Stereochemical Studies of the β-Elimination Reactions at Aldehydic Abasic Sites in DNA: Endonuclease III from Escherichia coli, Sodium Hydroxide, and Lys-Trp-Lys

The DNA strand cleavage reaction catalyzed by endonuclease III from Escherichia coli (endo III) on the 3′-side of aldehyde abasic sites proceeds by a syn β-elimination involving ABSTRACTion of the 2′-pro-S proton and formation of a trans α,β-unsaturated aldose product; we previously reported the same stereochemical course for the reaction catalyzed by UV endonuclease V from bacteriophage T₄ (UV endo V) [Mazumder, A., Gerlt, J. A., Rabow, L., Absalon, M. J., Stubbe, J., & Bolton, P. H. (1989) J. Am. Chem. Soc. 111, 8029-8030]. Since the UV endo V does not contain an 4Fe-4S center, the 4Fe-4S center present in endo III need not be assigned a unique role in the β-elimination reaction. The β-elimination reactions that occur under alkaline conditions (0.1 N NaOH) and in the presence of the tripeptide Lys-Trp-Lys proceed by anti β-elimination mechanisms involving ABSTRACTion of the 2′-pro-R proton and formation of a trans α,β-unsaturated aldose product. The different stereochemical outcomes of the enzymatic and nonenzymatic β-elimination reactions support the hypothesis that the enzyme-catalyzed reactions may involve general-base-catalyzed ABSTRACTion of the 2′-pro-S proton by the internucleotidic phosphodiester leaving group.