Trapping of an acyl-enzyme intermediate in a penicillin-binding protein (PBP)-catalyzed reaction |
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Authors: | Macheboeuf Pauline Lemaire David Teller Nathalie Martins Alexandre Dos Santos Luxen André Dideberg Otto Jamin Marc Dessen Andréa |
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Institution: | 1 Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 (CEA, CNRS, UJF, PSB), 41 rue Jules Horowitz, F-38027 Grenoble, France 2 Laboratoire des Interactions Protéine Métal, CEA-Cadarache, IBEB/SBVME, Bât 185, 13108 Saint Paul-lez-Durance, France 3 Unit of Virus Host Cell Interactions, UMR 5233 UJF-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France |
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Abstract: | Class A penicillin-binding proteins (PBPs) catalyze the last two steps in the biosynthesis of peptidoglycan, a key component of the bacterial cell wall. Both reactions, glycosyl transfer (polymerization of glycan chains) and transpeptidation (cross-linking of stem peptides), are essential for peptidoglycan stability and for the cell division process, but remain poorly understood. The PBP-catalyzed transpeptidation reaction is the target of β-lactam antibiotics, but their vast employment worldwide has prompted the appearance of highly resistant strains, thus requiring concerted efforts towards an understanding of the transpeptidation reaction with the goal of developing better antibacterials. This goal, however, has been elusive, since PBP substrates are rapidly deacylated. In this work, we provide a structural snapshot of a “trapped” covalent intermediate of the reaction between a class A PBP with a pseudo-substrate, N-benzoyl-d-alanylmercaptoacetic acid thioester, which partly mimics the stem peptides contained within the natural, membrane-associated substrate, lipid II. The structure reveals that the d-alanyl moiety of the covalent intermediate (N-benzoyl-d-alanine) is stabilized in the cleft by a network of hydrogen bonds that place the carbonyl group in close proximity to the oxyanion hole, thus mimicking the spatial arrangement of β-lactam antibiotics within the PBP active site. This arrangement allows the target bond to be in optimal position for attack by the acceptor peptide and is similar to the structural disposition of β-lactam antibiotics with PBP clefts. This information yields a better understanding of PBP catalysis and could provide key insights into the design of novel PBP inhibitors. |
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Keywords: | PBP penicillin-binding protein S2d d-alanylmercaptoacetic acid thioester" target="_blank">N-benzoyl-d-alanylmercaptoacetic acid thioester GT glycosyl transfer TP transpeptidation HMM high molecular mass d-ala" target="_blank">N-Bz-d-ala d-alanine" target="_blank">N-benzoyl-d-alanine |
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