Harnessing Protein Symmetry for Enzyme Design

Abstract

Cyclic protein oligomers are common in Nature. Here we show that the central pore of the pentameric ring-forming protein lumazine synthase from Saccharomyces cerevisiae (ScLS) can be rationally engineered to catalyze a retro-aldol reaction. The C5-symmetry of the complex was exploited to equip the protein tunnel with a ring of five closely spaced lysines adjacent to an apolar site for substrate binding. The resulting system utilizes amine catalysis to promote the cleavage of (±)-methodol to 6-methoxy-2-naphthaldehyde and acetone with a >103-fold rate acceleration. The ease of organizing convergent functional groups within a protein pore may make the tunnels of many symmetric ring-shaped proteins useful starting points for creating designer enzymes.