Enoyl-CoA carboxylase/reductases (ECRs) catalyze the selective α-carboxylation of α,β-unsaturated CoA-thioesters. Structure-based engineering of the active-site binding pocket of ECRs enabled significant alteration of their catalytic activity towards larger substrates. This facilitates the incorporation of unusual extender units into polyketide backbones, thus providing a novel method for the directed structural diversification of polyketides.