Abstract
Abstract Computer modeling based on a molecular mechanics approach was used to explore the mechanism of staphylococcal nuclease action on the thymidine 3′-phosphate 5′-(p-nitrophenyl phosphate)-calcium ion substrate complex. The active-site residues Asp-21, Asp-40, Glu-43, Arg-35, Tyr-113, Lys-84, Arg-87, and Tyr-85 were included in the calculation. Initially the X-ray coordinates were used for the enzyme active-site residues with the inhibitor substrate, thymidine 3′,5′-bis(phosphate) (pdTp), in place. Subsequently, introduction of the p-nitrophenyl group and energy minimization gave the coordinates for the active substrate. In-line attack by hydroxide was simulated by approach opposite the phosphoryl oxygen atom attached to the p-nitrophenyl group (path 1) and by approach opposite the phosphoryl oxygen atom attached to thymidine (path 2). The former pathway is the route that leads to products observed in nonenzymatic cleavage. The latter pathway is the enzymatic route. Computer simulation of the hydroly...
Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callMore From: Phosphorus, Sulfur, and Silicon and the Related Elements
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
