Evidence map›Paper›PMID 38729259›Full record

ArticleJournal of molecular biology2024

Structural and Dynamic Features of Acinetobacter baumannii OXA-66 β-Lactamase Explain Its Stability and Evolution of Novel Variants.

Zachary L Klamer, Cynthia M June, Zdzislaw Wawrzak, Magdalena A Taracila, Joshua A Grey, Alyssa M I Benn, Christopher P Russell, Robert A Bonomo, Rachel A Powers, David A Leonard and 1 more

Abstract read
In one paragraph

Article in Journal of molecular biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Zachary L KlamerDepartment of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA.
Cynthia M JuneDepartment of Chemistry, Grand Valley State University, Allendale, MI, USA.
Zdzislaw WawrzakLife Sciences Collaborative Access Team, Synchrotron Research Center, Northwestern University, Argonne, IL, USA.
Magdalena A TaracilaDepartment of Medicine, Case Western Reserve University, Cleveland, OH, USA; Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA.
Joshua A GreyDepartment of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA.
Alyssa M I BennDepartment of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA.
Christopher P RussellDepartment of Chemistry, Grand Valley State University, Allendale, MI, USA.
Robert A BonomoDepartment of Medicine, Case Western Reserve University, Cleveland, OH, USA; Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; Departments of Pharmacology, Biochemistry, and Molecular Biology and Microbiology, and Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH, USA. Electronic address: Rab14@case.edu.
Rachel A PowersDepartment of Chemistry, Grand Valley State University, Allendale, MI, USA. Electronic address: powersra@gvsu.edu.
David A LeonardDepartment of Chemistry, Grand Valley State University, Allendale, MI, USA. Electronic address: leonardd@gvsu.edu.
Agnieszka SzareckaDepartment of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA. Electronic address: szarecka@gvsu.edu.

Funding

Understanding B-Lactam Resistance in Acinetobacter baumanniiR01AI072219 · NIAID · CASE WESTERN RESERVE UNIVERSITY · PI ROBERT A. BONOMO, Philip N. Rather · 2007 to 2026
$6.6M
Investigations of the role of key active site residues of two class D lactamasesR15AI082416 · NIAID · GRAND VALLEY STATE UNIVERSITY · PI LEONARD, DAVID A · 2009 to 2015
$991k
Structure-based discovery and design of novel class D beta-lactamase inhibitorsR15AI094489 · NIAID · GRAND VALLEY STATE UNIVERSITY · PI POWERS, RACHEL · 2011 to 2014
$709k
The Continuing Challenge of Carbapenemases in K. pneumoniae: KPC-2 & NDM-1I01BX001974 · VA · LOUIS STOKES CLEVELAND VA MEDICAL CENTER · PI BONOMO, ROBERT A. · 2013 to 2024
–
BLRD VA I01 BX001974NIAID NIH HHS R01 AI072219NIAID NIH HHS R15 AI082416NIAID NIH HHS R15 AI094489
6 · The paper itself

Abstract

OXA-66 is a member of the OXA-51 subfamily of class D β-lactamases native to the Acinetobacter genus that includes Acinetobacter baumannii, one of the ESKAPE pathogens and a major cause of drug-resistant nosocomial infections. Although both wild type OXA-66 and OXA-51 have low catalytic activity, they are ubiquitous in the Acinetobacter genomes. OXA-51 is also remarkably thermostable. In addition, newly emerging, single and double amino acid variants show increased activity against carbapenems, indicating that the OXA-51 subfamily is growing and gaining clinical significance. In this study, we used molecular dynamics simulations, X-ray crystallography, and thermal denaturation data to examine and compare the dynamics of OXA-66 wt and its gain-of-function variants: I129L (OXA-83), L167V (OXA-82), P130Q (OXA-109), P130A, and W222L (OXA-234). Our data indicate that OXA-66 wt also has a high melting temperature, and its remarkable stability is due to an extensive and rigid hydrophobic bridge formed by a number of residues around the active site and harbored by the three loops, P, Ω, and β5-β6. Compared to the WT enzyme, the mutants exhibit higher flexibility only in the loop regions, and are more stable than other robust carbapenemases, such as OXA-23 and OXA-24/40. All the mutants show increased rotational flexibility of residues I129 and W222, which allows carbapenems to bind. Overall, our data support the hypothesis that structural features in OXA-51 and OXA-66 promote evolution of multiple highly stable variants with increased clinical relevance in A. baumannii.

Indexed as

Acinetobacter baumanniibeta-LactamasesMolecular Dynamics SimulationBacterial ProteinsCarbapenemsCatalytic DomainCrystallography, X-RayEnzyme StabilityEvolution, MolecularProtein ConformationBacterial Proteinsbeta-LactamasesCarbapenemsAntibiotic resistanceCarbapenem bindingOXA-109OXA-82Thermal stability

Identifiers

PMID38729259
PMCPMC11198252

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.