Summary: Transglycosylase SLT domain
The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.
Transglycosylase SLT domain Provide feedback
Mushegian AR, Fullner KJ, Koonin EV, Nester EW; , Proc Natl Acad Sci U S A 1996;93:7321-7326.: A family of lysozyme-like virulence factors in bacterial pathogens of plants and animals. PUBMED:8692991 EPMC:8692991
Thunnissen AM, Rozeboom HJ, Kalk KH, Dijkstra BW; , Biochemistry 1995;34:12729-12737.: Structure of the 70-kDa soluble lytic transglycosylase complexed with bulgecin A. Implications for the enzymatic mechanism. PUBMED:7548026 EPMC:7548026
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR008258
Bacterial lytic transglycosylases degrade murein via cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine, with the concomitant formation of a 1,6-anhydrobond in the muramic acid residue. There are both soluble (Slt enzymes) and membrane-bound (Mlt enzymes) lytic transglycosylases that differ in size, sequence, activity, specificity and location. The multi-domain structure of the 70 Kd soluble lytic transglycosylase Slt70 is known [PUBMED:10452894]. Slt70 has 3 distinct domains, each rich in alpha helices: an N-terminal superhelical U-shaped domain (U-domain; INTERPRO), a superhelical linker domain (L-domain, INTERPRO), and a C-terminal catalytic domain (INTERPRO). Both the U- and L-domain share a similar superhelical structure. These two domains are connected, and together form a closed ring with a large central hole; the catalytic domain is packed on top of, and interacts with, this ring. The catalytic domain has a lysosome-like fold.
This entry represents the catalytic domain, which is structurally conserved in some membrane-bound lytic glycosylases and in bacteriophage transglycosylases, even though their sequences can differ considerably proteins [PUBMED:8203016]. The most conserved part of this domain is its N-terminal extremity that contains two conserved serines and a glutamate, which have been shown [PUBMED:8107871] to be involved in the catalytic mechanism. This family is distantly related to INTERPRO.
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||Prodom_3175 (release 99.1)|
|Number in seed:||39|
|Number in full:||14235|
|Average length of the domain:||115.80 aa|
|Average identity of full alignment:||22 %|
|Average coverage of the sequence by the domain:||28.70 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
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 SLT domain has been found. There are 20 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 seqence.
Loading structure mapping...