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

Rawlings, Neil D.

The preference for individual amino acids is shown in Table 2 . It is clear from the table that cysteine is an S3 S2 S1 S1' S2' S3' A count is made whenever an amino acid occurs in one binding pocket in 40% or more of the substrates. There are 15 peptidases that have a preference for two amino acids in a binding pocket: walleye dermal sarcoma virus retropepsin (A02.063, Asn or Gln in S2), sapovirus 3C-like peptidase (C24.003, Glu or Gln in S1), SARS coronavirus picornain 3C-like peptidase (C30.005, Gly or Gln in S1), peptidyl-peptidase Acer (M02.002, Gly or Pro in S1), vimelysin (M04.010, Phe or Leu in S1), carboxypeptidase M (M14.006, Arg or Lys in S1 0 ), carboxypeptidase U (M14.009, Arg or Lys in S1 0 ), dactylysin (M9G.026, Leu or Phe in S1 0 ), chymase (S01.140, Phe or Tyr in S1), tryptase alpha (S01.143, Lys or Arg in S1), trypsin 1 (S01.151, Lys or Arg in S1), plasmin (S01.233, Lys or Arg in S1), flavivirin (S07.001, Lys or Arg in S2), dipeptidyl aminopeptidase A (S09.005, Ala or Pro in S1) and kumamolisin (S53, 004, Glu or Gly in S3). Many peptidases show a preference in more than one binding pocket. There are 13 peptidases with a preference for all eight binding pockets, another 13 with a preference in seven, five peptidases in six, three in five, eight in four, 24 in three, 47 in two and 89 in only one. The number of peptidases showing a preference for an amino acid in a binding site is shown. Only those 312 peptidases with 10 or more known substrate cleavages are included. An amino acid must occur at that position in 40% or more of substrates. Therefore, it is possible for two amino acids to be preferred in any one binding pocket, as is the case for trypsin 1 where there is a preference for either Lys (59% of substrates) or Arg (41%) in S1.