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MEROPS: the peptidase database.

Rawlings ND, Morton FR, Kok CY, Kong J, Barrett AJ - Nucleic Acids Res. (2007)

Bottom Line: Peptidases (proteolytic enzymes or proteases), their substrates and inhibitors are of great relevance to biology, medicine and biotechnology.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.

View Article: PubMed Central - PubMed

Affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. ndr@sanger.ac.uk

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.

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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.
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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.

Mentions: The MEROPS collection of cleavages in natural and synthetic substrates now exceeds 7000. For each cleavage we store up to four residues on either side of the scissile bond (residues P4–P4′). For any peptidase with more than ten known cleavages we now present a display that gives an indication of the amino acids preferred at its substrate-binding sites. This display uses the WebLogo software (7). For the purposes of this display, the eight residues P4–P4′ for all substrates of a peptidase are considered to be an alignment. The observed frequency of amino acids at each position is calculated as a bit score, with the maximum possible score being 4.32 bits. At each position, the single-letter code of an amino acid is shown if the bit score exceeds 0.1, and the height of the letter is proportional to the bit score. Acidic residues are shown in red, basic in blue, hydrophobic residues in black and others in green. Figure 1 shows the cleavage site sequence logo for caspase-3. The logo shows an absolute requirement for aspartate in P1 (position 4) and a preference for aspartate in P4, and this specificity has been confirmed by experimentation (8).Figure 1.


MEROPS: the peptidase database.

Rawlings ND, Morton FR, Kok CY, Kong J, Barrett AJ - Nucleic Acids Res. (2007)

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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238837&req=5

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.
Mentions: The MEROPS collection of cleavages in natural and synthetic substrates now exceeds 7000. For each cleavage we store up to four residues on either side of the scissile bond (residues P4–P4′). For any peptidase with more than ten known cleavages we now present a display that gives an indication of the amino acids preferred at its substrate-binding sites. This display uses the WebLogo software (7). For the purposes of this display, the eight residues P4–P4′ for all substrates of a peptidase are considered to be an alignment. The observed frequency of amino acids at each position is calculated as a bit score, with the maximum possible score being 4.32 bits. At each position, the single-letter code of an amino acid is shown if the bit score exceeds 0.1, and the height of the letter is proportional to the bit score. Acidic residues are shown in red, basic in blue, hydrophobic residues in black and others in green. Figure 1 shows the cleavage site sequence logo for caspase-3. The logo shows an absolute requirement for aspartate in P1 (position 4) and a preference for aspartate in P4, and this specificity has been confirmed by experimentation (8).Figure 1.

Bottom Line: Peptidases (proteolytic enzymes or proteases), their substrates and inhibitors are of great relevance to biology, medicine and biotechnology.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.

View Article: PubMed Central - PubMed

Affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. ndr@sanger.ac.uk

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.

Show MeSH