Control of the N-glycosylase reaction by the DNA repair enzyme, MutY, entails the organization of solvent molecules. Classical molecular dynamics and QM/MM simulations were used to investigate the solvent and environment effects contributing to catalysis. Our ?ndings suggest that the entire reaction is energetically neutral, in which the ?rst step is rate-determining, requiring protonation of adenine (N7) to initiate cleavage, and the second step is strongly exothermic, involving hydrolysis of an oxacarbenium ion intermediate. Although water molecules are catalytically active in both steps, the ?rst step requires an entirely different level of solvent organization compared to the second. Needed to secure protonation at N7, a long term solvation pattern is established which facilitates the involvement of three structured water molecules in the active site. This persistent arrangement coordinates the catalytic water molecules into prime positions to assist the proton transfer: (i) a water molecule frequently bridges the catalytic residues and (ii) the bridging water molecule is assisted by 1-2 other 'supporting' water molecules. To maintain this con?guration, MutY, surprisingly, uses hydrophobic residues in combination with hydrophilic residues to tune the microenvironment into a 'water trap'. Hydrophilic residues prolong solvent residence times by maintaining hydrogen bonding networks, whereas the hydrophobic residues constrain the positioning of the catalytic water molecules that assist the proton transfer event. In this way, the enzyme uses both entropic and enthalpic considerations to guide the water-assisted reaction. 

Role of environment in the catalysis of the MutY DNA repair enzyme

245th National Meeting (2013)

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