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
5ZGX 2018-08-22 0.95 Crystal structure of NDM-1 at pH7.5 (Succinate) with 1 molecule per asymmetric unit
5ZGW 2018-08-22 0.95 Crystal structure of NDM-1 at pH7.5 with 1 molecule per asymmetric unit (crystallized at succinate pH5.5 and soaked at succinate pH7.5)
5ZGY 2018-08-22 0.95 Crystal structure of NDM-1 at pH7.5 (Bis-Tris) with 1 molecule per asymmetric unit
5XP6 2018-03-07 0.95 native structure of NDM-1 crystallized at pH5.5
5ZGZ 2018-08-22 0.95 Crystal structure of NDM-1 at pH7.5 (Imidazole) with 1 molecule per asymmetric unit
5ZJ7 2019-03-20 0.96 Crystal structure of NDM-1 in complex with D-captopril derivative CY22
5ZJC 2019-03-20 0.96 Crystal structure of NDM-1 in complex with D-captopril derivative CY41
5ZJ1 2019-03-20 0.96 Crystal structure of NDM-1 in complex with D-captopril derivative CYT-14
5ZJ8 2019-03-20 0.96 Crystal structure of NDM-1 in complex with D-captopril derivative CY32
5ZGI 2018-08-22 0.98 Crystal structure of NDM-1 at pH6.5 (Succinate) with 1 molecule per asymmetric unit
5ZIO 2019-03-20 0.98 Crystal structure of NDM-1 in complex with L-captopril
5ZGE 2018-08-22 1.0 Crystal structure of NDM-1 at pH5.5 (Bis-Tris) in complex with hydrolyzed ampicillin
6Q2Y 2019-04-24 1.0 Crystal structure of NDM-1 beta-lactamase in complex with broad spectrum boronic inhibitor cpd3
5ZH1 2018-08-22 1.05 Crystal structure of NDM-1 at pH7.5 (Imidazole) with 2 molecules per asymmetric unit
4HL2 2012-12-12 1.05 New Delhi Metallo-beta-Lactamase-1 1.05 A structure Complexed with Hydrolyzed Ampicillin
6V1M 2020-03-25 1.05 Structure of NDM-1 bound to QPX7728 at 1.05 A
5ZJ2 2019-03-20 1.1 Crystal structure of NDM-1 in complex with D-captopril
6D1I 2019-04-17 1.1 Crystal structure of NDM-1 complexed with compound 12
5ZGV 2018-08-22 1.15 Crystal structure of NDM-1 at pH8.0 (Tris) with 2 molecules per asymmetric unit
5ZGR 2018-08-22 1.15 Crystal structure of NDM-1 at pH7.3 (HEPES) in complex with hydrolyzed ampicillin
5ZGP 2018-08-22 1.15 Crystal structure of NDM-1 at pH6.2 (Bis-Tris) in complex with hydrolyzed ampicillin
6D1G 2019-04-17 1.15 Crystal structure of NDM-1 complexed with compound 9
6D1E 2019-04-17 1.15 Crystal structure of NDM-1 complexed with compound 7
6D1J 2019-04-17 1.15 Crystal structure of NDM-1 complexed with compound 13
6D1F 2019-04-17 1.15 Crystal structure of NDM-1 complexed with compound 8
6MDU 2019-04-17 1.15 Crystal structure of NDM-1 with compound 7
4EYB 2012-08-15 1.16 Crystal structure of NDM-1 bound to hydrolyzed oxacillin
4EY2 2012-08-08 1.17 Crystal structure of NDM-1 bound to hydrolyzed methicillin
6D1K 2019-04-17 1.2 Crystal structure of NDM-1 complexed with compound 14
5ZGT 2018-08-22 1.2 Crystal structure of NDM-1 at pH7.5 (HEPES) with 2 molecules per asymmetric unit
5ZGF 2018-08-22 1.2 Crystal structure of NDM-1 Q123G mutant
6D1B 2019-04-17 1.25 Crystal structure of NDM-1 complexed with compound 2
6D1C 2019-04-17 1.25 Crystal structure of NDM-1 complexed with compound 3
6D1A 2019-04-17 1.25 Crystal structure of NDM-1 complexed with compound 1
6D1H 2019-04-17 1.25 Crystal structure of NDM-1 complexed with compound 11
4RAW 2014-11-26 1.3 Crystal Structure of New Delhi Metallo-beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin
5O2E 2018-12-26 1.3 Crystal structure of NDM-1 in complex with hydrolyzed cefuroxime - new refinement
6O3R 2019-09-25 1.3 Crystal Structure of NDM-1 D199N with Compound 7
4RL0 2014-11-19 1.3 Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins
4GYQ 2012-09-26 1.35 Crystal Structure of New Delhi Metallo-beta-Lactamase-1 D223A mutant from Klebsiella pneumoniae
6IBS 2019-04-24 1.37 Crystal structure of NDM-1 beta-lactamase in complex with boronic inhibitor cpd 6
5WIG 2017-10-18 1.4 Structure of New Delhi Metallo-Beta-lactamase 4 (NDM-4)
6IBV 2019-05-15 1.4 Crystal structure of NDM-1 beta-lactamase in complex with broad spectrum boronic inhibitor cpd 1
6D1D 2019-04-17 1.4 Crystal structure of NDM-1 complexed with compound 6
