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Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease
Author(s) -
Zahran Mai,
Berezniak Tomasz,
Imhof Petra,
Smith Jeremy C.
Publication year - 2011
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2011.07.036
Subject(s) - ecorv , dna , restriction enzyme , chemistry , cleavage (geology) , endonuclease , magnesium , ion , recognition sequence , bond cleavage , crystallography , stereochemistry , hindiii , catalysis , biochemistry , biology , organic chemistry , paleontology , fracture (geology)
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 thatMg B 2 +is crucial for achieving a tightly bound protein–DNA complex and stabilizing a conformation that allows cleavage. In the absence ofMg 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.