Impact of remote mutations on metallo-beta-lactamase substrate specificity: implications for the evolution of antibiotic resistance


Abstract

Metallo-beta-lactamases have raised concerns due to their ability to hydrolyze a broad spectrum of beta-lactam antibiotics. The G262S point mutation distinguishing the metallo-beta-lactamase IMP-1 from IMP-6 has no effect on the hydrolysis of the drugs cephalothin and cefotaxime, but significantly improves catalytic efficiency toward cephaloridine, ceftazidime, benzylpenicillin, ampicillin, and imipenem. This change in specificity occurs even though residue 262 is remote from the active site. We investigated the substrate specificities of five other point mutants resulting from single-nucleotide substitutions at positions near residue 262: G262A, G262V, S121G, F218Y, and F218I. The results suggest two types of substrates: type I (nitrocefin, cephalothin, and cefotaxime), which are converted equally well by IMP-6, IMP-1, and G262A, but even more efficiently by the other mutants, and type II (ceftazidime, benzylpenicillin, ampicillin, and imipenem), which are hydrolyzed much less efficiently by all the mutants. G262V, S121G, F218Y, and F218I improve conversion of type I substrates, whereas G262A and IMP-1 improve conversion of type II substrates, indicating two distinct evolutionary adaptations from IMP-6. Substrate structure may explain the catalytic efficiencies observed. Type I substrates have R2 electron donors, which may stabilize the substrate intermediate in the binding pocket. In contrast, the absence of these stabilizing interactions with type II substrates may result in poor conversion. This observation may assist future drug design. As the G262A and F218Y mutants confer effective resistance to Escherichia coli BL21(DE3) cells (high minimal inhibitory concentrations), they are likely to evolve naturally.

Submission Details

ID: u4wcvuXA

Submitter: Peter Oelschlaeger

Submission Date: Dec. 11, 2018, 4:23 p.m.

Version: 1

Publication Details
Oelschlaeger P;Mayo SL;Pleiss J,Protein Sci (2005) Impact of remote mutations on metallo-beta-lactamase substrate specificity: implications for the evolution of antibiotic resistance. PMID:15722450
Additional Information

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
6JED 2019-08-07 1.57 Crystal structure of IMP-1 metallo-beta-lactamase in a complex with MCR
5Y5B 2018-08-08 1.7 Crystal Structure Of IMP-1 Metallo-beta-lactamase
4C1G 2014-08-27 1.71 Crystal structure of the metallo-beta-lactamase IMP-1 with D-captopril
5EV6 2016-06-01 1.98 Crystal structure of the native, di-zinc metallo-beta-lactamase IMP-1
1DD6 2000-11-08 2.0 IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH A MERCAPTOCARBOXYLATE INHIBITOR
5HH4 2017-01-18 2.0 Crystal structure of metallo-beta-lactamase IMP-1 in complex with a phosphonate-based inhibitor
4C1F 2014-08-27 2.01 Crystal structure of the metallo-beta-lactamase IMP-1 with L-captopril
1WUO 2005-03-29 2.01 Crystal structure of metallo-beta-lactamase IMP-1 mutant (D81A)
5EV8 2016-06-01 2.3 Crystal structure of the metallo-beta-lactamase IMP-1 in complex with the bisthiazolidine inhibitor D-CS319
5EWA 2016-06-01 2.3 Crystal structure of the metallo-beta-lactamase IMP-1 in complex with the bisthiazolidine inhibitor L-VC26
1VGN 2005-06-21 2.63 Structure-based design of the irreversible inhibitors to metallo--lactamase (IMP-1)
1WUP 2005-03-29 3.0 Crystal structure of metallo-beta-lactamase IMP-1 mutant (D81E)

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
200.0 A,B Metallo-beta-lactamase type 2 P52699 BLAB_SERMA