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 β 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 βααβ-fold, with the two helices packing onto the same side of a two stranded anti-parallel β-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 α/β.
• 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.