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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

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Domain organisation

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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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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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...


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.

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Curation and family details

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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


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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 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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