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discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Chimeric Pathway: superpathway of lysine degradation

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
Superpathways

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.

Summary:
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 4.1.1.18) in MetaCyc pathway lysine degradation I; saccharopine dehydrogenase (EC 1.5.1.8) in lysine degradation II (mammalian); ε-N-acetylase (EC 2.3.1.32) in lysine degradation III; lysine 2-monooxygenase (EC 1.13.12.2) in lysine degradation IV; racemase (EC 5.1.1.5) in lysine degradation V; ε-transaminase (EC 2.6.1.36) in lysine degradation VI; α-oxidase (EC 1.4.3.14) in lysine degradation VII; ε-dehydrogenase (EC 1.4.1.18) in lysine degradation VIII; aminomutase (anaerobic) (EC 5.4.3.2) in lysine fermentation to acetate and butyrate; and a novel ε-transaminase (EC 2.6.1.71) 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 1.14.13.59) 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 1.4.1.15), 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

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

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


References

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

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

Bairoch, 1993: 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

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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Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sat Nov 22, 2014, biocyc13.