Rapid screening platform for discovering novel peptide prenyltransferases to expand the structural diversity of pseudo-natural prenylated peptides

Peptide lipidation can enhance stability and permeability, yet biocatalysts for late-stage, site- and mode-selective modification remain limited. We established a streamlined activity-profiling system that rapidly assesses peptide-prenylating activities using an artificial substrate set. Screening 19 recombinant, putative cyanobactin prenyltransferases (PTases) uncovered 14 active enzymes with diverse catalytic properties, including five unprecedented modes of prenylation, bifunctionality toward Trp/Tyr, and expanded donor utilization such as farnesylation. Co-crystal structures of seven PTases reveal how subtle active-site changes enable dual substrate recognition and accommodation of bulkier donors, highlighting the evolutionary diversification of catalytic functions. The enzymes tolerate non-native substrates, enabling late-stage, site- and mode-selective lipidation to construct pseudo-natural peptides. Together, these findings drastically expand the enzymatic and mechanistic landscape of cyanobactin PTases, substantially enlarging their functional repertoire and revealing the structural principles that govern the diversification of peptide prenylation chemistry.