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105  structures 7977  species 0  interactions 58761  sequences 1259  architectures

Family: LysM (PF01476)

Summary: LysM domain

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LysM domain Edit Wikipedia article

LysM domain
PDB 1e0g EBI.jpg

In molecular biology the LysM domain is a protein domain found in a wide variety of extracellular proteins and receptors. The LysM domain is named after the Lysin Motif which was the original name given to the sequence motif identified in bacterial proteins. The region was originally identified as a C-terminal repeat found in the Enterococcus hirae muramidase.[1] The LysM domain is found in a wide range of microbial extracellular proteins, where the LysM domain is thought to provide an anchoring to extracellular polysaccharides such as peptidoglycan and chitin. LysM domains are also found in plant receptors, including NFP, the receptor for Nod factor which is necessary for the root nodule symbiosis between legumes and symbiotic bacteria.[2] The LysM domain is typically between 44 and 65 amino acid residues in length.[3] The structure of the LysM domain showed that it is composed of a pair of antiparallel beta strands separated by a pair of short alpha helices.[4]

See also

Nod factor


  1. ^ Joris B, Englebert S, Chu CP, Kariyama R, Daneo-Moore L, Shockman GD, Ghuysen JM (March 1992). "Modular design of the Enterococcus hirae muramidase-2 and Streptococcus faecalis autolysin". FEMS Microbiology Letters. 70 (3): 257–64. doi:10.1016/0378-1097(92)90707-u. PMID 1352512.
  2. ^ Arrighi, Jean-François; Barre, Annick; Ben Amor, Besma; Bersoult, Anne; Soriano, Lidia Campos; Mirabella, Rossana; de Carvalho-Niebel, Fernanda; Journet, Etienne-Pascal; Ghérardi, Michèle; Huguet, Thierry; Geurts, René (2006). "The Medicago truncatula Lysine Motif-Receptor-Like Kinase Gene Family Includes NFP and New Nodule-Expressed Genes". Plant Physiology. 142 (1): 265–279. doi:10.1104/pp.106.084657. ISSN 0032-0889. PMC 1557615. PMID 16844829.
  3. ^ Buist G, Steen A, Kok J, Kuipers OP (May 2008). "LysM, a widely distributed protein motif for binding to (peptido)glycans". Molecular Microbiology. 68 (4): 838–47. doi:10.1111/j.1365-2958.2008.06211.x. PMID 18430080.
  4. ^ Bateman A, Bycroft M (June 2000). "The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD)". Journal of Molecular Biology. 299 (4): 1113–9. doi:10.1006/jmbi.2000.3778. PMID 10843862.

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LysM domain Provide feedback

The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation [1]. This domain may have a general peptidoglycan binding function. The structure of this domain is known [2].

Literature references

  1. Joris B, Englebert S, Chu CP, Kariyama R, Daneo-Moore L, Shockman GD, Ghuysen JM; , FEMS Microbiol Lett 1992;70:257-264.: Modular design of the Enterococcus hirae muramidase-2 and Streptococcus faecalis autolysin. PUBMED:1352512 EPMC:1352512

  2. Bateman A, Bycroft M; , J Mol Biol 2000;299:1113-1119.: The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD). PUBMED:10843862 EPMC:10843862

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018392

The LysM (lysin motif) domain is a small globular domain, approximately 40 amino acids long. It is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls [ PUBMED:1352512 ], but proteins involved in many other biological functions also contain this domain. It has been reported that the LysM domain functions as a signal for specific plant-bacteria recognition in bacterial pathogenesis [ PUBMED:15120137 ]. Many of these enzymes are modular and are composed of catalytic units linked to one or several repeats of LysM domains. LysM domains are found in bacteria and eukaryotes [ PUBMED:10369758 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan LysM (CL0187), which has the following description:

The LysM domain (Pfam:PF01476) is thought to be a general peptidoglycan-binding module. Although originally described in bacterial proteins, it has been also found in some eukaryotic sequences. It takes up a beta-alpha-alpha-beta conformation, with the beta strands forming an antiparallel beta sheet and the two alpha helices packing on one side of this sheet [1].

The clan contains the following 7 members:

gp37_C LysM OapA Phage-Gp8 Phage_gp53 Phage_tail_X T4_gp9_10


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Bateman A
Previous IDs: PG_binding_2;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 155
Number in full: 58761
Average length of the domain: 44.50 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 15.30 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.9 11.8
Trusted cut-off 20.9 11.8
Noise cut-off 20.8 11.7
Model length: 44
Family (HMM) version: 22
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Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the LysM domain has been found. There are 105 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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