Metallo-β-lactamase structure and function

Abstract

β-Lactam antibiotics are the most commonly used antibacterial agents and growing resistance to these drugs is a concern. Metallo-β-lactamases are a diverse set of enzymes that catalyze the hydrolysis of a broad range of β-lactam drugs including carbapenems. This diversity is reflected in the observation that the enzyme mechanisms differ based on whether one or two zincs are bound in the active site that, in turn, is dependent on the subclass of β-lactamase. The dissemination of the genes encoding these enzymes among Gram-negative bacteria has made them an important cause of resistance. In addition, there are currently no clinically available inhibitors to block metallo-β-lactamase action. This review summarizes the numerous studies that have yielded insights into the structure, function, and mechanism of action of these enzymes.

Figure 1

Illustration showing the acylation of β-lactam antibiotic by transpeptidases and β-lactamases and subsequent trapping of the transpeptidase versus deacylation and hydrolysis by the β-lactamases.

Figure 2

Classes of β-lactam antibiotics. A. Core structure of penicillin. Different R-groups distinguish various penicillins. B. Cephalosporin core structure. C. Monobactam core structure. D. Carbapenem core structure. Atoms are numbered for reference to discussion in the text.

Figure 3

Schematic illustration of the amino acid residues that serve as zinc binders in the active sites of subclass B1, B2, and B3 metallo-β-lactamases. A. Active site zinc chelator residues for the Bacteroidesfragilis subclass B1 CcrA enzyme (pdb ID: 1ZNB) . B. Active site zinc binding residues for Aeromonashydrophilamonozinc enzyme of subclass B2 (pdb ID: 1X8G). C. Active site zinc binding residues for Stenotrophomonasmaltophilia L1 enzyme of subclass B3 (pdb ID: 1SML). Zinc ions are labeled and shown as spheres.

Figure 4

Schematic illustration of cephalosporin binding to dizincmetallo-β-lactamase active site (subclasses B1 and B3). The zinc ions are labeled and interactions are shown with dashed lines. A. Cephalosporin substrate bound to active sites with interactions to both Zn1 and Zn2 via the carbonyl oxygen and carboxyl groups, respectively. The bound hydroxide is positioned to attack the carbonyl carbon of the substrate. B. Anionic intermediate bound in the active site via stabilizing interactions provided by Zn2.

Figure 5

Carbapenem substrate and anionic intermediate binding to monozincmetallo-β-lactamase active site (subclass B2). A. Carbapenem binding to monozinc active site. An active site water bonds with Asp120 and His118 and is activated for attack on the carbonyl carbon of the carbapenem. B. Anionic intermediate shown stabilized in the active site by interactions with the Zn2 ion.

Figure 6

Illustration showing the closure of loop L3 over bound inhibitor in the subclass B1 CcrAβ-lactamase. A. Active site structure with L3 loop shown in cartoon of the CcrA enzyme without inhibitor bound. Zn2 is closest to the loop to the left and Zn1 is on the right side of the figure (PDB ID: 2BMI). B. CcrA active site with L159,061 inhibitor bound (PDB ID: 1A8T). The bound inhibitor molecule is colored white. The Trp64 (class B numbering system) is shown on the tip of the L3 loop.