KEGG   PATHWAY: bic00020
Entry
bic00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Bradyrhizobium icense
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
bic00020  Citrate cycle (TCA cycle)
bic00020

Module
bic_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:bic00020]
bic_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:bic00020]
bic_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:bic00020]
bic_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:bic00020]
bic_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:bic00020]
Other DBs
GO: 0006099
Organism
Bradyrhizobium icense [GN:bic]
Gene
LMTR13_19065  citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
LMTR13_37720  aconitate hydratase 1 [KO:K01681] [EC:4.2.1.3]
LMTR13_15325  isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
LMTR13_37650  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
LMTR13_37645  dihydrolipoamide succinyltransferase [KO:K00658] [EC:2.3.1.61]
LMTR13_37635  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
LMTR13_08165  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
LMTR13_13855  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
LMTR13_19300  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
LMTR13_06690  ferredoxin oxidoreductase [KO:K00174] [EC:1.2.7.3 1.2.7.11]
LMTR13_06685  2-oxoglutarate ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
LMTR13_37655  succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
LMTR13_37665  succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
LMTR13_38000  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
LMTR13_38005  succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
LMTR13_37990  succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
LMTR13_37995  succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
LMTR13_27605  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
LMTR13_31240  fumarate hydratase, class II [KO:K01679] [EC:4.2.1.2]
LMTR13_37670  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
LMTR13_02380  phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
LMTR13_29065  transketolase [KO:K00163] [EC:1.2.4.1]
LMTR13_13845  pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
LMTR13_19280  pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
LMTR13_19285  pyruvate dehydrogenase complex E1 component subunit beta [KO:K00162] [EC:1.2.4.1]
LMTR13_13850  dihydrolipoamide acetyltransferase [KO:K00627] [EC:2.3.1.12]
LMTR13_19295  pyruvate dehydrogenase complex dihydrolipoamide 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
bic00010  Glycolysis / Gluconeogenesis
bic00053  Ascorbate and aldarate metabolism
bic00061  Fatty acid biosynthesis
bic00071  Fatty acid degradation
bic00190  Oxidative phosphorylation
bic00220  Arginine biosynthesis
bic00250  Alanine, aspartate and glutamate metabolism
bic00280  Valine, leucine and isoleucine degradation
bic00350  Tyrosine metabolism
bic00470  D-Amino acid metabolism
bic00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

DBGET integrated database retrieval system