A large and accurate collection of peptidase cleavages in the MEROPS database

Rawlings, Neil D.

There are 202 peptidases that show a preference, of which 13 show a preference at all eight sites, 13 for seven sites, five for six sites, three for five sites, eight for four sites, 23 for three sites, 49 for two sites and 88 for one site. unwelcome amino acid near a cleavage site. Only the peroxisomal transit peptide peptidase shows a preference for cysteine binding to the S2 and S1 pockets. Tryptophan is also rare around cleavage sites, with only tryptophanyl aminopeptidase (M9A.008, a preference in the S1 pocket) and mast cell peptidase 4 (Rattus) (S01.005, in the S2 pocket) showing a preference; however, this may have more to do with the fact that tryptophan is the rarest of the amino acids. Asparagine is also very rare in the proximity of a cleavage site, one of the few examples being the specialist peptidase legumain (C13.006) which only cleaves asparaginyl bonds (33) . Histidine is also a rare preference, with only three peptidases showing any preference for it, namely chymosin (A01.006; S4), carnosine dipeptidase I (M20.006; S1 0 ) and Xaa-methyl-His dipeptidase (M20.013; S1 0 ). Methionine is also not preferred by most peptidases, exceptions being methionyl aminopeptidases (M24.001, M24.002), where the preference is as expected for methionine binding in the S1 pocket, some members of the peptidase Clp family (S14) and the unsequenced Met-Xaa dipeptidase (M9B.004). The gpr peptidase (A25.001) shows a preference for Met binding to S4. The commonest preference is for arginine binding to the S1 pocket, which occurs in over fifty peptidases. However, arginine is relatively rare outside the P1 position. There are peptidases that show a preference for Gly, Pro and Val for every binding pocket in the range S4-S4 0 . Peptidases showing unique preferences are listed in Table 3 .