A Distal Disulfide Bridge in OXA-1 β-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Ω Loop.
Widespread antibiotic resistance, particularly when mediated by broad-spectrum β-lactamases, has major implications for public health. Substitutions in the active site often allow broad-spectrum enzymes to accommodate diverse types of β-lactams. Substitutions observed outside the active site are thought to compensate for the loss of thermal stability. The OXA-1 clade of class D β-lactamases contains a pair of conserved cysteines located outside the active site that forms a disulfide bond in the periplasm. Here, the effect of the distal disulfide bond on the structure and dynamics of OXA-1 was investigated via 4 μs molecular dynamics simulations. The results reveal that the disulfide promotes the preorganized orientation of the catalytic residues and affects the conformation of the functionally important Ω loop. Furthermore, principal component analysis reveals differences in the global dynamics between the oxidized and reduced forms, especially in the motions involving the Ω loop. A dynamical network analysis indicates that, in the oxidized form, in addition to its role in ligand binding, the KTG family motif is a central hub of the global dynamics. As activity of OXA-1 has been measured only in the reduced form, we suggest that accurate assessment of its functional profile would require oxidative conditions mimicking periplasm.
Carnegie Mellon University , Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania 15213, United States.|Center for Computational Research, SUNY at Buffalo , New York 14203, United States.
Nikolay
N
Simakov
David A
DA
Leonard
Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.
Jeremy C
JC
Smith
Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.|Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States.
Troy
T
Wymore
Agnieszka
A
Szarecka
D055162:Biocatalysis; D004220:Disulfides / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D013379:Substrate Specificity; D001618:beta-Lactamases / Q000737:chemistry / Q000378:metabolism*
D004220:Disulfides; C039404:beta-lactamase OXA-2; D001618:beta-Lactamases