title: Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease.
abstract: The restriction endonuclease EcoRV binds two magnesium ions. One of these ions, Mg(A)(2+), binds to the phosphate group where the cleavage occurs and is required for catalysis, but the role of the other ion, Mg(B)(2+) is debated. Here, multiple independent molecular dynamics simulations suggest that Mg(B)(2+) is crucial for achieving a tightly bound protein-DNA complex and stabilizing a conformation that allows cleavage. In the absence of Mg(B)(2+) in all simulations the protein-DNA hydrogen bond network is significantly disrupted and the sharp kink at the central base pair step of the DNA, which is observed in the two-metal complex, is not present. Also, the active site residues rearrange in such a way that the formation of a nucleophile, required for DNA hydrolysis, is unlikely.
authors.affiliation: Computational Molecular Biophysics, IWR, University of Heidelberg, Heidelberg, Germany.
authors.forename: Mai
authors.initials: M
authors.lastname: Zahran
authors.forename: Tomasz
authors.initials: T
authors.lastname: Berezniak
authors.forename: Petra
authors.initials: P
authors.lastname: Imhof
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
mesh_terms: D018360:Crystallography, X-Ray; D004247:DNA / Q000378:metabolism*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry* / Q000378:metabolism*; D006860:Hydrogen Bonding; D008274:Magnesium / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding
chemical_list: D004247:DNA; D015252:Deoxyribonucleases, Type II Site-Specific; C027440:GATATC-specific type II deoxyribonucleases; D008274:Magnesium