Molecular characterisation of the acyltransferase-acyl carrier protein interface in a fungal highly reducing polyketide synthase

Iterative polyketide synthases (iPKSs) rely on communication between acyl carrier protein (ACP) and acyltransferase (AT) domains to ensure efficient delivery of starter and extender substrates during biosynthesis. However, the molecular determinants governing the AT:ACP interface remain poorly understood. Here, we use the fungal highly reducing PKS, SimG, a component of the cyclosporin biosynthetic pathway, as a model system to dissect the AT:ACP interface. Using alanine scanning mutagenesis combined with a high-throughput intact-protein mass spectrometry assay, we identified epitope-forming residues that affect AT:ACP interaction. These experimental constraints were used to guide docking and molecular dynamics simulations to produce a data-driven structural model of the SimG AT:ACP complex in a catalytically competent geometry. We also demonstrate that the SimG AT domain transacylates ACP domains from a range of fungal PKS architectural classes, highlighting significant interface plasticity. These insights advance our fundamental understanding of domain communication in these enigmatic megasynthases and provide a foundation for rational engineering to expand substrate scope towards novel polyketide scaffolds.