Crystal structure of β‐ketoacyl‐acyl carrier protein synthase II from E.coli reveals the molecular architecture of condensing enzymes

In the biosynthesis of fatty acids, the β‐ketoacyl‐acyl carrier protein (ACP) synthases catalyze chain elongation by the addition of two‐carbon units derived from malonyl‐ACP to an acyl group bound to either ACP or CoA. The crystal structure of β‐ketoacyl synthase II from Escherichia coli has been determined with the multiple isomorphous replacement method and refined at 2.4 Å resolution. The subunit consists of two mixed five‐stranded β‐sheets surrounded by α‐helices. The two sheets are packed against each other in such a way that the fold can be described as consisting of five layers, α–β–α–β–α. The enzyme is a homodimer, and the subunits are related by a crystallographic 2‐fold axis. The two active sites are located near the dimer interface but are ∼25 Å apart. The proposed nucleophile in the reaction, Cys163, is located at the bottom of a mainly hydrophobic pocket which is also lined with several conserved polar residues. In spite of very low overall sequence homology, the structure of β‐ketoacyl synthase is similar to that of thiolase, an enzyme involved in the β‐oxidation pathway, indicating that both enzymes might have a common ancestor.