KEGG   PATHWAY: mety00020
Entry
mety00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Phytobacter sp. MRY16-398
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
mety00020  Citrate cycle (TCA cycle)
mety00020

Module
mety_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:mety00020]
mety_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:mety00020]
mety_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:mety00020]
mety_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:mety00020]
mety_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:mety00020]
Other DBs
GO: 0006099
Organism
Phytobacter sp. MRY16-398 [GN:mety]
Gene
MRY16398_28490  citrate synthase [KO:K01647] [EC:2.3.3.1]
MRY16398_40410  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
MRY16398_30520  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
MRY16398_42980  acnB; aconitate hydratase B [KO:K01682] [EC:4.2.1.3 4.2.1.99]
MRY16398_46990  aconitate hydratase B [KO:K01682] [EC:4.2.1.3 4.2.1.99]
MRY16398_21770  isocitrate dehydrogenase [NADP] [KO:K00031] [EC:1.1.1.42]
MRY16398_40360  sucA; 2-oxoglutarate dehydrogenase subunit E1 [KO:K00164] [EC:1.2.4.2]
MRY16398_40350  sucB; dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
MRY16398_47020  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
MRY16398_40330  sucD; succinate--CoA ligase [ADP-forming] subunit alpha [KO:K01902] [EC:6.2.1.5]
MRY16398_40340  sucC; succinate--CoA ligase [ADP-forming] subunit beta [KO:K01903] [EC:6.2.1.5]
MRY16398_40380  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
MRY16398_05540  oxidoreductase [KO:K00239] [EC:1.3.5.1]
MRY16398_40370  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
MRY16398_40400  sdhC; succinate dehydrogenase cytochrome b556 large subunit [KO:K00241]
MRY16398_40390  sdhD; succinate dehydrogenase hydrophobic membrane anchor subunit [KO:K00242]
MRY16398_51010  fumarate reductase flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
MRY16398_51020  succinate dehydrogenase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
MRY16398_51030  frdC; fumarate reductase subunit C [KO:K00246]
MRY16398_51040  frdD; fumarate reductase subunit D [KO:K00247]
MRY16398_23870  fumarate hydratase class I [KO:K01676] [EC:4.2.1.2]
MRY16398_32650  fumarate hydratase class I [KO:K01676] [EC:4.2.1.2]
MRY16398_23880  fumC; fumarate hydratase class II [KO:K01679] [EC:4.2.1.2]
MRY16398_22630  hypothetical protein [KO:K01675] [EC:4.2.1.2]
MRY16398_05400  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
MRY16398_16660  mqo; putative malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
MRY16398_03930  pckA; phosphoenolpyruvate carboxykinase [ATP] [KO:K01610] [EC:4.1.1.49]
MRY16398_47040  aceE; pyruvate dehydrogenase E1 component [KO:K00163] [EC:1.2.4.1]
MRY16398_47030  aceF; acetyltransferase component of pyruvate dehydrogenase complex [KO:K00627] [EC:2.3.1.12]
MRY16398_27910  nifJ2; pyruvate-flavodoxin oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
MRY16398_30070  ydbK; pyruvate-flavodoxin 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
mety00010  Glycolysis / Gluconeogenesis
mety00053  Ascorbate and aldarate metabolism
mety00061  Fatty acid biosynthesis
mety00071  Fatty acid degradation
mety00190  Oxidative phosphorylation
mety00220  Arginine biosynthesis
mety00250  Alanine, aspartate and glutamate metabolism
mety00280  Valine, leucine and isoleucine degradation
mety00350  Tyrosine metabolism
mety00470  D-Amino acid metabolism
mety00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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