Structure and Dynamics of the Penicillin-Binding Protein 3 from Staphylococcus Epidermidis Native and in Complex with Cefotaxime and Vaborbactam

Author(s): Martin Schwinzer, Hévila Brognaro, Holger Rohde Christian Betzel

Staphylococcus epidermidis (Se) is a highly abundant gram-positive bacterium predominantly found on human skin. It poses significant threat to immunocompromised patients due to its ability to form biofilms on medical devices. In this study, we determined and refined the first structure of a penicillin-binding protein (PBP) from SePBP3 to a resolution of 2.5 Å. The apo form analysis revealed a shift in the head sub-domain (HSD) relative to the homologous structure in Staphylococcus aureus (Sa). The discovery led us to conduct an analysis of SePBP3’s flexibility applying also X-ray solution scattering. Additional molecular dynamics simulations revealed a rigid transpeptidase domain paired with a flexible pedestal domain, displaying an open and closed interface between the N-terminal anchor domain and the HSD. Furthermore, we solved and refined the structure of SePBP3 in complex with the β-lactam antibiotic cefotaxime and the boron-based antibiotic vaborbactam to 2.51 and 2.3 Å resolution, respectively. Both ligands demonstrated high binding affinity, as confirmed by ITC measurements. Since Staphylococcus epidermidis is a potential major contributor to nosocomial infections, the new structural insights into a highly affine PBP capable of binding various classes of antibiotics provide valuable information for future drug design investigations.