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105  structures 7977  species 0  interactions 58761  sequences 1259  architectures

Family: LysM (PF01476)

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
PDB 1e0g EBI.jpg
Identifiers
SymbolLysM
PfamPF01476
InterProIPR000644
SMARTLysM
PROSITEPS51782
SCOPe1e0g / SUPFAM
CDDcd00118
Membranome1306

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

References

  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.

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

  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

Alignments

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)
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HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(155)
Full
(58761)
Representative proteomes UniProt
(248095)
RP15
(8182)
RP35
(27945)
RP55
(55843)
RP75
(92893)
Alignment:
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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 Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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 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
Download: download the raw HMM for this family

Species distribution

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

Selections

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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.

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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.

Protein Predicted structure External Information
A0A0B4K620 View 3D Structure Click here
A0A0P0V3S8 View 3D Structure Click here
A0A0P0V8Z1 View 3D Structure Click here
A0A0R0EC15 View 3D Structure Click here
A0A0R0F3A2 View 3D Structure Click here
A0A0R0F3G4 View 3D Structure Click here
A0A0R0GDN0 View 3D Structure Click here
A0A0R0GJZ6 View 3D Structure Click here
A0A0R0GJZ6 View 3D Structure Click here
A0A0R0L5N1 View 3D Structure Click here
A0A0R0LHZ4 View 3D Structure Click here
A0A1D6FJ52 View 3D Structure Click here
A0A1D6GP29 View 3D Structure Click here
A0A1D6H4H3 View 3D Structure Click here
A0A1D6HG05 View 3D Structure Click here
A0A1D6HW13 View 3D Structure Click here
A0A1D6JLC8 View 3D Structure Click here
A0A1D6JMW2 View 3D Structure Click here
A0A1D6JMW2 View 3D Structure Click here
A0A1D6JU71 View 3D Structure Click here
A0A1D6JU71 View 3D Structure Click here
A0A1D6JU71 View 3D Structure Click here
A0A1D6K716 View 3D Structure Click here
A0A1D6KSL3 View 3D Structure Click here
A0A1D6L0I7 View 3D Structure Click here
A0A1D6LUX5 View 3D Structure Click here
A0A1D6LUX5 View 3D Structure Click here
A0A1D6N9U5 View 3D Structure Click here
A0A1D6NC92 View 3D Structure Click here
A0A1D6NMX9 View 3D Structure Click here
A0A1D6NZG2 View 3D Structure Click here
A0A1D6QMA0 View 3D Structure Click here
A0A2R8QKC7 View 3D Structure Click here
A4HWW7 View 3D Structure Click here
A4HWW7 View 3D Structure Click here
A4I8L7 View 3D Structure Click here
A5JYU6 View 3D Structure Click here
A8R7E6 View 3D Structure Click here
B6SWT1 View 3D Structure Click here
B7ZXR1 View 3D Structure Click here
B7ZYI9 View 3D Structure Click here
B7ZYI9 View 3D Structure Click here
B9F1U2 View 3D Structure Click here
B9GB49 View 3D Structure Click here
B9GB49 View 3D Structure Click here
C0PJ37 View 3D Structure Click here
C0PNW8 View 3D Structure Click here
C0PNW8 View 3D Structure Click here
C6THY0 View 3D Structure Click here
D0UTL4 View 3D Structure Click here
D0UTL7 View 3D Structure Click here
F1LWN1 View 3D Structure Click here
F1R068 View 3D Structure Click here
F4IB81 View 3D Structure Click here
H2L003 View 3D Structure Click here
I1JB35 View 3D Structure Click here
I1JCT5 View 3D Structure Click here
I1JCT5 View 3D Structure Click here
I1JIK3 View 3D Structure Click here
I1JQ00 View 3D Structure Click here
I1JZ72 View 3D Structure Click here
I1JZ72 View 3D Structure Click here
I1K380 View 3D Structure Click here
I1K380 View 3D Structure Click here
I1KA91 View 3D Structure Click here
I1KA91 View 3D Structure Click here
I1KGI2 View 3D Structure Click here
I1KII7 View 3D Structure Click here
I1KQ51 View 3D Structure Click here
I1KXB8 View 3D Structure Click here
I1L3F5 View 3D Structure Click here
I1L3F6 View 3D Structure Click here
I1L6P2 View 3D Structure Click here
I1L9B7 View 3D Structure Click here
I1LHL9 View 3D Structure Click here
I1LIS3 View 3D Structure Click here
