Smith Clyde A, Stasyuk Anastasiya
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Department of Chemistry, Stanford University, Stanford, CA 94303, USA.
Pathogens. 2025 Aug 1;14(8):761. doi: 10.3390/pathogens14080761.
Class D β-lactamases (DBLs) represent a major threat to antibiotic efficacy by hydrolyzing β-lactam drugs, including last-resort carbapenems, thereby driving antimicrobial resistance in Gram-negative bacteria. The enzymes share a structurally conserved two-domain α/β architecture with seven active-site motifs and three flexible extended loops (the P-loop, Ω-loop, and newly designated B-loop) that surround the active site. While each of these loops is known to influence enzyme function, their coordinated roles have not been fully elucidated. To investigate the significance of their interplay, we compared the sequences and crystal structures of 40 DBLs from clinically relevant Gram-negative pathogens and performed molecular dynamics simulations on selected representatives. Combined structural and dynamical analyses revealed a strong correlation between B-loop architecture and carbapenemase activity in the pathogens and , particularly regarding loop length and spatial organization. These findings emphasize the B-loop's critical contribution, in concert with the P- and Ω-loops, in tuning active site versatility, substrate recognition, catalytic activity, and structural stability. A deeper understanding of how these motifs and loops govern DBL function may inform the development of novel antibiotics and inhibitors targeting this class of enzymes.
D类β-内酰胺酶（DBLs）通过水解β-内酰胺类药物（包括作为最后防线的碳青霉烯类药物）对抗生素疗效构成重大威胁，从而导致革兰氏阴性菌产生耐药性。这些酶具有结构保守的双结构域α/β结构，带有七个活性位点基序和三个围绕活性位点的柔性延伸环（P环、Ω环和新命名的B环）。虽然已知这些环中的每一个都会影响酶的功能，但其协同作用尚未完全阐明。为了研究它们相互作用的重要性，我们比较了来自临床相关革兰氏阴性病原体的40种DBLs的序列和晶体结构，并对选定的代表性序列进行了分子动力学模拟。结构和动力学分析相结合，揭示了病原体 和 中B环结构与碳青霉烯酶活性之间的强相关性，特别是在环长度和空间组织方面。这些发现强调了B环与P环和Ω环协同作用，在调节活性位点通用性、底物识别、催化活性和结构稳定性方面起着关键作用。深入了解这些基序和环如何控制DBL功能，可能为开发针对这类酶的新型抗生素和抑制剂提供思路。
