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11  structures 1275  species 0  interactions 7230  sequences 147  architectures

Family: Peptidase_S28 (PF05577)

Summary: Serine carboxypeptidase S28

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Serine carboxypeptidase S28 Provide feedback

These serine proteases include several eukaryotic enzymes such as lysosomal Pro-X carboxypeptidase, dipeptidyl-peptidase II, and thymus-specific serine peptidase.

Literature references

  1. Skidgel RA, Erdos EG; , Immunol Rev 1998;161:129-141.: Cellular carboxypeptidases. PUBMED:9553770 EPMC:9553770

  2. Shariat-Madar Z, Mahdi F, Schmaier AH; , J Biol Chem 2002;277:17962-17969.: Identification and characterization of prolylcarboxypeptidase as an endothelial cell prekallikrein activator. PUBMED:11830581 EPMC:11830581

  3. Senten K, Van der Veken P, Bal G, De Meester I, Lambeir AM, Scharpe S, Bauvois B, Haemers A, Augustyns K; , Bioorg Med Chem Lett 2002;12:2825-2828.: Development of potent and selective dipeptidyl peptidase II inhibitors. PUBMED:12270155 EPMC:12270155

  4. Araki H, Li Y, Yamamoto Y, Haneda M, Nishi K, Kikkawa R, Ohkubo I; , J Biochem (Tokyo) 2001;129:279-288.: Purification, molecular cloning, and immunohistochemical localization of dipeptidyl peptidase II from the rat kidney and its identity with quiescent cell proline dipeptidase. PUBMED:11173530 EPMC:11173530

  5. Fukasawa KM, Fukasawa K, Higaki K, Shiina N, Ohno M, Ito S, Otogoto J, Ota N; , Biochem J 2001;353:283-290.: Cloning and functional expression of rat kidney dipeptidyl peptidase II. PUBMED:11139392 EPMC:11139392

  6. Carrier A, Wurbel MA, Mattei MG, Kissenpfennig A, Malissen M, Malissen B; , Immunogenetics 2000;51:984-986.: Chromosomal localization of two mouse genes encoding thymus-specific serine peptidase and thymus-expressed acidic protein. PUBMED:11003393 EPMC:11003393

  7. Bowlus CL, Ahn J, Chu T, Gruen JR; , Cell Immunol 1999;196:80-86.: Cloning of a novel MHC-encoded serine peptidase highly expressed by cortical epithelial cells of the thymus. PUBMED:10527559 EPMC:10527559


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008758

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 group of serine peptidases belong to MEROPS peptidase family S28 (clan SC). The predicted active site residues for members of this family and family S10 occur in the same order in the sequence: S, D, H.

These serine proteases include several eukaryotic enzymes such as lysosomal Pro-X carboxypeptidase, dipeptidyl-peptidase II, and thymus-specific serine peptidase [ PUBMED:10527559 , PUBMED:11003393 , PUBMED:11139392 , PUBMED:11173530 ].

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...

