Yeast aspartic protease 3 (Yap3) prefers substrates with basic residues in the P2, P1 and P2′ positions

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Abstract
The yeast aspartic protease Yap3 is localised to the secretory pathway and correctly cleaves pro-α-mating factor at its dibasic sites. We determined the specificity of Yap3 for mono-, di- and multi-basic cleavage sites in the context of 15 residue synthetic proalbumin peptides. Yap3 cleaved after dibasic ArgArg and LysArg sites but not after monobasic Arg sites even when there was an additional arginine at −6 and/or −4. Yap3 did not cleave a tetra-arginine site and tribasic sites (RRR and RRK) were poor substrates. Cleavage always occurred C-terminal to the last arginine in the di- or tri-basic sequence. The optimal cleavage site sequence was RR ↓ DR and this substrate was cleaved 8–9-fold faster than the normal RR ↓ DA sequence. In contrast to Kex2, Yap3 did not remove the propeptide from normal proalbumin or a range of natural or recombinant proalbumin variants. However at pH 4.0 Yap3 slowly cleaved proalbumin and albumin between domains 2 and 3.