Summary: Germination protease
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Germination protease Provide feedback
No Pfam abstract.
Internal database links
|SCOOP:||Pex19 DUF1256 DUF3337 MRP-S26|
|Similarity to PfamA using HHSearch:||DUF1256|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005080
Metalloproteases are the most diverse of the four main types of protease, with more than 30 families identified to date [PUBMED:7674922]. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site [PUBMED:7674922]. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as abXHEbbHbc, where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases [PUBMED:7674922].
This group of metallopeptidases belong to MEROPS peptidase family A25 (gpr protease family, clan AE). These are tetrameric proteases that makes the rate-limiting first cut in the small, acid-soluble spore proteins (SASP) of Bacillus subtilis and related species during spore germination. The enzyme lacks clear homology to other known proteases. It processes its own amino end before becoming active to cleave SASPs.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||peptidase activity (GO:0008233)|
|Biological process||proteolysis (GO:0006508)|
|spore germination (GO:0009847)|
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This clan contains HybD-like domains. HybD is a nickel binding endopeptidase. Structural and sequences analyses have highlighted the presence of two highly conserved motifs that are shared with germination proteases and HybD . Members of this clan adopt an alpha/beta fold, comprised of a central beta sheet, surrounded by alpha helices.
The clan contains the following 3 members:DUF1256 HycI Peptidase_A25
We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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Curation and family details
|Previous IDs:||Peptidase_U3; Peptidase_M63;|
|Number in seed:||18|
|Number in full:||1777|
|Average length of the domain:||212.70 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||94.81 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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_A25 domain has been found. There are 2 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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