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20  structures 3793  species 0  interactions 14235  sequences 167  architectures

Family: SLT (PF01464)

Summary: Transglycosylase SLT domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

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.

Transglycosylase SLT domain Provide feedback

This family is distantly related to PF00062. Members are found in phages, type II, type III and type IV secretion systems (reviewed in [4]).

Literature references

  1. Koonin EV, Rudd KE; , Trends Biochem Sci 1994;19:106-107.: A conserved domain in putative bacterial and bacteriophage transglycosylases. PUBMED:8203016 EPMC:8203016

  2. 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

  3. 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

  4. Koraimann G; , Cell Mol Life Sci 2003;60:2371-2388.: Lytic transglycosylases in macromolecular transport systems of Gram-negative bacteria. PUBMED:14625683 EPMC:14625683


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.

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 Lysozyme (CL0037), which has the following description:

Barley chitinase, bacterial chitosanase, and lysozymes from phage and animals all hydrolyse related polysaccharides. The proteins little amino-acid similarity, but have a structurally invariant core consisting of two helices and a three-stranded beta-sheet which form the substrate-binding and catalytic cleft [1].

The clan contains the following 12 members:

Glucosaminidase Glyco_hydro_108 Glyco_hydro_19 Glyco_hydro_46 Lys Lysozyme_like Phage_lysozyme REGB_T4 SLT SLT_2 TraH_2 Transglycosylas

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(39)
Full
(14235)
Representative proteomes NCBI
(11652)
Meta
(3304)
RP15
(900)
RP35
(1993)
RP55
(2657)
RP75
(3295)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(39)
Full
(14235)
Representative proteomes NCBI
(11652)
Meta
(3304)
RP15
(900)
RP35
(1993)
RP55
(2657)
RP75
(3295)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(39)
Full
(14235)
Representative proteomes NCBI
(11652)
Meta
(3304)
RP15
(900)
RP35
(1993)
RP55
(2657)
RP75
(3295)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: Prodom_3175 (release 99.1)
Previous IDs: none
Type: Family
Author: Bateman A
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 121
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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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...

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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 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.

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