If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.
|Superclasses:||Degradation/Utilization/Assimilation → Amino Acids Degradation → 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
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.
Please note: This pathway does not represent a single organism. Rather, it is a superpathway assembled from pathways found in a variety of organisms. Its purpose is to provide an overview of the diversity of ways that organisms can degrade lysine.
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 18.104.22.168) in MetaCyc pathway lysine degradation I; saccharopine dehydrogenase (EC 22.214.171.124) in lysine degradation II (mammalian); ε-N-acetylase (EC 126.96.36.199) in lysine degradation III; lysine 2-monooxygenase (EC 188.8.131.52) in lysine degradation IV; racemase (EC 184.108.40.206) in lysine degradation V; ε-transaminase (EC 220.127.116.11) in lysine degradation VI; α-oxidase (EC 18.104.22.168) in lysine degradation VII; ε-dehydrogenase (EC 22.214.171.124) in lysine degradation VIII; aminomutase (anaerobic) (EC 126.96.36.199) in lysine fermentation to acetate and butyrate; and a novel ε-transaminase (EC 188.8.131.52) in lysine degradation IX. Reviewed in [Zabriskie00].
Common intermediates leading to central metabolism include: (S)-2-amino-6-oxohexanoate/(S)-2,3,4,5-tetrahydropiperidine-2-carboxylate; 2-keto-6-aminocaproate/Δ1-piperideine-2-carboxylate; L-2-aminoadipate; 2-oxoadipate; 5-aminopentanoate; glutarate semialdehyde; and glutarate.
In addition, a L-lysine 6-monooxygenase (EC 184.108.40.206) 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 220.127.116.11), was suggested by an early paper [Burgi66] but was not subsequently verified (in [Heydari04]).
Subpathways: lysine fermentation to acetate and butyrate , lysine degradation III , lysine degradation II (mammalian) , lysine degradation IV , lysine degradation V , lysine degradation VI , lysine degradation VII , lysine degradation VIII , lysine degradation IX , lysine degradation I
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
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
Alber06a: 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
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
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
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
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
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
Blemings94: Blemings KP, Crenshaw TD, Swick RW, Benevenga NJ (1994). "Lysine-alpha-ketoglutarate reductase and saccharopine dehydrogenase are located only in the mitochondrial matrix in rat liver." J Nutr 124(8);1215-21. PMID: 8064371
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