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632  structures 6885  species 0  interactions 43467  sequences 557  architectures

Family: Peptidase_S9 (PF00326)

Summary: Prolyl oligopeptidase family

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 annotation information from the InterPro database.

InterPro entry IPR001375

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes [ PUBMED:7845208 ]. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence [ PUBMED:7845208 ]. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases [ PUBMED:7845208 ].

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base [ PUBMED:7845208 ]. The geometric orientations of the catalytic residues are similar between families, despite different protein folds [ PUBMED:7845208 ]. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [ PUBMED:7845208 , PUBMED:8439290 ].

This domain covers the active site serine of the serine peptidases belonging to MEROPS peptidase family S9 (prolyl oligopeptidase family, clan SC). The protein fold of the peptidase domain for members of this family resembles that of serine carboxypeptidase D, the type example of clan SC. Examples of protein families containing this domain are:

  • Prolyl endopeptidase ( EC ) (PE) (also called post-proline cleaving enzyme). PE is an enzyme that cleaves peptide bonds on the C-terminal side of prolyl residues. The sequence of PE has been obtained from a mammalian species (pig) and from bacteria (Flavobacterium meningosepticum and Aeromonas hydrophila); there is a high degree of sequence conservation between these sequences.
  • Escherichia coli protease II ( EC ) (oligopeptidase B) (gene prtB) which cleaves peptide bonds on the C-terminal side of lysyl and argininyl residues.
  • Dipeptidyl peptidase IV ( EC ) (DPP IV). DPP IV is an enzyme that removes N-terminal dipeptides sequentially from polypeptides having unsubstituted N-termini provided that the penultimate residue is proline.
  • Saccharomyces cerevisiae (Baker's yeast) vacuolar dipeptidyl aminopeptidases A and B (DPAP A and DPAP B), encoded by the STE13 and DAP2 genes respectively. DPAP A is responsible for the proteolytic maturation of the alpha-factor precursor.
  • Acylamino-acid-releasing enzyme ( EC ) (acyl-peptide hydrolase). This enzyme catalyses the hydrolysis of the amino-terminal peptide bond of an N-acetylated protein to generate a N-acetylated amino acid and a protein with a free amino-terminus.

These proteins belong to MEROPS peptidase families S9A, S9B and S9C.

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...

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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 and the UniProtKB 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
(58)
Full
(43467)
Representative proteomes UniProt
(158952)
RP15
(5925)
RP35
(18721)
RP55
(41100)
RP75
(68069)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(58)
Full
(43467)
Representative proteomes UniProt
(158952)
RP15
(5925)
RP35
(18721)
RP55
(41100)
RP75
(68069)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(58)
Full
(43467)
Representative proteomes UniProt
(158952)
RP15
(5925)
RP35
(18721)
RP55
(41100)
RP75
(68069)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: Prosite
Previous IDs: Prolyl_oligopep;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 58
Number in full: 43467
Average length of the domain: 195.30 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 29.72 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.6 22.6
Trusted cut-off 22.6 22.6
Noise cut-off 22.5 22.5
Model length: 212
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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

Selections

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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 Peptidase_S9 domain has been found. There are 632 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A096RDK9 View 3D Structure Click here
A0A0C4DHM8 View 3D Structure Click here
A0A0G2L866 View 3D Structure Click here
A0A0P0VHT5 View 3D Structure Click here
A0A0R0ERN7 View 3D Structure Click here
A0A0R0FXW8 View 3D Structure Click here
A0A0R0GGG0 View 3D Structure Click here
A0A0R0GNR8 View 3D Structure Click here
A0A0R0HYJ0 View 3D Structure Click here
A0A0R0IVG1 View 3D Structure Click here
A0A0R0JDW0 View 3D Structure Click here
A0A0R0KWG6 View 3D Structure Click here
A0A0R0L7B5 View 3D Structure Click here
A0A0R4ISU8 View 3D Structure Click here
A0A0R4IZS8 View 3D Structure Click here
A0A1D6E3C1 View 3D Structure Click here
A0A1D6ER97 View 3D Structure Click here
A0A1D6ER99 View 3D Structure Click here
A0A1D6F149 View 3D Structure Click here
A0A1D6GQN1 View 3D Structure Click here
A0A1D6H4R4 View 3D Structure Click here
A0A1D6JRD1 View 3D Structure Click here
A0A1D6KV33 View 3D Structure Click here
A0A1D6LLT2 View 3D Structure Click here
A0A1D6NS68 View 3D Structure Click here
A0A1D6NS94 View 3D Structure Click here
A0A1D6QK76 View 3D Structure Click here
A0A1D8PNK0 View 3D Structure Click here
A0A1P8ATN7 View 3D Structure Click here
A0A1P8AW81 View 3D Structure Click here
A0A2R8QP51 View 3D Structure Click here
A0A2R8QSL0 View 3D Structure Click here
A2RVG6 View 3D Structure Click here
A4HSS5 View 3D Structure Click here
A4HTZ8 View 3D Structure Click here
A4ICB5 View 3D Structure Click here
A4IDL6 View 3D Structure Click here
B0R1C4 View 3D Structure Click here
B8JJX2 View 3D Structure Click here
D3ZHQ1 View 3D Structure Click here