Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Jan;36(Database issue):D320-5.
doi: 10.1093/nar/gkm954. Epub 2007 Nov 8.

MEROPS: the peptidase database

Neil D Rawlings  1 , Fraser R Morton, Chai Yin Kok, Jun Kong, Alan J Barrett
Affiliations

MEROPS: the peptidase database

Neil D Rawlings et al. Nucleic Acids Res. 2008 Jan.

Abstract

Peptidases (proteolytic enzymes or proteases), their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these. The organizational principle of the database is a hierarchical classification in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families and in turn grouped into clans. Important additions to the database include newly written, concise text annotations for peptidase clans and the small molecule inhibitors that are outside the scope of the standard classification; displays to show peptidase specificity compiled from our collection of known substrate cleavages; tables of peptidase-inhibitor interactions; and dynamically generated alignments of representatives of each protein species at the family level. New ways to compare peptidase and inhibitor complements between any two organisms whose genomes have been completely sequenced, or between different strains or subspecies of the same organism, have been devised.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Cleavage site sequence logo showing specificity for caspase-3. Amino acids preferred in positions P4–P4′ are shown in single-letter code. The specificity is shown as a string where each position is separated by a forward slash character and multiple letters in a position indicate a wide specificity for these amino acids. The scissile bond is shown by a red cross symbol. In the diagram, the height of the letter is proportional to the number of cleavage sites in which it is present. Positions P4–P4′ are numbered one to eight, with the scissile bond between residues four and five. Caspase-3, like most caspases, has a preference for Asp in P1 and a majority of substrates also have Asp in P4.
Figure 2.
Figure 2.
Example SMI page. The summary page for the inhibitor pepstatin is shown.
Figure 3.
Figure 3.
Peptidase–inhibitor interactions for aprotinin.
Figure 4.
Figure 4.
Comparison between the peptidase complements of the human and the C. albicans genomes. Only the top and bottom portions of the table are shown.
See this image and copyright information in PMC

References

    1. Rawlings ND, Barrett AJ. Evolutionary families of peptidases. Biochem. J. 1993;290:205–218. - PMC - PubMed
    1. Rawlings ND, Tolle DP, Barrett AJ. Evolutionary families of peptidase inhibitors. Biochem. J. 2004;378:705–716. - PMC - PubMed
    1. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, et al. Pfam: clans, web tools and services. Nucleic Acids Res. 2006;34(Database issue):D247–D251. - PMC - PubMed
    1. Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 2004;32(Database issue):D226–D229. - PMC - PubMed
    1. Schechter I, Berger A. On the active site of proteases. 3. Mapping the active site of papain; specific peptide inhibitors of papain. Biochem. Biophys. Res. Commun. 1968;32:898–902. - PubMed

Publication types