MEROPS: the peptidase database

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 a hierarchical classification 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 classification framework is used for attaching information at each level. An important focus of the database has become distinguishing one peptidase from another through identifying the specificity of the peptidase in terms of where it will cleave substrates and with which inhibitors it will interact. We have collected over 39,000 known cleavage sites in proteins, peptides and synthetic substrates. These allow us to display peptidase specificity and alignments of protein substrates to give an indication of how well a cleavage site is conserved, and thus its probable physiological relevance. While the number of new peptidase families and clans has only grown slowly the number of complete genomes has greatly increased. This has allowed us to add an analysis tool to the relevant species pages to show significant gains and losses of peptidase genes relative to related species.

Figure 1.

A summary analysis for the peptidase homologues from the completely sequence genome of the archaean Cenarchium symbiosum. The figure is taken from the species page in the MEROPS website. A list of peptidase homologues arranged alphabetically by MEROPS identifier is shown in the top panel and the genome analysis is shown at the bottom of the page. The peptidase portion of the proteome of C. symbiosum (12) has been compared with those of 17 other species from the class Thermoprotei. There are unexpected absences of members of peptidase families C26, C44, M38, M48, S9 and U62, and an unexpected presence of a homologue from peptidase family M3. Of the species compared, C. symbiosum had the fewest number of peptidase family M20 homologues, but the most for peptidase family S8. The large number of absent peptidase families may indicates that this endosymbiont genome is degenerate.

Figure 2.

The domain architectures for holotypes in peptidase subfamily M12B. The figure is taken from the domain architecture page for peptidase subfamily M12B (the adamalysins) from the MEROPS website. The arrangement of regions and domains are shown for a selection of holotype proteins. The structures are arranged from the top of the page in order of MEROPS identifier. The name of the peptidase is given on the left-hand side. All the structures are drawn to the same scale. The sequence length is denoted by the pale blue line. Regions and domains as determined by MEROPS, the Pfam database and Swiss-Prot entries in the UniProt database (7), are shown as coloured rectangles on this bar. The domains that are classified within the MEROPS database are shown as slightly larger boxes, in green for a peptidase unit and grey for an inhibitor unit (not shown). The MEROPS identifier is displayed in the centre in black text. Domains derived from the Pfam database (13) are shown as smaller rectangles in crimson, with the domain name in white text. On clicking on the box, the user will be taken to the relevant Pfam entry. Regions from Swiss-Prot include signal peptides and transmembrane regions (shown as even smaller boxes in black) and propeptides (in dark grey). Active site residues (red ‘lollipops’) and metal ligands (blue ‘lollipops’) are shown along the bottom edge. Carbohydrate-binding residues (orange ‘lollipops’) and disulphide bridges (black lines connecting the cysteines) are shown along the top edge. Mouse-over text gives details of the feature displayed in all cases.

Figure 3.

An example of a substrate protein sequence alignment. The figure is taken from the MEROPS website and shows a protein sequence alignment of human C–X–C motif chemokine 11 and its close homologues, showing conservation around the matrix metallopeptidase 8 (MMP8, M10.002) cleavage site at residue 84 (14). The sequence of the protein in which the cleavage was discovered is highlighted in green. Residues are numbered according to this sequence. The MEROPS identifiers of the peptidases known to cleave this substrate are shown below the residue numbers on the left. The arrows next to each MEROPS identifier show the residue range of the peptide fragment used in the experiment, which in most cases is the mature protein without the signal peptide (the signal peptidase cleavage at residue 22 is shown). A question mark instead of an angled bracket would indicate that the terminus has not been determined. The scissile bond symbol () shows where cleavage occurs. Each symbol can be clicked, and the alignment will be highlighted to show conservation around that cleavage site. Four residues either side of each cleavage site (P4–P4′) (6) are highlighted. Completely conserved residues are highlighted in orange. Although not shown in this example, a residue highlighted in pink would not be conserved, but the amino acid would have been observed in the same position in another MMP8 substrate. Ile84 in the sequence from the European ferret (Mustela putorius fero), labelled UniProt A8DBL7, is shown with a black background because isoleucine is unknown in this position for any MMP8 substrate. The last line shows the secondary structure: an alpha helix is shown as a series of ‘a’s highlighted in red, and a strand as a series of ‘b’s highlighted in green. This example shows that MMP8 is capable of cleaving this protein substrate within an alpha helix.

Figure 4.

Comparison of peptidase specificity. The figure shows a portion of a page from the MEROPS website. Peptidase preference for the amino acid proline is shown. The MEROPS identifiers and names of the peptidases are shown on the left, along with the number of substrate cleavages in the MEROPS collection. Where proline occurs in the same position in 40% or more of substrates, the cell is highlighted in green and the percentage of substrates with proline in this position is shown. Cells are only highlighted if 10 or more substrates are known for the peptidase. Where there can be no binding pocket to accommodate a substrate residue, for example in position P4, P3 and P2 for an aminopeptidase or P2′, P3′ and P4′ for a carboxypeptidase, these cells are highlighted in grey.