The structure of a doripenem‐bound OXA‐51 class D β‐lactamase variant with enhanced carbapenemase activity

Journal Article · Mon Sep 26 00:00:00 EDT 2016 · Protein Science

DOI:https://doi.org/10.1002/pro.3040· OSTI ID:1401875

June, Cynthia M. ^[1]; Muckenthaler, Taylor J. ^[1]; Schroder, Emma C. ^[1]; Klamer, Zachary L. ^[2]; Wawrzak, Zdzislaw ^[3]; Powers, Rachel A. ^[1]; Szarecka, Agnieszka ^[2]; Leonard, David A. ^[1]

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1. Department of Chemistry Grand Valley State University Allendale Michigan 49401
2. Department of Cell and Molecular Biology Grand Valley State University Allendale Michigan 49401
3. Life Sciences Collaborative Access Team, Synchrotron Research Center, Northwestern University Argonne Illinois 60439

Abstract OXA‐51 is a class D β‐lactamase that is thought to be the native carbapenemase of Acinetobacter baumannii . Many variants of OXA‐51 containing active site substitutions have been identified from A. baumannii isolates, and some of these substitutions increase hydrolytic activity toward carbapenem antibiotics. We have determined the high‐resolution structures of apo OXA‐51 and OXA‐51 with one such substitution (I129L) with the carbapenem doripenem trapped in the active site as an acyl‐intermediate. The structure shows that acyl‐doripenem adopts an orientation very similar to carbapenem ligands observed in the active site of OXA‐24/40 (doripenem) and OXA‐23 (meropenem). In the OXA‐51 variant/doripenem complex, the indole ring of W222 is oriented away from the doripenem binding site, thereby eliminating a clash that is predicted to occur in wildtype OXA‐51. Similarly, in the OXA‐51 variant complex, L129 adopts a different rotamer compared to I129 in wildtype OXA‐51. This alternative position moves its side chain away from the hydroxyethyl moiety of doripenem and relieves another potential clash between the enzyme and carbapenem substrates. Molecular dynamics simulations of OXA‐51 and OXA‐51 I129L demonstrate that compared to isoleucine, a leucine at this position greatly favors a rotamer that accommodates the ligand. These results provide a molecular justification for how this substitution generates enhanced binding affinity for carbapenems, and therefore helps explain the prevalence of this substitution in clinical OXA‐51 variants.

• Sponsoring Organization: USDOE
• Grant/Contract Number: DE‐AC02‐06CH11357
• OSTI ID: 1401875
• Journal Information: Protein Science, Journal Name: Protein Science Vol. 25 Journal Issue: 12; ISSN 0961-8368
• Publisher: Wiley Blackwell (John Wiley & Sons)
• Country of Publication: United Kingdom
• Language: English