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MetaCyc Chimeric Pathway: superpathway of L-lysine degradation

Pathway diagram: superpathway of L-lysine degradation

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Degradation/Utilization/AssimilationAmino Acids DegradationProteinogenic Amino Acids DegradationL-lysine Degradation

Some taxa known to possess parts of the pathway include : Agrobacterium tumefaciens, Anaerovibrio lipolyticus, Bos taurus, Candida maltosa L4, Candida tropicalis, Clostridium peptidivorans, Clostridium SB4 , Clostridium subterminale, Cyberlindnera saturnus, Escherichia coli K-12 substr. MG1655, Fusobacterium nucleatum, Geobacillus stearothermophilus, Homo sapiens, Meyerozyma guilliermondii, Mus musculus, Neurospora crassa 15069, Neurospora crassa 33933, Porphyromonas gingivalis, Pseudomonas fluorescens, Pseudomonas putida, Rattus norvegicus, Rhizoctonia leguminicola, Saccharomyces cerevisiae, Selenomonas ruminantium, Streptomyces clavuligerus, Trichoderma harzianum, Trichoderma viride, Veillonella parvula, Yarrowia lipolytica, [Clostridium] sticklandii, [Flavobacterium] lutescens

Expected Taxonomic Range: Bacteria , Eukaryota

Note: This is a chimeric pathway, comprising reactions from multiple organisms, and typically will not occur in its entirety in a single organism. The taxa listed here are likely to catalyze only subsets of the reactions depicted in this pathway.

L-Lysine degradation is varied among microorganisms, animals and plants. Although many initiating reactions have been studied, in some organisms not all subsequent reactions have been described. Initiating reactions include: decarboxylase (EC in MetaCyc pathway L-lysine degradation I; saccharopine dehydrogenase (EC in L-lysine degradation XI (mammalian); ε-N-acetylase (EC in L-lysine degradation III; lysine 2-monooxygenase (EC in L-lysine degradation IV; racemase (EC in L-lysine degradation V; ε-transaminase (EC in L-lysine degradation VI; α-oxidase (EC in L-lysine degradation VII; ε-dehydrogenase (EC in L-lysine degradation VIII; aminomutase (anaerobic) (EC in L-lysine fermentation to acetate and butanoate; and a novel ε-transaminase (EC in L-lysine degradation IX. Reviewed in [Zabriskie00].

Common intermediates leading to central metabolism include: (S)-2-amino-6-oxohexanoate/ 1-piperideine 6-carboxylate; 2-keto-6-aminocaproate/ 1-piperideine-2-carboxylate; L-2-aminoadipate; 2-oxoadipate; 5-aminopentanoate; glutarate semialdehyde; and glutarate.

In addition, a L-lysine 6-monooxygenase (EC is involved in aerobactin bioxynthesis (see MetaCyc pathway aerobactin biosynthesis). An enzyme in human liver catalyzing the deamination of the lysine α-amino group, L-lysine 2-dehydrogenase (EC, was suggested by an early paper [Burgi66] but was not subsequently verified (in [Heydari04]).

Subpathways: L-lysine fermentation to acetate and butanoate, L-lysine degradation III, L-lysine degradation XI (mammalian), L-lysine degradation IV, L-lysine degradation V, L-lysine degradation VI, L-lysine degradation VII, L-lysine degradation VIII, L-lysine degradation IX, L-lysine degradation I

Variants: L-lysine degradation II (L-pipecolate pathway), L-lysine degradation X

Created 12-Sep-2006 by Fulcher CA, SRI International


Burgi66: Burgi W, Richterich R, Colombo JP (1966). "L-Lysine dehydrogenase deficiency in a patient with congenital lysine intolerance." Nature 211(51);854-5. PMID: 4291003

Heydari04: Heydari M, Ohshima T, Nunoura-Kominato N, Sakuraba H (2004). "Highly stable L-lysine 6-dehydrogenase from the thermophile Geobacillus stearothermophilus isolated from a Japanese hot spring: characterization, gene cloning and sequencing, and expression." Appl Environ Microbiol 70(2);937-42. PMID: 14766574

Zabriskie00: Zabriskie TM, Jackson MD (2000). "Lysine biosynthesis and metabolism in fungi." Nat Prod Rep 17(1);85-97. PMID: 10714900

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

Aceti88: Aceti DJ, Ferry JG (1988). "Purification and characterization of acetate kinase from acetate-grown Methanosarcina thermophila. Evidence for regulation of synthesis." J Biol Chem 1988;263(30);15444-8. PMID: 2844814

Alber06: Alber BE, Spanheimer R, Ebenau-Jehle C, Fuchs G (2006). "Study of an alternate glyoxylate cycle for acetate assimilation by Rhodobacter sphaeroides." Mol Microbiol 61(2);297-309. PMID: 16856937