I1LZI6 View 3D Structure Click here
I1M5G4 View 3D Structure Click here
I1M8G4 View 3D Structure Click here
I1MI67 View 3D Structure Click here
I1MQ37 View 3D Structure Click here
I1N7P2 View 3D Structure Click here
I1NAL6 View 3D Structure Click here
I1NCX7 View 3D Structure Click here
I1NIZ6 View 3D Structure Click here
I3ISS4 View 3D Structure Click here
I6YA32 View 3D Structure Click here
K7L2M0 View 3D Structure Click here
K7L566 View 3D Structure Click here
K7L7S5 View 3D Structure Click here
K7LC82 View 3D Structure Click here
K7LG03 View 3D Structure Click here
K7LGK8 View 3D Structure Click here
K7M3U3 View 3D Structure Click here
K7M924 View 3D Structure Click here
K7MIN1 View 3D Structure Click here
K7MK21 View 3D Structure Click here
K7MNT9 View 3D Structure Click here
K7MUF0 View 3D Structure Click here
K7WFN8 View 3D Structure Click here
K7WFN8 View 3D Structure Click here
O02055 View 3D Structure Click here
O16237 View 3D Structure Click here
O16237 View 3D Structure Click here
O16237 View 3D Structure Click here
O16237 View 3D Structure Click here
O16237 View 3D Structure Click here
O16237 View 3D Structure Click here
O16237 View 3D Structure Click here
O16237 View 3D Structure Click here
O16237 View 3D Structure Click here
O16237 View 3D Structure Click here
O16237 View 3D Structure Click here
O16237 View 3D Structure Click here
O22808 View 3D Structure Click here
O23006 View 3D Structure Click here
O23006 View 3D Structure Click here
O64825 View 3D Structure Click here
O64825 View 3D Structure Click here
P02976 View 3D Structure Click here
P0ADA3 View 3D Structure Click here
P0ADE6 View 3D Structure Click here
P0AEZ7 View 3D Structure Click here
P0AEZ7 View 3D Structure Click here
P0AFS9 View 3D Structure Click here
P75954 View 3D Structure Click here
P76193 View 3D Structure Click here
P9WM39 View 3D Structure Click here
P9WM39 View 3D Structure Click here
P9WM39 View 3D Structure Click here
Q0DX82 View 3D Structure Click here
Q0DX82 View 3D Structure Click here
Q0IZU8 View 3D Structure Click here
Q0IZU8 View 3D Structure Click here
Q2FYF1 View 3D Structure Click here
Q2G0D4 View 3D Structure Click here
Q2G0D4 View 3D Structure Click here
Q2G0U9 View 3D Structure Click here
Q2G0U9 View 3D Structure Click here
Q2G0U9 View 3D Structure Click here
Q2G278 View 3D Structure Click here
Q2R2M3 View 3D Structure Click here
Q46798 View 3D Structure Click here
Q4CM37 View 3D Structure Click here
Q4CM37 View 3D Structure Click here
Q4CS31 View 3D Structure Click here
Q4CS31 View 3D Structure Click here
Q4D6W9 View 3D Structure Click here
Q4DEM5 View 3D Structure Click here
Q4DEM5 View 3D Structure Click here
Q4KMM3 View 3D Structure Click here
Q4V8B0 View 3D Structure Click here
Q54BN6 View 3D Structure Click here
Q54DD6 View 3D Structure Click here
Q54PL5 View 3D Structure Click here
Q54PL5 View 3D Structure Click here
Q54PL6 View 3D Structure Click here
Q54VE7 View 3D Structure Click here
Q55BK6 View 3D Structure Click here
Q5HZA4 View 3D Structure Click here
Q5M836 View 3D Structure Click here
Q67UE8 View 3D Structure Click here
Q67UE8 View 3D Structure Click here
Q69T51 View 3D Structure Click here
Q69TY8 View 3D Structure Click here
Q6DEF4 View 3D Structure Click here
Q6DFV7 View 3D Structure Click here
Q6IQA2 View 3D Structure Click here
Q6NPN4 View 3D Structure Click here
Q6NPN4 View 3D Structure Click here
Q7K4J7 View 3D Structure Click here
Q7KWK0 View 3D Structure Click here
Q7XD97 View 3D Structure Click here
Q7Z3D4 View 3D Structure Click here
Q851T1 View 3D Structure Click here
Q8H095 View 3D Structure Click here
Q8H8C7 View 3D Structure Click here
Q8H8C7 View 3D Structure Click here
Q8IV50 View 3D Structure Click here
Q8N573 View 3D Structure Click here
Q8NI08 View 3D Structure Click here
Q8VYP8 View 3D Structure Click here
Q93ZH0 View 3D Structure Click here
Q93ZH0 View 3D Structure Click here
Q94298 View 3D Structure Click here
Q94298 View 3D Structure Click here
Q94298 View 3D Structure Click here
Q94298 View 3D Structure Click here
Q94298 View 3D Structure Click here
Q961C8 View 3D Structure Click here
Q96S90 View 3D Structure Click here
Q99LE3 View 3D Structure Click here
Q9D0E3 View 3D Structure Click here
Q9D7V2 View 3D Structure Click here
Q9FZ32 View 3D Structure Click here
Q9LXI6 View 3D Structure Click here
Q9SGI7 View 3D Structure Click here
Q9W4G8 View 3D Structure Click here
Q9ZNI1 View 3D Structure Click here