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Significance Acyltransferases (ATs) are responsible for the selection and incorporation of acyl building blocks in the biosynthesis of various polyketide natural products. Proper protein–protein interactions between AT and cognate acyl carrier protein (ACP) are critical for the functional transfer of acyl groups. However, the ACP recognition mechanism has remained elusive because the structural determination of an AT–ACP complex is hampered by the weak and transient interactions between them. Herein, we describe the first crystal structure of the AT–ACP complex. To stabilize the weak protein–protein interaction sufficiently for analysis, we prepared a covalent AT–ACP complex using a cross-linking reagent for crystallization. The determined AT–ACP complex structure provides detailed mechanistic insights into ACP recognition by AT.

Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis