Dynamic control of the prolyl isomerase function of the dual-domain SlyD protein

Local dynamics on variable timescales are important to facilitate high catalytic efficiency in enzymes. In this study, we examined the dual-domain peptidyl-prolyl cis/trans-isomerase (PPIase) SlyD with regard to its catalytic cycle. Fluorescence- and NMR-based experiments were performed to understand the high catalytic efficiency of SlyD compared to single domain FKBP proteins. We probed local conformational changes for amino acids involved in substrate-binding (IF domain) and substrate-catalysis (FKBP domain) taking place on the timescale of substrate turnover. Binding of the PPIase activity inhibitors to the FKBP domain suppressed the conformational freedom of the remote IF domain. A single side-chain mutation in the active site strongly reduced the rate of substrate turnover and changed the conformational dynamics of all amino acids involved in catalysis. This dynamic interplay between substrate-binding domain and PPIase domain determines the high catalytic activity of SlyD and inhibitor-binding modulates the backbone plasticity required for enzyme activity.

Highlights► The chaperone domain of the SlyD protein facilitates its high catalytic efficiency. ► We find a dynamic coupling of the two domains at various time scales. ► Inhibitor binding and point mutations modify the dynamics and catalysis. ► A proposed model connects the local dynamics to the steps of catalysis.