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Significance The essential role of acyltransferases (ATs) in fatty acid synthase (FAS) and polyketide synthase (PKS) pathways, namely the selection and loading of starter and extender units onto acyl carrier proteins (ACPs), relies on catalytically productive ACP–AT interactions. Here, we describe and interrogate the structure of a type II FAS malonyl-CoA:ACP-transacylase (MAT) in the covalent complex with its cognate ACP. We combine structural, mutational, crosslinking, and kinetic data with molecular dynamics simulations to describe a highly flexible and robust protein–protein interface, substrate-induced active site reorganization, and key subdomain motions that likely govern AT function. These findings strengthen a mechanistic understanding of molecular recognition between ACPs and partner enzymes and provide insights for engineering AT-dependent biosynthetic pathways.

Interfacial plasticity facilitates high reaction rate of E. coli FAS malonyl-CoA:ACP transacylase, FabD