KEGG   PATHWAY: nim00020
Entry
nim00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Candidatus Nitrotoga sp. AM1P
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
nim00020  Citrate cycle (TCA cycle)
nim00020

Module
nim_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:nim00020]
nim_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:nim00020]
nim_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:nim00020]
nim_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:nim00020]
Other DBs
GO: 0006099
Organism
Candidatus Nitrotoga sp. AM1P [GN:nim]
Gene
W01_10890  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
W01_24870  acnA; aconitate hydratase [KO:K01681] [EC:4.2.1.3]
W01_26200  icd; isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
W01_10880  sucA; 2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
W01_10870  sucB; dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex [KO:K00658] [EC:2.3.1.61]
W01_10860  lpd; lipoamide dehydrogenase, E3 component is part of three enzyme complexes [KO:K00382] [EC:1.8.1.4]
W01_22720  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
W01_14250  sucD_2; succinate--CoA ligase [ADP-forming], alpha subunit [KO:K01902] [EC:6.2.1.5]
W01_14260  sucC_2; succinate--CoA ligase [ADP-forming], beta subunit [KO:K01903] [EC:6.2.1.5]
W01_10930  sdhA; succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
W01_10910  sdhB; succinate dehydrogenase, iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
W01_10950  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
W01_10940  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
W01_05910  fumC; fumarate hydratase class II [KO:K01679] [EC:4.2.1.2]
W01_07550  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
W01_16740  aceE; pyruvate dehydrogenase, E1 component [KO:K00163] [EC:1.2.4.1]
W01_16750  aceF; acetyltransferase component of pyruvate dehydrogenase complex [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
nim00010  Glycolysis / Gluconeogenesis
nim00061  Fatty acid biosynthesis
nim00071  Fatty acid degradation
nim00190  Oxidative phosphorylation
nim00220  Arginine biosynthesis
nim00250  Alanine, aspartate and glutamate metabolism
nim00280  Valine, leucine and isoleucine degradation
nim00350  Tyrosine metabolism
nim00470  D-Amino acid metabolism
nim00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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