Structural comparison of substrate-binding pockets of serine β-lactamases in classes A, C, and D

beta-lactams have been the most successful antibiotics, but the rise of multi-drug resistant (MDR) bacteria threatens their effectiveness. Serine beta-lactamases (SBLs), among the most common causes of resistance, are classified as A, C, and D, with numerous variants complicating structural and substrate spectrum comparisons. This study compares representative SBLs of these classes, focusing on the substrate-binding pocket (SBP). SBP is kidney bean-shaped on the indented surface, formed mainly by loops L1, L2, and L3, and an additional loop Lc in class C. beta-lactams bind in a conserved orientation, with the beta-lactam ring towards L2 and additional rings towards the space between L1 and L3. Structural comparison shows each class has distinct SBP structures, but subclasses share a conserved scaffold. The SBP structure, accommodating complimentary beta-lactams, determines the substrate spectrum of SBLs. The systematic comparison of SBLs, including structural compatibility between beta-lactams and SBPs, will help understand their substrate spectrum.