title: Kinetic isotope effect studies of the reaction catalyzed by uracil DNA glycosylase: evidence for an oxocarbenium ion-uracil anion intermediate.
abstract: The DNA repair enzyme uracil DNA glycosylase catalyzes the first step in the uracil base excision repair pathway, the hydrolytic cleavage of the N-glycosidic bond of deoxyuridine in DNA. Here we report kinetic isotope effect (KIE) measurements that have allowed the determination of the transition-state structure for this important reaction. The small primary (13)C KIE (=1.010 +/- 0.009) and the large secondary alpha-deuterium KIE (=1.201 +/- 0.021) indicate that (i) the glycosidic bond is essentially completely broken in the transition state and (ii) there is significant sp(2) character at the anomeric carbon. Large secondary beta-deuterium KIEs were observed when [2'R-(2)H] = 1.102 +/- 0.011 and [2'S-(2)H] = 1.106 +/- 0.010. The nearly equal and large magnitudes of the two stereospecific beta-deuterium KIEs indicate strong hyperconjugation between the elongated glycosidic bond and both of the C2'-H2' bonds. Geometric interpretation of these beta-deuterium KIEs indicates that the furanose ring adopts a mild 3'-exo sugar pucker in the transition state, as would be expected for maximal stabilization of an oxocarbenium ion. Taken together, these results strongly indicate that the reaction proceeds through a dissociative transition state, with complete dissociation of the uracil anion followed by addition of water. To our knowledge, this is the first transition-state structure determined for enzymatic cleavage of the glycosidic linkage in a pyrimidine deoxyribonucleotide.
authors.affiliation: Center for Advanced Research in Biotechnology of the University of Maryland Biotechnology Institutes and National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.
authors.forename: R M
authors.initials: RM
authors.lastname: Werner
authors.forename: J T
authors.initials: JT
authors.lastname: Stivers
mesh_terms: D000838:Anions; D001665:Binding Sites; D002384:Catalysis; D002851:Chromatography, High Pressure Liquid; D045647:DNA Glycosylases; D004260:DNA Repair; D004277:DNA, Single-Stranded / Q000138:chemical synthesis; D003857:Deoxyuridine / Q000737:chemistry; D003903:Deuterium; D006027:Glycosides / Q000737:chemistry; D007700:Kinetics; D009699:N-Glycosyl Hydrolases / Q000737:chemistry*; D055672:Static Electricity; D013379:Substrate Specificity; D014316:Tritium / Q000737:chemistry; D014498:Uracil / Q000737:chemistry*; D051981:Uracil-DNA Glycosidase
chemical_list: D000838:Anions; D004277:DNA, Single-Stranded; D006027:Glycosides; D014316:Tritium; D014498:Uracil; D003903:Deuterium; D045647:DNA Glycosylases; D009699:N-Glycosyl Hydrolases; D051981:Uracil-DNA Glycosidase; D003857:Deoxyuridine