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.
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
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
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
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
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
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
|SCOOP:||Tannase PGAP1 DUF1749 DUF2305 DUF2920|
|Similarity to PfamA using HHSearch:||Peptidase_S9 Abhydrolase_1 Peptidase_S37 Hydrolase_4|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR008758
In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:
- Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
- Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases.
In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding.
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].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||serine-type peptidase activity (GO:0008236)|
|Biological process||proteolysis (GO:0006508)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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This catalytic domain is found in a very wide range of enzymes.
The clan contains the following 67 members:Abhydro_lipase Abhydrolase_1 Abhydrolase_2 Abhydrolase_3 Abhydrolase_4 Abhydrolase_5 Abhydrolase_6 Abhydrolase_7 Abhydrolase_8 Acyl_transf_2 Arb2 AXE1 BAAT_C Chlorophyllase Chlorophyllase2 COesterase Cutinase DLH DUF1057 DUF1100 DUF1350 DUF1400 DUF1749 DUF2048 DUF2235 DUF2305 DUF2424 DUF2920 DUF2974 DUF3089 DUF3141 DUF3530 DUF452 DUF676 DUF726 DUF818 DUF829 DUF900 DUF915 EHN Esterase Esterase_phd FSH1 Hydrolase_4 LCAT LIP Lipase Lipase_2 Lipase_3 Ndr PAF-AH_p_II Palm_thioest PE-PPE Peptidase_S10 Peptidase_S15 Peptidase_S28 Peptidase_S37 Peptidase_S9 PGAP1 PhaC_N PHB_depo_C PhoPQ_related Ser_hydrolase Tannase Thioesterase UPF0227 VirJ
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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Curation and family details
|Number in seed:||12|
|Number in full:||2459|
|Average length of the domain:||332.50 aa|
|Average identity of full alignment:||23 %|
|Average coverage of the sequence by the domain:||80.27 %|
|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:||8|
|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_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 seqence.
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