4MLL

The 1.4 A structure of the class D beta-lactamase OXA-1 K70D complexed with oxacillin

Replaces:  4F7Y

Summary for 4MLL

• Entry DOI: 10.2210/pdb4mll/pdb
• Related: 4F94
• Descriptor: Beta-lactamase OXA-1, (2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid, PHOSPHATE ION, ... (5 entities in total)
• Functional Keywords: hydrolase, oxacillinase, antibiotic resistance, hydrolase-antibiotic complex, hydrolase/antibiotic
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 115220.08

Authors

June, C.M.,Vallier, B.C.,Bonomo, R.A.,Leonard, D.A.,Powers, R.A. (deposition date: 2013-09-06, release date: 2013-10-09, Last modification date: 2024-10-16)

Primary citation

June, C.M.,Vallier, B.C.,Bonomo, R.A.,Leonard, D.A.,Powers, R.A.
Structural Origins of Oxacillinase Specificity in Class D beta-Lactamases.
Antimicrob.Agents Chemother., 58:333-341, 2014

PubMed Abstract: Since the discovery and use of penicillin, the increase of antibiotic resistance among bacterial pathogens has become a major health concern. The most prevalent resistance mechanism in Gram-negative bacteria is due to β-lactamase expression. Class D β-lactamases are of particular importance due to their presence in multidrug-resistant Acinetobacter baumannii and Pseudomonas aeruginosa. The class D enzymes were initially characterized by their ability to efficiently hydrolyze isoxazolyl-type β-lactams like oxacillin. Due to this substrate preference, these enzymes are traditionally referred to as oxacillinases or OXAs. However, this class is comprised of subfamilies characterized by diverse activities that include oxacillinase, carbapenemase, or cephalosporinase substrate specificity. OXA-1 represents one subtype of class D enzyme that efficiently hydrolyzes oxacillin, and OXA-24/40 represents another with weak oxacillinase, but increased carbapenemase, activity. To examine the structural basis for the substrate selectivity differences between OXA-1 and OXA-24/40, the X-ray crystal structures of deacylation-deficient mutants of these enzymes (Lys70Asp for OXA-1; Lys84Asp for OXA-24) in complexes with oxacillin were determined to 1.4 Å and 2.4 Å, respectively. In the OXA-24/40/oxacillin structure, the hydrophobic R1 side chain of oxacillin disrupts the bridge between Tyr112 and Met223 present in the apo OXA-24/40 structure, causing the main chain of the Met223-containing loop to adopt a completely different conformation. In contrast, in the OXA-1/oxacillin structure, a hydrophobic pocket consisting of Trp102, Met99, Phe217, Leu161, and Leu255 nicely complements oxacillin's nonpolar R1 side chain. Comparison of the OXA-1/oxacillin and OXA-24/40/oxacillin complexes provides novel insight on how substrate selectivity is achieved among subtypes of class D β-lactamases. By elucidating important active site interactions, these findings can also inform the design of novel antibiotics and inhibitors.

PubMed: 24165180
DOI: 10.1128/AAC.01483-13

Experimental method

X-RAY DIFFRACTION (1.37 Å)