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Antimicrob Agents Chemother. 2018 Oct 24;62(11). pii: e01579-18. doi: 10.1128/AAC.01579-18. Print 2018 Nov.

Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1.

Zhang H1,2, Ma G3,2, Zhu Y3,2, Zeng L4, Ahmad A3,2, Wang C3,2, Pang B4, Fang H5, Zhao L5, Hao Q6.

Author information

1
Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China zhanghm@sustc.edu.cn qhao@hku.hk.
2
Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China.
3
Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China.
4
School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China.
5
College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, China.
6
School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China zhanghm@sustc.edu.cn qhao@hku.hk.

Abstract

β-Lactam antibiotics are the mainstay for the treatment of bacterial infections. However, elevated resistance to these antibiotics mediated by metallo-β-lactamases (MBLs) has become a global concern. New Delhi metallo-β-lactamase-1 (NDM-1), a newly added member of the MBL family that can hydrolyze almost all β-lactam antibiotics, has rapidly spread all over the world and poses serious clinical threats. Broad-spectrum and mechanism-based inhibitors against all MBLs are highly desired, but the differential mechanisms of MBLs toward different antibiotics pose a great challenge. To facilitate the design of mechanism-based inhibitors, we investigated the active-site conformational changes of NDM-1 through the determination of a series of 15 high-resolution crystal structures in native form and in complex with products and by using biochemical and biophysical studies, site-directed mutagenesis, and molecular dynamics computation. The structural studies reveal the consistency of the active-site conformations in NDM-1/product complexes and the fluctuation in native NDM-1 structures. The enzymatic measurements indicate a correlation between enzymatic activity and the active-site fluctuation, with more fluctuation favoring higher activity. This correlation is further validated by structural and enzymatic studies of the Q123G mutant. Our combinational studies suggest that active-site conformational fluctuation promotes the enzymatic activity of NDM-1, which may guide further mechanism studies and inhibitor design.

KEYWORDS:

NDM-1; conformational change; metallo-β-lactamase; microbial antibiotic resistance; structure-based drug design

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