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Acyl acceptor recognition by Enterococcus faecium L,D-transpeptidase Ldtfm.

Sébastien Triboulet^1,2,3, Catherine M Bougault^4,5,6, Cédric Laguri^4,5,6

¹INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Equipe 12, F-75006, Paris, France.

Molecular Microbiology

|June 24, 2015

Summary

Researchers identified the acceptor site of L,D-transpeptidase (Ldt) in Enterococcus faecium, a key enzyme in antibiotic resistance. This discovery aids in designing novel inhibitors to combat drug-resistant bacteria like Mycobacterium tuberculosis.

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Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Published on: December 12, 2017

Area of Science:

Microbiology
Structural Biology
Drug Discovery

Background:

L,D-transpeptidases (Ldts) confer resistance to β-lactam antibiotics in bacteria like Enterococcus faecium and Mycobacterium tuberculosis by forming unique peptidoglycan cross-links.
Carbapenem antibiotics, such as ertapenem, function by inactivating Ldts through acylation of their catalytic cysteine residue.

Purpose of the Study:

To elucidate the molecular interactions at the acyl acceptor site of E. faecium Ldt(fm) when bound to ertapenem.
To identify critical residues involved in substrate binding and catalysis within the Ldt(fm) active site.

Main Methods:

Nuclear Magnetic Resonance (NMR) spectroscopy to analyze chemical shift perturbations upon binding of peptidoglycan fragments to the ertapenem-inactivated Ldt(fm) (acylenzyme).
NMR-guided molecular docking to generate a structural model of the acylenzyme-acceptor complex.
Site-directed mutagenesis and a novel cross-linking assay to validate key interactions and identify essential residues.

Main Results:

The acyl acceptor site of Ldt(fm) was successfully mapped using NMR chemical shift perturbation analysis.
An NMR-driven docking model revealed crucial hydrogen bonding interactions between the peptidoglycan acceptor and Ldt(fm).
Three specific residues were identified as critical for stabilizing the acceptor substrate and orienting it for catalysis.

Conclusions:

The identification of the acceptor substrate-binding pocket in Ldt(fm) provides a new target for antimicrobial drug development.
These findings open avenues for designing novel inhibitors that can act independently or synergistically with existing β-lactam antibiotics to overcome bacterial resistance.