Structural and Biochemical Characterization of the Interaction between KPC-2 β-Lactamase and β-Lactamase Inhibitor Protein

KPC β-lactamases hydrolyze the “last resort” β-lactam antibiotics (carbapenems) used to treat multidrug resistant infections and are compromising efforts to combat life-threatening Gram-negative bacterial infections in hospitals worldwide. Consequently, the development of novel inhibitors is essential for restoring the effectiveness of existing antibiotics. The β-lactamase inhibitor protein (BLIP) is a competitive inhibitor of a number of class A β-lactamases. In this study, we characterize the previously unreported interaction between KPC-2 β-lactamase and BLIP. Biochemical results show that BLIP is an extremely potent inhibitor of KPC enzymes, binding KPC-2 and KPC-3 with subnanomolar affinity. To understand the basis of affinity and specificity in the β-lactamase−BLIP system, the crystallographic structure of the KPC-2−BLIP complex was determined to 1.9 Å resolution. Computational alanine scanning was also conducted to identify putative hot spots in the KPC-2−BLIP interface. Interestingly, the two complexes making up the KPC-2−BLIP asymmetric unit are distinct, and in one structure, the BLIP F142 loop is absent, in contrast to homologous structures in which it occupies the active site. This finding and other sources of structural plasticity appear to contribute to BLIP’s promiscuity, enabling it to respond to mutations at the β-lactamase interface. Given the continuing emergence of antibiotic resistance, the high-resolution KPC-2−BLIP structure will facilitate its use as a template for the rational design of new inhibitors of this problematic enzyme.