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, 40 (Database issue), D343-50

MEROPS: The Database of Proteolytic Enzymes, Their Substrates and Inhibitors

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MEROPS: The Database of Proteolytic Enzymes, Their Substrates and Inhibitors

Neil D Rawlings et al. Nucleic Acids Res.

Abstract

Peptidases, 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 database has hierarchical classifications in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. The database has been expanded to include proteolytic enzymes other than peptidases. Special identifiers for peptidases from a variety of model organisms have been established so that orthologues can be detected in other species. A table of predicted active-site residue and metal ligand positions and the residue ranges of the peptidase domains in orthologues has been added to each peptidase summary. New displays of tertiary structures, which can be rotated or have the surfaces displayed, have been added to the structure pages. New indexes for gene names and peptidase substrates have been made available. Among the enhancements to existing features are the inclusion of small-molecule inhibitors in the tables of peptidase-inhibitor interactions, a table of known cleavage sites for each protein substrate, and tables showing the substrate-binding preferences of peptidases derived from combinatorial peptide substrate libraries.

Figures

Figure 1.
Figure 1.
Sequence features display. The sequence features are shown for orthologues of thimet oligopeptidase.
Figure 2.
Figure 2.
Displays of tertiary structure. The Structure page for thermolysin (M04.001) is shown. The table provides the cross-reference to the PDB entry, source organism, resolution, a comment and a description of the elements displayed in the images below. The image on the left-hand side is a rendered Richardson image generated using the programs RasMol (22), Molscript (23) and Render (24). The image on the right shows the surface of the molecule using the AstexViewer. This image can be rotated in any direction by the user, and the surface hidden by clicking the ‘hide surface’ button. The third image shows secondary structure, active-site residues and metal ligands as they appear in the protein sequence.
Figure 3.
Figure 3.
Growth in number of determined putative peptidase sequences. The curves shown are (A) all sequences, (B) sequences assigned to identifiers, (C) sequences assigned to identifiers excluding model organisms, (D) all identifiers and (E) identifiers excluding model organisms.
Figure 4.
Figure 4.
Display of cleavages in a protein substrate. Known cleavages in the DSPP600 protein from pig are shown. The full sequence is shown at the top with cleaved bonds indicated by the ‘dagger’ symbol. More details of each cleavage are shown in the table beneath.
Figure 5.
Figure 5.
Specificity from combinatorial peptide libraries. The amino acid preferences within each substrate-binding pocket (labeled P4–P4′) are shown for experiments using combinatorial libraries of peptide substrates for the peptidase papain.

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References

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    1. Rawlings ND, Tolle DP, Barrett AJ. Evolutionary families of peptidase inhibitors. Biochem. J. 2004;378:705–716. - PMC - PubMed

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