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InterPro-Version: 108.0
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{
"metadata": {
"accession": "IPR000667",
"entry_id": null,
"type": "family",
"go_terms": [
{
"identifier": "GO:0004185",
"name": "serine-type carboxypeptidase activity",
"category": {
"code": "F",
"name": "molecular_function"
}
},
{
"identifier": "GO:0006508",
"name": "proteolysis",
"category": {
"code": "P",
"name": "biological_process"
}
}
],
"source_database": "interpro",
"member_databases": {
"pfam": {
"PF02113": "D-Ala-D-Ala carboxypeptidase 3 (S13) family"
},
"panther": {
"PTHR30023": "D-ALANYL-D-ALANINE CARBOXYPEPTIDASE"
},
"ncbifam": {
"TIGR00666": "D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine endopeptidase"
},
"prints": {
"PR00922": "DADACBPTASE3"
}
},
"integrated": null,
"hierarchy": {
"accession": "IPR000667",
"name": "Peptidase S13, D-Ala-D-Ala carboxypeptidase C",
"type": "Family",
"children": []
},
"name": {
"name": "Peptidase S13, D-Ala-D-Ala carboxypeptidase C",
"short": "Peptidase_S13"
},
"description": [
{
"text": "<p>This family of serine peptidases belong to MEROPS peptidase family S13 (D-Ala-D-Ala carboxypeptidase C, clan SE). The active site residues occur in the motif SXXK.</p>\n\n<p>D-Ala-D-Ala carboxypeptidase C is involved in the metabolism of cell components [[cite:PUB00000120], [cite:PUB00035543]]; it is synthesised with a leader peptide to target it to the cell membrane [[cite:PUB00003576]]. After cleavage of the leader peptide, the enzyme is retained in the membrane by a C-terminal anchor [[cite:PUB00003576]]. There are three families of serine-type D-Ala-D-Ala peptidase (designated S11, S12 and S13), which are also known as low molecular weight penicillin-binding proteins [[cite:PUB00003576], [cite:PUB00035543]]. Family S13 comprises D-Ala-D-Ala peptidases that have sufficient sequence similarity around their active sites to assume a distant evolutionary relationship to other clan members; members of the S13 family also bind penicillin and have D-amino-peptidase activity. Proteases of family S11 have exclusive D-Ala-D-Ala peptidase activity, while some members of S12 are C beta-lactamases [[cite:PUB00003576]].</p>",
"llm": false,
"checked": false,
"updated": false
},
{
"text": "<p>Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes [[cite:PUB00003576]]. 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 [[cite:PUB00003576]]. 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 [[cite:PUB00003576]].</p>\r\n\r\n<p>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 [[cite:PUB00003576]]. The geometric orientations of the catalytic residues are similar between families, despite different protein folds [[cite:PUB00003576]]. 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) [[cite:PUB00003576], [cite:PUB00000522]].</p>",
"llm": false,
"checked": false,
"updated": false
}
],
"wikipedia": null,
"literature": {
"PUB00003576": {
"PMID": 7845208,
"ISBN": null,
"volume": "244",
"issue": null,
"year": 1994,
"title": "Families of serine peptidases.",
"URL": null,
"raw_pages": "19-61",
"medline_journal": "Methods Enzymol",
"ISO_journal": "Meth. Enzymol.",
"authors": [
"Rawlings ND",
"Barrett AJ."
],
"DOI_URL": "http://dx.doi.org/10.1016/0076-6879(94)44004-2"
},
"PUB00000522": {
"PMID": 8439290,
"ISBN": null,
"volume": "290 ( Pt 1)",
"issue": null,
"year": 1993,
"title": "Evolutionary families of peptidases.",
"URL": null,
"raw_pages": "205-18",
"medline_journal": "Biochem J",
"ISO_journal": "Biochem. J.",
"authors": [
"Rawlings ND",
"Barrett AJ."
],
"DOI_URL": "http://www.pubmedcentral.nih.gov/picrender.fcgi?tool=EBI&pubmedid=8439290&action=stream&blobtype=pdf"
},
"PUB00000120": {
"PMID": 1741619,
"ISBN": null,
"volume": "45",
"issue": null,
"year": 1991,
"title": "Serine beta-lactamases and penicillin-binding proteins.",
"URL": null,
"raw_pages": "37-67",
"medline_journal": "Annu Rev Microbiol",
"ISO_journal": "Annu. Rev. Microbiol.",
"authors": [
"Ghuysen JM."
],
"DOI_URL": "http://dx.doi.org/10.1146/annurev.mi.45.100191.000345"
},
"PUB00035543": {
"PMID": 16411754,
"ISBN": null,
"volume": "45",
"issue": "3",
"year": 2006,
"title": "Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics.",
"URL": null,
"raw_pages": "783-92",
"medline_journal": "Biochemistry",
"ISO_journal": "Biochemistry",
"authors": [
"Kishida H",
"Unzai S",
"Roper DI",
"Lloyd A",
"Park SY",
"Tame JR."
],
"DOI_URL": "http://dx.doi.org/10.1021/bi051533t"
}
},
"set_info": null,
"overlaps_with": [
{
"accession": "IPR012338",
"name": "Beta-lactamase/transpeptidase-like",
"type": "homologous_superfamily"
}
],
"counters": {
"subfamilies": 0,
"domain_architectures": 32,
"interactions": 0,
"matches": 24245,
"pathways": 2,
"proteins": 18035,
"proteomes": 9934,
"sets": 0,
"structural_models": {
"alphafold": 13333,
"bfvd": 0
},
"structures": 35,
"taxa": 15573
},
"entry_annotations": {
"alignment:seed": 9,
"alignment:full": 9070
},
"cross_references": {
"ec": {
"displayName": "ENZYME",
"description": "ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.",
"rank": 19,
"accessions": [
{
"accession": "3.4.16.4",
"url": "https://enzyme.expasy.org/EC/3.4.16.4"
}
]
}
},
"is_llm": false,
"is_reviewed_llm": false,
"is_updated_llm": false,
"representative_structure": {
"accession": "2ex2",
"name": "Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli"
}
}
}
