title: Stereochemical studies of the beta-elimination reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys.
abstract: 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 beta-elimination involving abstraction of the 2'-pro-S proton and formation of a trans alpha,beta-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 beta-elimination reaction. The beta-elimination reactions that occur under alkaline conditions (0.1 N NaOH) and in the presence of the tripeptide Lys-Trp-Lys proceed by anti beta-elimination mechanisms involving abstraction of the 2'-pro-R proton and formation of a trans alpha,beta-unsaturated aldose product. The different stereochemical outcomes of the enzymatic and nonenzymatic beta-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.
authors.affiliation: Department of Chemistry and Biochemistry, University of Maryland, College Park 20742.
authors.forename: A
authors.initials: A
authors.lastname: Mazumder
authors.forename: J A
authors.initials: JA
authors.lastname: Gerlt
authors.forename: M J
authors.initials: MJ
authors.lastname: Absalon
authors.forename: J
authors.initials: J
authors.lastname: Stubbe
authors.forename: R P
authors.initials: RP
authors.lastname: Cunningham
authors.forename: J
authors.initials: J
authors.lastname: Withka
authors.forename: P H
authors.initials: PH
authors.lastname: Bolton
mesh_terms: D000447:Aldehydes / Q000737:chemistry*; D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid; D004247:DNA / Q000378:metabolism*; D043224:Deoxyribonuclease (Pyrimidine Dimer); D004706:Endodeoxyribonucleases / Q000378:metabolism*; D004926:Escherichia coli / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics; D029968:Escherichia coli Proteins; D006859:Hydrogen; D006868:Hydrolysis; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000378:metabolism*; D010727:Phosphoric Diester Hydrolases / Q000737:chemistry; D012972:Sodium Hydroxide / Q000494:pharmacology; D013237:Stereoisomerism; D014466:Ultraviolet Rays
chemical_list: D000447:Aldehydes; D029968:Escherichia coli Proteins; D009842:Oligopeptides; C029535:lysyl-tryptophyl-alpha-lysine; D012972:Sodium Hydroxide; D006859:Hydrogen; D004247:DNA; D004706:Endodeoxyribonucleases; D043224:Deoxyribonuclease (Pyrimidine Dimer); C106403:NTH protein, E coli; D010727:Phosphoric Diester Hydrolases