{PDOC51782}
{PS51782; LYSM}
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* LysM domain profile *
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A highly  conserved  carbohydrate  binding module, LysM (lysin-like motif), is
found in  proteins  from  viruses,  bacteria, fungi, plants and mammals. It is
present in bacterial extracellular proteins including hydrolases, adhesins and
virulence factors  such  as  Protein  A from Staphylococcus aureus. It is also
found in  proteins  produced  by fungal pathogens acting as modulators of host
immunity, and  is  present in a large number of proteins from insects, mammals
and plants  involved  in  defence  against pathogens and symbiotic signalling.
LysM modules recognize polysaccharides containing N-acetylglucosamine (GlcNAc)
residues including peptidoglycan, an essential component of the bacterial cell
wall. Prokaryotic  LysM  modules bind peptidoglycan, the main component of the
bacterial cell  wall,  made of alternating N-acetylglycosamine (GlcNac) and N-
acetylmuramic acid  (MurNac)  residues, substituted by short peptide stems. In
eukaryotes, LysM domains have been shown to bind mainly to chitin, a beta 1,4-
linked GlcNac  polymer  that  is the main constituent of fungal cell walls, as
well as to peptidoglycan [1,2].

LysM modules  consist  of  43-50  amino  acids  that  adopt a highly conserved
BetaAlphaAlphaBeta-fold, with  the two helices packing onto the same side of a
two stranded   anti-parallel   beta-sheet   (see   <PDB:1E0G>).  The  sequence
conservation is particularly high in the first 16 residues [1,2].

Some proteins known to contain a LysM domain are listed below:

 - Caenorhabditis elegans LysM Domain (Peptidoglycan binding) protein.
 - Kluyveromyces lactis killer toxin subunits alpha/beta.
 - Arabidopsis thaliana LysM domain receptor-like kinases.
 - Listeria probable endopeptidase p60.
 - Haemophilus influenzae probable N-acetylmuramoyl-L-alanine amidase AmiB.
 - Enterococcus faecalis autolysin.
 - Staphylococci  immunoglobulin  G-binding  protein  A, helps the bacteria to
   avoid the immune response.
 - Mycobacterium tuberculosis uncharacterized protein Rv1288.
 - Escherichia  coli  murein  hydrolase  activator NlpD, activator of the cell
   wall hydrolase AmiC.
 - Escherichia coli probable L,D-transpeptidase YnhG.
 - Escherichia  coli  membrane-bound lytic murein transglycosylase D (mltD), a
   murein-degrading enzyme.
 - Enterohaemorrhagic  and enteropathogenic Escherichia coli intimin, an outer
   membrane protein required for intimate attachment to mammalian cells.
 - Bacillus subtilis N-acetylmuramoyl-L-alanine amidase XlyA.
 - Bacillus  phage phi29 lysozyme, helps to release the mature phage particles
   from the cell wall by breaking down the peptidoglycan.

The profile we developed covers the entire LysM domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: November 2015 / First entry.

[ 1] Bateman A., Bycroft M.
     "The structure of a LysM domain from E. coli membrane-bound lytic
     murein transglycosylase D (MltD)."
     J. Mol. Biol. 299:1113-1119(2000).
     PubMed=10843862; DOI=10.1006/jmbi.2000.3778
[ 2] Mesnage S., Dellarole M., Baxter N.J., Rouget J.-B., Dimitrov J.D.,
     Wang N., Fujimoto Y., Hounslow A.M., Lacroix-Desmazes S., Fukase K.,
     Foster S.J., Williamson M.P.
     "Molecular basis for bacterial peptidoglycan recognition by LysM
     domains."
     Nat. Commun. 5:4269-4269(2014).
     PubMed=24978025; DOI=10.1038/ncomms5269

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