This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.
Synonyms: δ-aminovalerate pathway, δ-aminovaleric acid pathway
|Superclasses:||Degradation/Utilization/Assimilation → Amino Acids Degradation → Proteinogenic Amino Acids Degradation → L-lysine Degradation|
Expected Taxonomic Range:
Fluorescent pseudomonads such as Pseudomonas putida can catabolize L-lysine and other amino acids as a sole carbon and nitrogen source, giving them the ability to grow in the rhizosphere of plants where amino acids are part of the root exudates. These soil bacteria are believed to promote the growth and health of crop plants (in [Revelles05, Revelles04, EspinosaUrgel01].
Pseudomonas putida can catabolize L-lysine via the 5-aminopentanoate (δ-aminovalerate) pathway to glutarate. In this pathway, L-lysine is transported into the cell by basic amino acid transport systems [Fan72]. It is oxidatively decarboxylated to 5-aminopentanamide (δ-aminovaleramide), which is then hydrolyzed to 5-aminopentanoate (δ-aminovalerate) and ammonia. The conversion of 5-aminopentanoate to glutarate involves gene products of the davDT operon (in [Revelles05]). Activation of glutarate to glutaryl-CoA by an as yet uncharacterized reaction(s) and further metabolism of glutaryl-CoA to carbon dioxide and acetyl-CoA have been demonstrated in Pseudomonas fluorescens (in [Numa64]).
Some Pseudomonas putida strains also catabolize D-lysine via a separate, pipecolate pathway (see MetaCyc pathway L-lysine degradation V). This pathway involves a lysine racemase that converts L-lysine to D-lysine, which is then converted to cyclic, six-carbon intermediates [Chang71] and in [Muramatsu05, Revelles05, Chang77a]. It is also known as the α-aminoadipate (AMA) pathway, and some of the enzymes, as well as a transporter, may be encoded on the OCT plasmid [Cao93] and in [Revelles05]. The cyclic intermediate substrates Δ1-piperideine-2-carboxylate and Δ1-piperideine-6-carboxylate exist in equilibrium with their open chain forms, α-keto-ε-aminoadipate and α-aminoadipate δ-semialdehyde (also named 2-aminoadipate-6-semialdehyde), respectively [Broquist91, Calvert66, Rodwell71].
L-lysine catabolism in Pseudomonas varies as to species and strain. Pseudomonas aeruginosa does not use the δ-aminovalerate pathway. It was proposed to catabolizes L-lysine via decarboxylation to cadaverine (see MetaCyc pathway L-lysine degradation I) (in [Revelles05]).
Superpathways: superpathway of L-lysine degradation
Variants: L-lysine degradation I, L-lysine degradation II (L-pipecolate pathway), L-lysine degradation III, L-lysine degradation V, L-lysine degradation VI, L-lysine degradation VII, L-lysine degradation VIII, L-lysine degradation IX, L-lysine degradation X, L-lysine degradation XI (mammalian), L-lysine fermentation to acetate and butanoate
Calvert66: Calvert AF, Rodwell VW (1966). "Metabolism of pipecolic acid in a Pseudomonas species. 3. L-alpha-aminoadipate delta-semialdehyde:nicotinamide adenine dinucleotide oxidoreductase." J Biol Chem 241(2);409-14. PMID: 4285660
Chang77a: Chang YF, Adams E (1977). "Factors influencing growth on L-lysine by Pseudomonas. Regulation of terminal enzymes in the delta-aminovalerate pathway and growth stimulation by alpha ketoglutarate." J Biol Chem 252(22);7987-91. PMID: 914858
EspinosaUrgel01: Espinosa-Urgel M, Ramos JL (2001). "Expression of a Pseudomonas putida aminotransferase involved in lysine catabolism is induced in the rhizosphere." Appl Environ Microbiol 67(11);5219-24. PMID: 11679348
Muramatsu05: Muramatsu H, Mihara H, Kakutani R, Yasuda M, Ueda M, Kurihara T, Esaki N (2005). "The putative malate/lactate dehydrogenase from Pseudomonas putida is an NADPH-dependent delta1-piperideine-2-carboxylate/delta1-pyrroline-2-carboxylate reductase involved in the catabolism of D-lysine and D-proline." J Biol Chem 280(7);5329-35. PMID: 15561717
Revelles04: Revelles O, Espinosa-Urgel M, Molin S, Ramos JL (2004). "The davDT operon of Pseudomonas putida, involved in lysine catabolism, is induced in response to the pathway intermediate delta-aminovaleric acid." J Bacteriol 186(11);3439-46. PMID: 15150230
Revelles05: Revelles O, Espinosa-Urgel M, Fuhrer T, Sauer U, Ramos JL (2005). "Multiple and interconnected pathways for L-lysine catabolism in Pseudomonas putida KT2440." J Bacteriol 187(21);7500-10. PMID: 16237033
Marlaire13: Marlaire S, Van Schaftingen E, Veiga-da-Cunha M (2013). "C7orf10 encodes succinate-hydroxymethylglutarate CoA-transferase, the enzyme that converts glutarate to glutaryl-CoA." J Inherit Metab Dis. PMID: 23893049
Yamanishi07: Yamanishi Y, Mihara H, Osaki M, Muramatsu H, Esaki N, Sato T, Hizukuri Y, Goto S, Kanehisa M (2007). "Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa." FEBS J 274(9);2262-73. PMID: 17388807
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