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.
Submitter: Paulie Dang
Submission Date: Sept. 24, 2019, 10:10 a.m.
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.
|Number of data points||382|
|Proteins||Metallo-beta-lactamase type 2|
|Assays/Quantities/Protocols||Experimental Assay: Kcat ; Experimental Assay: Kcat/Km ; Experimental Assay: Km ; Experimental Assay: MIC Absolute ; Experimental Assay: Melting Temperature ; Experimental Assay: MIC Relative ; Experimental Assay: Resistance ; Derived Quantity: SD of Melting Temperature ; Derived Quantity: SD of Km|
|Libraries||MIC Assay Data ; Melting Temperature Data ; Kinetic Assay Data|
|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)|
|5ZJ7||2018-03-19T00:00:00+0000||0.96||Crystal structure of NDM-1 in complex with D-captopril derivative CY22|
|5ZJ8||2018-03-19T00:00:00+0000||0.96||Crystal structure of NDM-1 in complex with D-captopril derivative CY32|
|5ZGP||2018-03-10T00:00:00+0000||1.15||Crystal structure of NDM-1 at pH6.2 (Bis-Tris) in complex with hydrolyzed ampicillin|
|5ZH1||2018-03-10T00:00:00+0000||1.05||Crystal structure of NDM-1 at pH7.5 (Imidazole) with 2 molecules per asymmetric unit|
|6LJ7||2019-12-13T00:00:00+0000||1.16||Crystal structure of NDM-1 in complex with D-captopril derivative wss05010|
|3SBL||2011-06-05T00:00:00+0000||2.31||Crystal Structure of New Delhi Metal-beta-lactamase-1 from Klebsiella pneumoniae|
|Percent Identity||Matching Chains||Protein||Accession||Entry Name|
|200.0||A,B||Metallo-beta-lactamase type 2||C7C422||BLAN1_KLEPN|