MetaCyc Pathway: L-lysine degradation IV
Inferred from experiment

Enzyme View:

Pathway diagram: L-lysine degradation IV

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/AssimilationAmino Acids DegradationProteinogenic Amino Acids DegradationL-lysine Degradation

Some taxa known to possess this pathway include : Pseudomonas fluorescens, Pseudomonas putida

Expected Taxonomic Range: Bacteria

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

Created 16-Aug-2006 by Fulcher CA, SRI International


Broquist91: Broquist HP (1991). "Lysine-pipecolic acid metabolic relationships in microbes and mammals." Annu Rev Nutr 11;435-48. PMID: 1909881

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

Cao93: Cao X, Kolonay J, Saxton KA, Hartline RA (1993). "The OCT plasmid encodes D-lysine membrane transport and catabolic enzymes in Pseudomonas putida." Plasmid 30(2);83-9. PMID: 8234494

Chang71: Chang YF, Adams E (1971). "Induction of separate catabolic pathways for L- and D-lysine in Pseudomonas putida." Biochem Biophys Res Commun 45(3);570-7. PMID: 5128165

Chang74a: Chang YF, Adams E (1974). "D-lysine catabolic pathway in Pseudomonas putida: interrelations with L-lysine catabolism." J Bacteriol 117(2);753-64. PMID: 4359655

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

Fan72: Fan CL, Miller DL, Rodwell VW (1972). "Metabolism of basic amino acids in Pseudomonas putida. Transport of lysine, ornithine, and arginine." J Biol Chem 247(8);2283-8. PMID: 5019949

Flashner74: Flashner MI, Massey V (1974). "Purification and properties of L-lysine monooxygenase from Pseudomonas fluorescens." J Biol Chem 249(8);2579-86. PMID: 4207122

Miller71: Miller DL, Rodwell VW (1971). "Metabolism of basic amino acids in Pseudomonas putida. Properties of the inducible lysine transport system." J Biol Chem 246(6);1765-71. PMID: 5547703

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

Numa64: Numa S, Ishimura Y, Nakazawa T, Ooazaki T, Hayaishi O (1964). "Enzymic studies on the metabolism of glutarate in Pseudomonas." J Biol Chem 239;3915-26. PMID: 14257627

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

Rodwell71: Rodwell V.W. (1971). 1-Piperideine-6-carboxylic acid and α-aminoadipic acid δ-semialdehyde." Methods Enzymol. 178:188-199.

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Chang71a: Chang YF, Adams E (1971). "Glutaric semialdehyde dehydrogenase (Pseudomonas putida)." Methods Enzymol. 17B:166-171.

Chang77b: Chang YF, Adams E (1977). "Glutarate semialdehyde dehydrogenase of Pseudomonas. Purification, properties, and relation to L-lysine catabolism." J Biol Chem 252(22);7979-86. PMID: 914857

Deana92: Deana R (1992). "Substrate specificity of a dicarboxyl-CoA: dicarboxylic acid coenzyme A transferase from rat liver mitochondria." Biochem Int 26(4);767-73. PMID: 1610380

Flashner74a: Flashner MI, Massey V (1974). "Regulatory properties of the flavoprotein L-lysine monooxygenase." J Biol Chem 249(8);2587-92. PMID: 4207123

Large91: Large PJ, Robertson A (1991). "The route of lysine breakdown in Candida tropicalis." FEMS Microbiol Lett 66(2);209-13. PMID: 1682209

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

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

Nakazawa72: Nakazawa T, Hori K, Hayaishi O (1972). "Studies on monooxygenases. V. Manifestation of amino acid oxidase activity by L-lysine monooxygenase." J Biol Chem 247(11);3439-44. PMID: 4624115

Reitz70: Reitz MS, Rodwell VW (1970). "Delta-aminovaleramidase of Pseudomonas putida." J Biol Chem 245(12);3091-6. PMID: 5432799

Takeda69: Takeda H, Yamamoto S, Kojima Y, Hayaishi O (1969). "Studies on monooxygenases. I. General properties of crystalline L-lysine monooxygenase." J Biol Chem 244(11);2935-41. PMID: 5772467

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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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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