KEGG   PATHWAY: npp00020
Entry
npp00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Novosphingobium sp. PP1Y
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
npp00020  Citrate cycle (TCA cycle)
npp00020

Module
npp_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:npp00020]
npp_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:npp00020]
npp_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:npp00020]
npp_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:npp00020]
npp_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:npp00020]
Other DBs
GO: 0006099
Organism
Novosphingobium sp. PP1Y [GN:npp]
Gene
PP1Y_AT27179  citrate synthase [KO:K01647] [EC:2.3.3.1]
PP1Y_AT35121  aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
PP1Y_AT11916  aconitate hydratase 2 [KO:K01682] [EC:4.2.1.3 4.2.1.99]
PP1Y_AT30385  isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
PP1Y_AT17276  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
PP1Y_AT17267  2-oxoglutarate dehydrogenase E2 component (dihydrolipoamide succinyltransferase) [KO:K00658] [EC:2.3.1.61]
PP1Y_AT17260  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
PP1Y_AT25757  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
PP1Y_AT30563  2-oxoglutarate ferredoxin oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
PP1Y_AT30556  2-oxoglutarate ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
PP1Y_AT17301  succinyl-CoA synthetase alpha subunit [KO:K01902] [EC:6.2.1.5]
PP1Y_AT433  succinyl-CoA synthetase beta subunit [KO:K01903] [EC:6.2.1.5]
PP1Y_AT30672  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
PP1Y_AT21737  succinate dehydrogenase iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
PP1Y_AT30692  succinate dehydrogenase cytochrome b-556 subunit [KO:K00241]
PP1Y_AT30686  succinate dehydrogenase hydrophobic membrane anchor protein [KO:K00242]
PP1Y_AT37168  fumarate hydratase, class I [KO:K01676] [EC:4.2.1.2]
PP1Y_AT4446  fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
PP1Y_AT17313  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
PP1Y_AT28221  phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
PP1Y_AT26309  pyruvate dehydrogenase E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
PP1Y_AT26298  pyruvate dehydrogenase E1 component subunit beta [KO:K00162] [EC:1.2.4.1]
PP1Y_AT13756  pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [KO:K00627] [EC:2.3.1.12]
PP1Y_Mpl5575  pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [KO:K00627] [EC:2.3.1.12]
PP1Y_AT25743  pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [KO:K00627] [EC:2.3.1.12]
PP1Y_AT22962  pyruvate ferredoxin/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
npp00010  Glycolysis / Gluconeogenesis
npp00053  Ascorbate and aldarate metabolism
npp00061  Fatty acid biosynthesis
npp00071  Fatty acid degradation
npp00190  Oxidative phosphorylation
npp00220  Arginine biosynthesis
npp00250  Alanine, aspartate and glutamate metabolism
npp00280  Valine, leucine and isoleucine degradation
npp00350  Tyrosine metabolism
npp00470  D-Amino acid metabolism
npp00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

DBGET integrated database retrieval system