6NY7 2019-09-25 1.4 Crystal Structure of NDM-1 D199N with Compound 16
4EXY 2012-08-08 1.47 Crystal structure of NDM-1 bound to ethylene glycol
5N0I 2017-04-05 1.47 Crystal structure of NDM-1 in complex with beta-mercaptoethanol - new refinement
4H0D 2012-09-26 1.5 New Delhi Metallo-beta-Lactamase-1 Complexed with Mn from Klebsiella pneumoniae
6Q30 2019-04-24 1.5 Crystal structure of NDM-1 beta-lactamase in complex with boronic inhibitor cpd 5
4HL1 2012-12-12 1.5 Crystal Structure of New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Ampicillin
5ZGQ 2018-08-22 1.5 Crystal structure of NDM-1 at pH7.5 (Tris-HCl, (NH4)2SO4) in complex with hydrolyzed ampicillin
4RAM 2014-09-24 1.5 Crystal Structure of New Delhi Metallo-beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G
6RMF 2019-09-11 1.51 Crystal structure of NDM-1 with VNRX-5133
5XP9 2018-03-07 1.55 Crystal structure of Bismuth bound NDM-1
5ZGU 2018-08-22 1.55 Crystal structure of NDM-1 at pH7.0 (HEPES) with 2 molecules per asymmetric unit
6MGY 2018-10-03 1.6 Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 from Klebsiella pneumoniae
6EFJ 2019-04-17 1.65 Crystal structure of NDM-1 with compound 9
6MGZ 2018-10-03 1.65 Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 from Klebsiella pneumoniae
6C6I 2018-10-17 1.65 Crystal structure of a chimeric NDM-1 metallo-beta-lactamase harboring the IMP-1 L3 loop
5JQJ 2017-05-10 1.67 Directed evolutionary changes in MBL super family - NDM-1 Round 10 crystal-1
6CAC 2018-10-17 1.79 Crystal structure of NDM-1 metallo-beta-lactamase harboring an insertion of a Pro residue in L3 loop
4EYF 2012-08-08 1.8 Crystal structure of NDM-1 bound to hydrolyzed benzylpenicillin
4GYU 2012-09-26 1.8 Crystal Structure of New Delhi Metallo-beta-Lactamase-1 A121F mutant from Klebsiella pneumoniae
4EYL 2012-08-08 1.9 Crystal structure of NDM-1 bound to hydrolyzed meropenem
4U4L 2014-08-20 1.9 Crystal structure of the metallo-beta-lactamase NDM-1 in complex with a bisthiazolidine inhibitor
5N0H 2017-04-05 1.9 Crystal structure of NDM-1 in complex with hydrolyzed meropenem - new refinement
3ZR9 2011-06-29 1.91 Structure of New Delhi Metallo-Beta-lactamase 1 (NDM-1)
6EX7 2017-12-13 1.95 Crystal structure of NDM-1 metallo-beta-lactamase in complex with Cd ions and a hydrolyzed beta-lactam ligand - new refinement
5K4M 2017-04-26 1.98 Directed evolutionary changes in MBL super family - NDM-1 Round 10 crystal-3
3PG4 2011-11-16 2.0 The crystal structure of New Delhi Metallo-beta lactamase (NDM-1)
4HKY 2013-01-23 2.0 New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Faropenem
3RKJ 2011-05-18 2.0 Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pnueumoniae
4RL2 2014-11-19 2.01 Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins
5O2F 2018-12-26 2.01 Crystal structure of NDM-1 in complex with hydrolyzed ampicillin - new refinement
4RM5 2014-11-19 2.1 Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins
3SPU 2011-08-03 2.1 apo NDM-1 Crystal Structure
3SFP 2011-06-29 2.27 Crystal Structure of the Mono-Zinc-boundform of New Delhi Metallo-beta-Lactamase-1 from Klebsiella pneumoniae
3SBL 2011-06-29 2.31 Crystal Structure of New Delhi Metal-beta-lactamase-1 from Klebsiella pneumoniae
3RKK 2011-05-18 2.35 Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pneumoniae
4EXS 2012-08-08 2.4 Crystal structure of NDM-1 bound to L-captopril
4RBS 2014-11-26 2.4 Crystal Structure of New Delhi Metallo-beta-Lactamase-1 in the Complex with Hydrolyzed Meropenem
6JKB 2020-03-25 2.44 Crystal structure of metallo-beta-lactamse, NDM-1, in complex with hydrolyzed ampicillin
3SRX 2011-07-20 2.5 New Delhi Metallo-beta-Lactamase-1 Complexed with Cd
5NBK 2018-10-03 2.6 NDM-1 metallo-beta-lactamase: a parsimonious interpretation of the diffraction data
5A5Z 2015-07-08 2.6 Approved Drugs Containing Thiols as Inhibitors of Metallo-beta- lactamases: Strategy To Combat Multidrug-Resistant Bacteria

Relevant UniProtKB Entries

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