Aluri15: Aluri S, Rex K, Varshney U (2015). "Simultaneous presence of fhs and purT genes is disadvantageous for the fitness of Escherichia coli growth." FEMS Microbiol Lett 362(14). PMID: 26100103

Atteia06: Atteia A, van Lis R, Gelius-Dietrich G, Adrait A, Garin J, Joyard J, Rolland N, Martin W (2006). "Pyruvate formate-lyase and a novel route of eukaryotic ATP synthesis in Chlamydomonas mitochondria." J Biol Chem 281(15);9909-18. PMID: 16452484

Auger89: Auger EA, Redding KE, Plumb T, Childs LC, Meng SY, Bennett GN (1989). "Construction of lac fusions to the inducible arginine- and lysine decarboxylase genes of Escherichia coli K12." Mol Microbiol 3(5);609-20. PMID: 2527331

Avison01: Avison MB, Horton RE, Walsh TR, Bennett PM (2001). "Escherichia coli CreBC is a global regulator of gene expression that responds to growth in minimal media." J Biol Chem 276(29);26955-61. PMID: 11350954

Baginsky67: Baginsky ML, Rodwell VW (1967). "Metabolism of pipecolic acid in a Pseudomonas species. V. Pipecolate oxidase and dehydrogenase." J Bacteriol 94(4);1034-9. PMID: 6051341

Bairoch93a: Bairoch A, Boeckmann B (1993). "The SWISS-PROT protein sequence data bank, recent developments." Nucleic Acids Res. 21:3093-3096. PMID: 8332529

Baker72: Baker JJ, Jeng I, Barker HA (1972). "Purification and properties of L-erythro-3,5-diaminohexanoate dehydrogenase from a lysine-fermenting Clostridium." J Biol Chem 247(23);7724-34. PMID: 4344229

Baker73: Baker JJ, van der Drift C, Stadtman TC (1973). "Purification and properties of -lysine mutase, a pyridoxal phosphate and B 12 coenzyme dependent enzyme." Biochemistry 12(6);1054-63. PMID: 4540127

Barak98: Barak R, Abouhamad WN, Eisenbach M (1998). "Both acetate kinase and acetyl coenzyme A synthetase are involved in acetate-stimulated change in the direction of flagellar rotation in Escherichia coli." J Bacteriol 1998;180(4);985-8. PMID: 9473056

Barker78: Barker HA, Jeng IM, Neff N, Robertson JM, Tam FK, Hosaka S (1978). "Butyryl-CoA:acetoacetate CoA-transferase from a lysine-fermenting Clostridium." J Biol Chem 253(4);1219-25. PMID: 624727

Barker82: Barker HA, Kahn JM, Hedrick L (1982). "Pathway of lysine degradation in Fusobacterium nucleatum." J Bacteriol 152(1);201-7. PMID: 6811551

BaronaGomez04: Barona-Gomez F, Wong U, Giannakopulos AE, Derrick PJ, Challis GL (2004). "Identification of a cluster of genes that directs desferrioxamine biosynthesis in Streptomyces coelicolor M145." J Am Chem Soc 126(50);16282-3. PMID: 15600304

Beckerich94: Beckerich JM, Lambert M, Gaillardin C (1994). "LYC1 is the structural gene for lysine N-6-acetyl transferase in yeast." Curr Genet 25(1);24-9. PMID: 8082161

Bennett84: Bennett MJ, Hosking GP, Smith MF, Gray RG, Middleton B (1984). "Biochemical investigations on a patient with a defect in cytosolic acetoacetyl-CoA thiolase, associated with mental retardation." J Inherit Metab Dis 7(3);125-8. PMID: 6150136

Bennett91: Bennett MJ, Pollitt RJ, Goodman SI, Hale DE, Vamecq J (1991). "Atypical riboflavin-responsive glutaric aciduria, and deficient peroxisomal glutaryl-CoA oxidase activity: a new peroxisomal disorder." J Inherit Metab Dis 14(2);165-73. PMID: 1909402

Beretskene80: Beretskene SIa, Bruzgulis PA, Ragavichus AB (1980). "[Conditions of the synthesis of lysine decarboxylase by Escherichia coli MRE 600]." Prikl Biokhim Mikrobiol 16(3);351-5. PMID: 7001435

Berg07: Berg IA, Kockelkorn D, Buckel W, Fuchs G (2007). "A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea." Science 318(5857);1782-6. PMID: 18079405

Bergmeyer63: Bergmeyer, H.U., Holz, G., Klotzsch, H., Lang, G. (1963). "[Phosphotransacetylase from Clostridium kluyveri. Culture of the bacterium, isolation, crystallization and properties of the enzyme.]." Biochem Z 338;114-21. PMID: 14087284

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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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