Evolution of New Delhi metallo-β-lactamase (NDM) in the clinic: Effects of NDM mutations on stability, zinc affinity, and mono-zinc activity.


Abstract

Infections by carbapenem-resistant Enterobacteriaceae are difficult to manage owing to broad antibiotic resistance profiles and because of the inability of clinically used β-lactamase inhibitors to counter the activity of metallo-β-lactamases often harbored by these pathogens. Of particular importance is New Delhi metallo-β-lactamase (NDM), which requires a di-nuclear zinc ion cluster for catalytic activity. Here, we compare the structures and functions of clinical NDM variants 1-17. The impact of NDM variants on structure is probed by comparing melting temperature and refolding efficiency and also by spectroscopy (UV-visible,

Submission Details

ID: ZaNao4tc3

Submitter: Paulie Dang

Submission Date: March 31, 2020, 9:47 a.m.

Version: 1

Publication Details
Cheng Z;Thomas PW;Ju L;Bergstrom A;Mason K;Clayton D;Miller C;Bethel CR;VanPelt J;Tierney DL;Page RC;Bonomo RA;Fast W;Crowder MW,J Biol Chem (2018) Evolution of New Delhi metallo-β-lactamase (NDM) in the clinic: Effects of NDM mutations on stability, zinc affinity, and mono-zinc activity. PMID:29909397
Additional Information

S, I, and R indicate susceptible, intermediate, and resistant, respectively. SDD indicates Susceptible-Dose Dependent for Cefepime.

Study Summary

Number of data points 1164
Proteins Metallo-beta-lactamase NDM-2 ; Metallo-beta-lactamase type 2
Unique complexes 149
Assays/Quantities/Protocols Experimental Assay: Kd for L-Captopril ; Experimental Assay: L-captopril Binding ; Experimental Assay: Zinc Content (Purified) ; Experimental Assay: MIC (relative) in normal conditions ; Experimental Assay: MIC (absolute) in normal conditions ; Experimental Assay: Resistance (SIR) ; Experimental Assay: MIC (relative) in zinc limited conditions ; Experimental Assay: MIC (absolute) in zinc limited conditions ; Experimental Assay: Kcat ; Experimental Assay: Activity % at low Zinc on Ampicillin ; Experimental Assay: Kd, Zn2 ; Experimental Assay: Km ; Experimental Assay: Fluorescence Intensity (%) ; Experimental Assay: Tm ; Experimental Assay: Refolding efficiency using High Protein Concentration (350 μM) ; Experimental Assay: Resistance (SIR) for Zinc Limited Assays ; Experimental Assay: kcat/Km ; Derived Quantity: SD of Tm ; Derived Quantity: SD of Fluorescence Intensity (%) ; Derived Quantity: SD of Km ; Derived Quantity: SD of Kcat ; Derived Quantity: SD of Zinc Content (Purified) ; Derived Quantity: SD of L-captopril Binding ; Derived Quantity: SD of Kd for L-Captopril ; Derived Quantity: SD of Kd, Zn2 ; Derived Quantity: SD of Activity % at low Zinc on Ampicillin
Libraries NDM-2 Zinc Excess MIC ; NDM-2 Limited Zinc MIC ; Fluorescence & Tm & Refolding ; Activity in excess Zinc ; MIC Zinc Limited ; MIC Standard Conditions ; Kd and Purified Zinc Count ; Activity (Low Zinc on Ampicillin)

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
5ZJ1 2018-03-18T00:00:00+0000 0.96 Crystal structure of NDM-1 in complex with D-captopril derivative CYT-14
6C6I 2018-01-18T00:00:00+0000 1.65 Crystal structure of a chimeric NDM-1 metallo-beta-lactamase harboring the IMP-1 L3 loop
5ZJ2 2018-03-18T00:00:00+0000 1.1 Crystal structure of NDM-1 in complex with D-captopril
3PG4 2010-10-29T00:00:00+0000 2.0 The crystal structure of New Delhi Metallo-beta lactamase (NDM-1)
6LIP 2019-12-12T00:00:00+0000 0.98 Crystal structure of NDM-1 in complex with D-captopril derivative wss0218
6LJ1 2019-12-13T00:00:00+0000 1.15 Crystal structure of NDM-1 in complex with D-captopril derivative wss02127 monomer
6LJ2 2019-12-13T00:00:00+0000 1.35 Crystal structure of NDM-1 in complex with heterodimer of D-captopril derivative wss02127 stereoisomer
6LJ7 2019-12-13T00:00:00+0000 1.16 Crystal structure of NDM-1 in complex with D-captopril derivative wss05010
4H0D 2012-09-07T00:00:00+0000 1.5 New Delhi Metallo-beta-Lactamase-1 Complexed with Mn from Klebsiella pneumoniae
4EYL 2012-05-01T00:00:00+0000 1.9 Crystal structure of NDM-1 bound to hydrolyzed meropenem

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
200.0 A,B Metallo-beta-lactamase type 2 C7C422 BLAN1_KLEPN