NAR Molecular Biology Database Collection entry number 177
Neil D. Rawlings, Alan J. Barrett and Alex Bateman
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
Proteolytic enzymes, commonly termed proteases, but known scientifically as peptidases, are of enormous importance in human health, disease and technology. The MEROPS database provides a wealth of information about peptidases to the many scientists working on them in academia and industry. The database is organised around a structural classification of peptidases in which the enzymes are grouped into families on the basis of amino acid sequence homology. The families are further assembled into clans in the light of evidence (usually from similarities in tertiary structure) that they share common ancestry. The database contains four major types of documents: PepCards, FamCards, ClanCards and SpecCards, each giving information on a single peptidase, family, clan or organism, respectively. Access to the Card files is through links from indexes, or by online searches, and each of them gives information on classification and nomenclature as well as an interface to entries in other databases. Each PepCard includes data for human and mouse genetics, and links to the nucleic acid and amino acid sequences. If tertiary structural coordinates have been deposited, PDB entries are listed, and usually a rendered molecular image is provided. There is a PepCard even for a peptidase that cannot yet be assigned to a family (because no complete amino acid sequence is available) so long as it has been characterised biochemically. A FamCard includes links to other databases of sequence motifs and secondary and tertiary structure, a protein sequence alignment for the peptidase units of members of the family and a tree showing how the members of the family are related. The sequence alignments are annotated to highlight catalytic residues, disulfide bridges, carbohydrate attachment sites and transmembrane domains. Each FamCard includes a diagram showing distribution of homologues amongst completely sequenced genomes. Each ClanCard includes a diagram showing conservation of amino acid sequence around catalytic residues. Each SpecCard includes an abbreviated taxonomy, and a list of all the peptidases known from the species. The FamCards and ClanCards also show the distribution of peptidases in the group across the major kingdoms of living creatures. Each PepCard, FamCard and ClanCard includes literature references with links to Medline. Online searches provide rapid navigation of the database and the user can search for a peptidase by its name (partial or complete) or by a known accession number in a database such as SwissProt, TrEMBL, PIR, EMBL/GenBank and PDB. The user can also retrieve all the peptidases assigned to a specified human or mouse chromosome, and, for any given family or clan, may find all the peptidases for which structural coordinates have been deposited. Amongst the forms of biochemical information is data on the specificity of peptidases, accessed by additional online searches. A collection of known cleavage sites in synthetic substrates, peptides and proteins can be searched by providing the name of a substrate or peptidase, or by filling substrate specificity subsites. The database is maintained by a team consisting of N. D. Rawlings, D. P. Tolle and A. J. Barrett.
Supported by the Medical Research Council (UK) and the Biotechnology and Biological Sciences Research Council (UK).
Category: Protein sequence databases
Subcategory: Databases of individual protein families
Go to the abstract in the NAR 2010 Database Issue.
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