Alanine-scanning of the yeast killer toxin K2 reveals key residues for activity, gain-of-function variants, and supports prediction of precursor processing and 3D structure.
Yeast killer toxins (YKTs) are antimicrobial proteins secreted by yeast with potential applications ranging from food preservation to therapeutic agents in human health. However, the practical use of many YTKs is limited by specific pH requirements, low temperature stability, low production yields, and narrow target specificity. While protein engineering could potentially overcome these challenges, progress is hindered by a lack of detailed knowledge about sequence-function relationships and structural data for these often multi-step processed proteins. In this study, we focused on the YKT K2, encoded by the M2 dsRNA satellite virus in Saccharomyces cerevisiae. Using alanine scanning mutagenesis of the full open reading frame and structure predictions combined with molecular dynamics simulations, we generated a comprehensive sequence-function map, refined the model for the proteolytic processing of the K2 precursor, and predicted the mature toxin structure. Our findings also demonstrate that K2 can be engineered towards enhanced toxicity and altered target specificity through single-site mutations. Furthermore, we identified structural homology between K2 and the SMK toxin from the yeast Millerozyma farinosa. Our cost-effective workflow provides a platform to broadly map YKT sequence-structure-function relationships, facilitating the engineering towards toxin-based technologies. The workflow could also serve as a template to resolve the processing and conformations of other proteins within the secretory pathway - a dynamic multi-step process that is challenging to structurally capture by purification and solving structures of intermediates.