Mutational replacements in subtilisin 309

Abstract

The previous notion that the amino acid side chain at position 104 of subtilisins is involved in the binding of the side chain at position P4 of the substrate has becn invcstigated. The amino acid residue Val104 in subtilisin 309 has been replaced by Ala, Arg, Asp, Phei Ser, Trp and Tyr by site-directed mutagenesis. It is shown that the P4 specificity of this enzyme is not determined solely by the amino acid residue occupying position 104, as the enzyme exhibits a marked preference for aromatic groups in P4, regardless of the nature of the position-104 residue. With hydrophilic amino acid residues at this position, no involvement is seen in binding of either hydrophobic or hydrophilic amino acid residues at position P4 of the substrates. The substrate with Asp in P4 is an exception, as the preference for this substrate is increased dramatically by introduction of an arginine residue at position 104 in the enzyme, presumably due to a substrate-induced conformational change. However, when position 104 is occupied by hydrophobic residues, it is highly involved in binding of hydrophobic amino acid residues, either by increasing the hydrophobicity of S4 or by determining the size of the pocket. The results suggest that the amino acid residue at position 104 is mobile such that it is positioned in the S4 binding site only when it can interact favourably with the substrate's side chain at position P4.According to their substrate specificities, the endopeptidases can be divided into several groups. A number of endopeptidases, e.g. trypsin [3], have a very high specificity for particular amino acid residues at position PI, while others are less specific. In some of these enzymes with broadcr substrate preference, a binding subsite rcmote from the scissile bond is of primary importance, e.g. the S2 subsites of a-lytic protease [4] and papain [5], and the S4 subsites of elastase [6] and the subtilisins [7]. X-ray crystallographic studies of subtilisins BPN' and Carlsberg complexed with various inhibitor proteins [8 -121, and extensive kinetic characterisation of two subtilisins, subtilisin 309 from Bacillus lentils and subtilisin BPN' from Bacillus amyloliquefuciens [I 31, suggest that interaction between the substrate and the S4 binding pocket is at least as important for substrate preference as interaction in the S1 region.Subtilisin BPN' exhibits a marked preferencc for aromatic groups in P4 [13]; this has been claimed to be due to a tyrosine Enzyme. Subtilisin 309, a protease from Bacillus lentus (EC 3.4.21.14).Note. The binding-site notation is that of Schechter and Berger [I]. Accordingly, amino acid residues in the suhstrate are referred to as PI, Pz, . . . Pi and P;, P;, . . . Pi away from the scissile bond towards the N-and C-terminal amino acid residues of the substrate, respectively. Enzymc subsites are denoted S, , Sz, ... Si and S;, S;, ... SI in correspondcnce with the substrate. The numbering of amino acid residues is that of subtilisin BPN' from Bacillus miyloliquefaciens (21. residue, TyrlO4 located...

Portion-mixing peptide libraries of quenched fluorogenic substrates for complete subsite mapping of endoprotease specificity.

“…The donor-acceptor amino acid pair o-aminobenzamide (ABz)-3-nitrotyrosine [Tyr(NO2)] (13) for which excellent quenching of fluorescence is observed has recently been described (5). This donor-acceptor pair is conveniently introduced in parallel multiple-column peptide synthesis (MCPS) (14) of numerous substrates and has been used for subsite mapping of a variety of proteases (6,(15)(16)(17)(18)(19)(20)(21). However, substantial effort is still required to identify the optimal substrates.…”

The effect of changing the hydrophobic S1′ subsite of thermolysin‐like proteases on substrate specificity

“…[32] and its interactions with the enzyme are therefore more likely to be affected by mutation of residue 202. Several mutagenesis studies of proteases have shown that it is possible to manipulate substrate preferences by changing the size and/or character of hydrophobic binding pockets [41][42][43][44][45][46][47][48][49][50]. For example, diminishing the space in the S 1 subsite of subtilisin YaB [41] and subtilisin E [42] by increasing the size of the subsite residues led to reduced activity towards substrates with large P 1 residues while yielding higher activity towards substrates with smaller P 1 residues.…”

Plasticity of Extended Subsites Facilitates Divergent Substrate Recognition by Kex2 and Furin

“…Based on these structural studies, several groups have mutated the S 4 pocket in an attempt to alter the P 4 substrate specificity of subtilisin (21)(22)(23)(24)(25)(26). Wells and co-workers (27,28) found that substitutions of Asp for Tyr 104 in subtilisin BPNЈ increased cleavage of substrates containing a P 4 Arg, but the resulting mutant protease did not discriminate between Arg and Phe at this position.…”