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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
(12)
Full
(7230)
Representative proteomes UniProt
(13291)
RP15
(1783)
RP35
(3921)
RP55
(5997)
RP75
(7651)
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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
(12)
Full
(7230)
Representative proteomes UniProt
(13291)
RP15
(1783)
RP35
(3921)
RP55
(5997)
RP75
(7651)
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
(12)
Full
(7230)
Representative proteomes UniProt
(13291)
RP15
(1783)
RP35
(3921)
RP55
(5997)
RP75
(7651)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Merops
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Studholme DJ
Number in seed: 12
Number in full: 7230
Average length of the domain: 318.80 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 77.52 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.9 19.9
Trusted cut-off 19.9 19.9
Noise cut-off 19.8 19.8
Model length: 434
Family (HMM) version: 14
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_S28 domain has been found. There are 11 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
A0A0R0FXY0 View 3D Structure Click here
A0A0R0H7D8 View 3D Structure Click here
A0A0R0JTP4 View 3D Structure Click here
A0A0R0JTP4 View 3D Structure Click here
A0A0R0KM72 View 3D Structure Click here
A0A0R0KRX0 View 3D Structure Click here
A0A0R0L1E8 View 3D Structure Click here
A0A0R0L358 View 3D Structure Click here
A0A1D6GJU0 View 3D Structure Click here
A0A1D6GN16 View 3D Structure Click here
A0A1D6HMG2 View 3D Structure Click here
A0A1D6HMG2 View 3D Structure Click here
A0A1D6JLE0 View 3D Structure Click here
A0A1D6KR27 View 3D Structure Click here
A0A1D6MN36 View 3D Structure Click here
A0A1D6NEM4 View 3D Structure Click here
A0A1D6P500 View 3D Structure Click here
A0A1D6P503 View 3D Structure Click here
A0A1D6P505 View 3D Structure Click here
A0A1D6P506 View 3D Structure Click here
A0A1D6Q5C1 View 3D Structure Click here
A0A1D6QC03 View 3D Structure Click here
A0A6H2EEF7 View 3D Structure Click here
A4VCL8 View 3D Structure Click here
B4F9I1 View 3D Structure Click here
D4AA31 View 3D Structure Click here
F1Q7G9 View 3D Structure Click here
F4J0D0 View 3D Structure Click here
G5EFJ8 View 3D Structure Click here
G5EFJ8 View 3D Structure Click here
I1J655 View 3D Structure Click here
I1JQ57 View 3D Structure Click here
I1LTP5 View 3D Structure Click here
I1MN82 View 3D Structure Click here
I1MVH2 View 3D Structure Click here
K7MZA3 View 3D Structure Click here
K7U741 View 3D Structure Click here
K7V4K2 View 3D Structure Click here
O02252 View 3D Structure Click here
O02252 View 3D Structure Click here
P34528 View 3D Structure Click here
P34610 View 3D Structure Click here
P34676 View 3D Structure Click here
P42785 View 3D Structure Click here
P90893 View 3D Structure Click here
Q18198 View 3D Structure Click here
Q19589 View 3D Structure Click here
Q19590 View 3D Structure Click here
Q1JPM1 View 3D Structure Click here
Q1PF50 View 3D Structure Click here
Q337C4 View 3D Structure Click here
Q3MHS0 View 3D Structure Click here
Q4CW86 View 3D Structure Click here
Q4DM56 View 3D Structure Click here
Q4DW34 View 3D Structure Click here
Q53ND8 View 3D Structure Click here
Q54CF7 View 3D Structure Click here
Q54D54 View 3D Structure Click here
Q54G47 View 3D Structure Click here
Q54GI7 View 3D Structure Click here
Q54H23 View 3D Structure Click here
Q54HT4 View 3D Structure Click here
Q54YD0 View 3D Structure Click here
Q555E5 View 3D Structure Click here
Q5CZT1 View 3D Structure Click here
Q5ZAM8 View 3D Structure Click here
Q67WZ5 View 3D Structure Click here
Q6DG46 View 3D Structure Click here
Q7TMR0 View 3D Structure Click here
Q7XCY0 View 3D Structure Click here
Q8SXS7 View 3D Structure Click here
Q93Z34 View 3D Structure Click here
Q94CC6 View 3D Structure Click here
Q9EPB1 View 3D Structure Click here
Q9ET22 View 3D Structure Click here
Q9FFC2 View 3D Structure Click here
Q9GRV9 View 3D Structure Click here
Q9GRV9 View 3D Structure Click here
Q9NQE7 View 3D Structure Click here
Q9QXE5 View 3D Structure Click here
Q9UHL4 View 3D Structure Click here
Q9VDX5 View 3D Structure Click here
Q9VDX6 View 3D Structure Click here
Q9VIM0 View 3D Structure Click here
Q9VS02 View 3D Structure Click here