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Escherichia Coli Uracil DNA Glycosylase: NMR Characterization of the Short Hydrogen Bond From His 187 to Uracil 02



A C. Drohat, J T. Stivers


Uracil DNA glycosylase (UDG) cleaves the glycosidic bond of deoxyuridine in DNA using a hydrolytic mechanism, with an overall catalytic rate enhancement of 1012-fold over the solution reaction. The nature of the enzyme-substrate interactions that lead to this large rate enhancement are key to understanding enzymatic DNA repair. Using 1H and heteronuclear NMR spectroscopy, we have characterized one such interaction in the ternary product complex of Escherichia coli UDG, the short (2.7 ) H bond between His187 Ne2 and uracil O2. The H bond proton is highly desheilded at 15.6 ppm, indicating a short N-O distance, and exhibits a solvent exchange rate that is 400- and 105-fold slower than free imidazole at pH 7.5 and pH 10, respectively. Heteronuclear NMR experiments at neutral pH show that this H bond involves the neutral imidazole form of His187 and the N1-O2 imidate form of uracil. The excellent correspondence of the pKa for disappearance of the H bond (pKa = 6.3 0.1) with the previously determined pKa = 6.4 for the N1 proton of enzyme-bound uracil indicates that the H bond requires negative charge on uracil O2 [Drohat, A. C. and Stivers, J. T. (2000) J. Am. Chem. Soc. 122, 1840-1841]. Although the above characteristics suggest a short strong H bond, the D/H fractionation factor of diameter} = 1.0 is more typical of a normal H bond. This unexpected observation may reflect a large donor-acceptor pKa mismatch, or the net result of two opposing effects on vibrational frequencies: decreased N-H bond stretching frequencies (diameter} < 1), and increased bending frequencies (diameter} > 1) relative to the O-H bonds of water. The role of this H bond in catalysis by UDG, and several approaches to quantify the H bond energy are discussed.
No. 39


H/D fractionation, histidine 187, hydrogen bond energy, NMR spectroscopy, pH dependence, proton exchange rates, short hydrogen bond


Drohat, A. and Stivers, J. (2000), Escherichia Coli Uracil DNA Glycosylase: NMR Characterization of the Short Hydrogen Bond From His 187 to Uracil 02, Biochemistry (Accessed May 21, 2024)


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Created September 30, 2000, Updated October 12, 2021