Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
1  structure 49  species 0  interactions 67  sequences 13  architectures

Family: Peptidase_M66 (PF10462)

Summary: Peptidase M66

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.

Peptidase M66 Provide feedback

This family of metallopeptidases contains StcE, a virulence factor found in Shiga toxigenic Escherichia coli organisms. StcE peptidase cleaves C1 esterase inhibitor [1].

Literature references

  1. Lathem WW, Grys TE, Witowski SE, Torres AG, Kaper JB, Tarr PI, Welch RA; , Mol Microbiol. 2002;45:277-288.: StcE, a metalloprotease secreted by Escherichia coli O157:H7, specifically cleaves C1 esterase inhibitor. PUBMED:12123444 EPMC:12123444


This tab holds annotation information from the InterPro database.

InterPro entry IPR019503

The peptidase family M66 domain is a zinc metalloprotease found in:

  • Enterohemorrhagic Escherichia coli (EHEC) neutral zinc metalloprotease StcE.
  • Aeromonas hydrophila ToxR-regulated lipoprotein TagA.
  • Vibrio cholerae ToxR-activated gene A lipoprotein TagA.

The peptidase family M66 domain adopts a characteristic mixed alpha+beta and a conserved Met-turn, features that place it within the metzincin superfamily of metalloproteases including astacins, ADAMs (a disintegrin and metalloprotease) and matrixins. Notably, a central substrate-binding cleft containing the active site separates the peptidase family M66 domain into two subdomains SD1 and SD2. SD1 consists of a twisted beta sheet packed on both sides by three helices. A sharp turn introduced by a conserved Gly in the zinc-binding motif along the active site helix then leads to SD2, which, after a series of convoluted loops, terminates in an helix. The peptidase family M66 coordinates an essential zinc ion in the characteristic tetrahedral fashion and possesses the extended zinc-binding motif HExxHxxGxxH [PUBMED:22483117].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

Loading domain graphics...

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, the UniProtKB sequence database, 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
(10)
Full
(67)
Representative proteomes UniProt
(434)
NCBI
(1413)
Meta
(20)
RP15
(30)
RP35
(59)
RP55
(90)
RP75
(173)
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(10)
Full
(67)
Representative proteomes UniProt
(434)
NCBI
(1413)
Meta
(20)
RP15
(30)
RP35
(59)
RP55
(90)
RP75
(173)
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
(10)
Full
(67)
Representative proteomes UniProt
(434)
NCBI
(1413)
Meta
(20)
RP15
(30)
RP35
(59)
RP55
(90)
RP75
(173)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Manual
Previous IDs: none
Type: Family
Author: Rawlings N, Mistry J
Number in seed: 10
Number in full: 67
Average length of the domain: 253.10 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 30.99 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.4
Model length: 306
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Loading sunburst data...

Tree controls

Hide

The 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 Peptidase_M66 domain has been found. There are 1 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...