Specificity of damage recognition and catalysis of DNA repair

A common feature of DNA repair enzymes is their ability to recognize the da mage independently of sequence in which they are found. The presence of a f lipped out base inserted into the protein in several DNA-enzyme complexes s uggests a contribution to enzyme specificity. Molecular simulations of dama ged DNA indicate that the damage produces changes in DNA structure and chan ges the dynamics of DNA bending. The reduced bending force constant can be used by the enzyme to induce DNA bending and facilitate base flipping. We s how that a thymine dimer (TD) containing DNA requires less energy to bend, lowering the barrier for base flipping. On the other hand, bending in DNA w ith U-G mismatch is affected only by a small amount and flipping is not enh anced significantly. T4 endonuclease V (endoV), which recognizes TD, utiliz es the reduced barrier for flipping as a specific recognition element. In u racil DNA glycosylase (UDG), which recognizes U-G mismatches, base flipping is not enhanced and recognition is encoded in a highly specific binding po cket for the flipped base. Simulations of UDG and endoV in complex with dam aged DNA provide insight into the essential elements of the catalytic mecha nism. Calculations of pK(a)s of active site residues in endoV and endoV-DNA complex show that the pK(a) of the N-terminus is reduced from 8.01 to 6.52 while that of Glu-23 increases from 1.52 to 7.82. Thus, the key catalytic residues are in their neutral form. The simulations also show that Glu-23 i s also H-bonded to O'(4) of the 5'-TD enhancing the nucleophilic attack on C'(1) and that Arg-26 enhances the hydrolysis by electrostatic stabilizatio n but does not participate in proton transfer. In the enzyme-substrate comp lex of UDG, the role of electrostatic stabilization is played by His-268, w hose pK(a) increases to 7.1 from 4.9 in the free enzyme. The pK(a) of Asp-1 45, the other important catalytic residue, remains around 4.2 in the free e nzyme and in the complex. Thus, it can not act as a proton acceptor. In the complex the 3'-phosphate of uracil is stabilized next to Asp-145 by two br idging water molecules. Such a configuration activates one water molecule t o act as a proton acceptor to produce a stabilizing hydronium ion and the o ther as a proton donor to produce the nucleophilic hydroxide. It appears th at DNA glycosylases share commonalties in recognition of damage but differ in their catalytic mechanisms. (C) 2000 Elsevier Science Ltd. All rights re served.