phosphoenolpyruvate carboxykinase [GTP] [KO:K01596] [EC:4.1.1.32]
MSR1_12930  acoA; Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit alpha [KO:K00161] [EC:1.2.4.1]
MSR1_12920  bfmBAB; 2-oxoisovalerate dehydrogenase subunit beta [KO:K00162] [EC:1.2.4.1]
MSR1_12910  pdhC; Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex [KO:K00627] [EC:2.3.1.12]
MSR1_11920  porA; Pyruvate synthase subunit PorA [KO:K00169] [EC:1.2.7.1]
MSR1_11930  porB; Pyruvate synthase subunit PorB [KO:K00170] [EC:1.2.7.1]
MSR1_11910  porC; Pyruvate synthase subunit PorC [KO:K00172] [EC:1.2.7.1]
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
mgry00010  Glycolysis / Gluconeogenesis
mgry00053  Ascorbate and aldarate metabolism
mgry00061  Fatty acid biosynthesis
mgry00071  Fatty acid degradation
mgry00190  Oxidative phosphorylation
mgry00220  Arginine biosynthesis
mgry00250  Alanine, aspartate and glutamate metabolism
mgry00280  Valine, leucine and isoleucine degradation
mgry00350  Tyrosine metabolism
mgry00470  D-Amino acid metabolism
mgry00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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