KEGG   PATHWAY: rhk00020
Entry
rhk00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Rhizobium sp. Kim5
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
rhk00020  Citrate cycle (TCA cycle)
rhk00020

Module
rhk_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:rhk00020]
rhk_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:rhk00020]
rhk_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:rhk00020]
rhk_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:rhk00020]
Other DBs
GO: 0006099
Organism
Rhizobium sp. Kim5 [GN:rhk]
Gene
Kim5_CH02082  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
Kim5_CH02295  citrate synthase protein [KO:K01647] [EC:2.3.3.1]
Kim5_CH02296  citA; citrate synthase [KO:K01647] [EC:2.3.3.1]
Kim5_CH04307  acnA; aconitate hydratase [KO:K01681] [EC:4.2.1.3]
Kim5_CH02443  icd; isocitrate dehydrogenase (NADP(+)) [KO:K00031] [EC:1.1.1.42]
Kim5_CH04248  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
Kim5_CH04246  sucB; dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
Kim5_CH02095  lpdA; dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Kim5_CH04241  dihydrolipoamide dehydrogenase protein [KO:K00382] [EC:1.8.1.4]
Kim5_PD00073  lpdV; dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
Kim5_CH04249  sucD; succinyl-CoA synthetase (ADP-forming) subunit alpha [KO:K01902] [EC:6.2.1.5]
Kim5_CH04250  sucC; succinyl-CoA synthetase (ADP-forming) subunit beta [KO:K01903] [EC:6.2.1.5]
Kim5_CH04255  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
Kim5_CH04254  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
Kim5_CH04257  sdhC; succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
Kim5_CH04256  sdhD; succinate dehydrogenase SdhD subunit [KO:K00242]
Kim5_CH02510  fumA; fumarate hydratase class 1 [KO:K01676] [EC:4.2.1.2]
Kim5_CH02507  fumC; fumarate hydratase class 2 [KO:K01679] [EC:4.2.1.2]
Kim5_CH04251  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
Kim5_CH04368  pyc; pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
Kim5_CH00037  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
Kim5_CH02090  pdhA; pyruvate dehydrogenase E1 component alpha subunit [KO:K00161] [EC:1.2.4.1]
Kim5_CH02091  pdhB; pyruvate dehydrogenase E1 component subunit beta [KO:K00162] [EC:1.2.4.1]
Kim5_CH02092  pdhC; pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase [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
rhk00010  Glycolysis / Gluconeogenesis
rhk00053  Ascorbate and aldarate metabolism
rhk00061  Fatty acid biosynthesis
rhk00071  Fatty acid degradation
rhk00190  Oxidative phosphorylation
rhk00220  Arginine biosynthesis
rhk00250  Alanine, aspartate and glutamate metabolism
rhk00280  Valine, leucine and isoleucine degradation
rhk00350  Tyrosine metabolism
rhk00470  D-Amino acid metabolism
rhk00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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