Summary: Peptidase propeptide and YPEB domain
Peptidase propeptide and YPEB domain Provide feedback
This region is likely to have an protease inhibitory function (personal obs:C Yeats). This model is likely to miss some members of this family as the separation from signal to noise is not clear. The name is derived from Peptidase & Bacillus subtilis YPEB.
McIver KS, Kessler E, Ohman DE; , Microbiology 2004;150:3969-3977.: Identification of residues in the Pseudomonas aeruginosa elastase propeptide required for chaperone and secretion activities. PUBMED:15583150 EPMC:15583150
Internal database links
|Similarity to PfamA using HHSearch:||PepSY_2|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR025711
This domain is likely to have a protease inhibitory function. The name is derived from peptidase (M4) and YpeB of Bacillus subtilis [PUBMED:15124630].
This domain is found in the propeptide of members of the MEROPS peptidase family M4 (clan MA(E)), which contains the thermostable thermolysins (EC), and related thermolabile neutral proteases (bacillolysins) (EC) from various species of Bacillus. It is also in many non-peptidase proteins, including Bacillus subtilis YpeB protein - a regulator of SleB spore cortex lytic enzyme - and a large number of eubacterial and archaeal cell wall-associated and secreted proteins which are mostly annotated as 'hypothetical protein'.
Many extracellular bacterial proteases are produced as proenzymes. The propeptides usually have a dual function, i.e. they function as an intramolecular chaperone required for the folding of the polypeptide and as an inhibitor preventing premature activation of the enzyme. Analysis of the propeptide region of the M4 family of peptidases reveals two regions of conservation, the PepSY domain and a second domain, proximate to the N terminus, the FTP domain (INTERPRO), which is also found in isolation in the propeptide of eukaryotic peptidases belonging to MEROPS peptidase family M36.
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Gladomain, followed by two consecutive
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We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Yeats C|
|Author:||Bateman A, Yeats C, Rawlings N|
|Number in seed:||348|
|Number in full:||4684|
|Average length of the domain:||65.70 aa|
|Average identity of full alignment:||19 %|
|Average coverage of the sequence by the domain:||24.77 %|
|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:||14|
|Download:||download the raw HMM for this family|
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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 PepSY domain has been found. There are 4 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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