Summary: LysM domain
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "LysM domain". More...
LysM domain Edit Wikipedia article
| LysM domain | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 | |||||||||
| Identifiers | |||||||||
| Symbol | LysM | ||||||||
| Pfam | PF01476 | ||||||||
| InterPro | IPR000644 | ||||||||
| SMART | LysM | ||||||||
| PROSITE | PS51782 | ||||||||
| SCOPe | 1e0g / SUPFAM | ||||||||
| CDD | cd00118 | ||||||||
| Membranome | 1306 | ||||||||
| |||||||||
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
References
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
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
-
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
-
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
| SCOOP: | CVNH Glyco_hydro_18 Lipase_GDSL OapA Phage_tail_X |
| Similarity to PfamA using HHSearch: | OapA |
External database links
| SCOP: | 1e0g |
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...
Loading domain graphics...
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_10Alignments
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...
View options
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
| Seed (155) |
Full (58761) |
Representative proteomes | UniProt (248095) |
||||
|---|---|---|---|---|---|---|---|
| RP15 (8182) |
RP35 (27945) |
RP55 (55843) |
RP75 (92893) |
||||
| Jalview | |||||||
| HTML | |||||||
| PP/heatmap | 1 | ||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
Download options
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
| Seed (155) |
Full (58761) |
Representative proteomes | UniProt (248095) |
||||
|---|---|---|---|---|---|---|---|
| RP15 (8182) |
RP35 (27945) |
RP55 (55843) |
RP75 (92893) |
||||
| Raw Stockholm | |||||||
| Gzipped | |||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
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.
Note: You can also download the data file for the tree.
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
| 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
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
| Model details: |
|
||||||||||||
| Model length: | 44 | ||||||||||||
| Family (HMM) version: | 22 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
Archea
|
Eukaryota
|
Bacteria
|
Other sequences
|
Viruses
|
Unclassified
|
Viroids
|
Unclassified sequence
|
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
Structures
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.
Loading structure mapping...
AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
