Biochemical characterization of New Delhi metallo-β-lactamase variants reveals differences in protein stability.


OBJECTIVES: Metallo-β-lactamase (MBL)-based resistance is a threat to the use of most β-lactam antibiotics. Multiple variants of the New Delhi MBL (NDM) have recently been reported. Previous reports indicate that the substitutions affect NDM activity despite being located outside the active site. This study compares the biochemical properties of seven clinically reported NDM variants. METHODS: NDM variants were generated by site-directed mutagenesis; recombinant proteins were purified to near homogeneity. Thermal stability and secondary structures of the variants were investigated using differential scanning fluorimetry and circular dichroism; kinetic parameters and MIC values were investigated for representative carbapenem, cephalosporin and penicillin substrates. RESULTS: The substitutions did not affect the overall folds of the NDM variants, within limits of detection; however, differences in thermal stabilities were observed. NDM-8 was the most stable variant with a melting temperature of 72°C compared with 60°C for NDM-1. In contrast to some previous studies, kcat/KM values were similar for carbapenem and penicillin substrates for NDM variants, but differences in kinetics were observed for cephalosporin substrates. Apparent substrate inhibition was observed with nitrocefin for variants containing the M154L substitution. In all cases, cefoxitin and ceftazidime were poorly hydrolysed with kcat/KM values <1 s(-1) μM(-1). CONCLUSIONS: These results do not define major differences in the catalytic efficiencies of the studied NDM variants and carbapenem or penicillin substrates. Differences in the kinetics of cephalosporin hydrolysis were observed. The results do reveal that the clinically observed substitutions can make substantial differences in thermodynamic stability, suggesting that this may be a factor in MBL evolution.

Submission Details


Submitter: Paulie Dang

Submission Date: Sept. 24, 2019, 10:10 a.m.

Version: 1

Publication Details
Makena A;Brem J;Pfeffer I;Geffen RE;Wilkins SE;Tarhonskaya H;Flashman E;Phee LM;Wareham DW;Schofield CJ,J Antimicrob Chemother (2015) Biochemical characterization of New Delhi metallo-β-lactamase variants reveals differences in protein stability. PMID:25324420
Additional Information

Additional Ki data for Nitrocefin: For NDM-1, NDM-3, NDM-4, NDM-5, NDM-6, NDM-7, and NDM-8: Ki (μM) is not reported (NR), NR, 102 ± 32, 139 ± 28, NR, 79 ± 18, and 146 ± 47, respectively. MIC Assay Data with the ISAba125 promoter were chosen for input into ProtaBank. For MIC Assay Absolute Data with > symbols the next higher multiplier was used to calculate the MIC Relative data.

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
3PG4 2010-10-29T00:00:00+0000 2.0 The crystal structure of New Delhi Metallo-beta lactamase (NDM-1)
3RKJ 2011-04-18T00:00:00+0000 2.0 Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pnueumoniae
3RKK 2011-04-18T00:00:00+0000 2.35 Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pneumoniae
3SBL 2011-06-05T00:00:00+0000 2.31 Crystal Structure of New Delhi Metal-beta-lactamase-1 from Klebsiella pneumoniae
3SFP 2011-06-13T00:00:00+0000 2.27 Crystal Structure of the Mono-Zinc-boundform of New Delhi Metallo-beta-Lactamase-1 from Klebsiella pneumoniae
3SPU 2011-07-03T00:00:00+0000 2.1 apo NDM-1 Crystal Structure
3SRX 2011-07-07T00:00:00+0000 2.5 New Delhi Metallo-beta-Lactamase-1 Complexed with Cd
3ZR9 2011-06-15T00:00:00+0000 1.91 Structure of New Delhi Metallo-Beta-lactamase 1 (NDM-1)
4EXS 2012-04-30T00:00:00+0000 2.4 Crystal structure of NDM-1 bound to L-captopril
4EXY 2012-05-01T00:00:00+0000 1.47 Crystal structure of NDM-1 bound to ethylene glycol

Relevant UniProtKB Entries

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