AP lyases and dRPases: commonality of mechanism

Abstract

Enzymes that release 5′-deoxyribose-5-phosphate (dRP) residues from preincised apurinic/apyrimidinic (AP) DNA have been collectively termed DNA deoxyribophosphodiesterases (dRPases), but they fall into two distinct categories: the hydrolytic dRPases and AP lyases. In order to resolve a number of conflicting reports in the dRPase literature, we examined two putative hydrolytic dRPases (Escherichia coli exonuclease I (exo I) and RecJ) and four AP lyases (E. coli 2,6-dihydroxy-5N-formamidopyrimidine (Fapy) DNA glycosylase (Fpg) and endonuclease III (endo III), bacteriophage T4 endonuclease V (endo V), and rat polymerase β (β-pol)) for their abilities to (i) excise dRP from preincised AP DNA and (ii) incise AP DNA. Although exo I and RecJ exhibited robust 3′ to 5′ and 5′ to 3′ exonucleolytic activities, respectively, on appropriate substrates, they failed to demonstrate detectable dRPase activity. All four AP lyases possessed both dRPase and traditional AP lyase activities, albeit to varying degrees. Moreover, as best illustrated with Fpg, AP lyase enzymes could be trapped on both preincised and unincised AP DNA using NaBH4 as the reducing agent. These results further support the assertion that the catalytic mechanism of the AP lyases, the β-elimination reaction, does proceed through an imine enzyme–DNA intermediate and that the active site residues responsible for dRP release must contain primary amines. Further, these data indicate a biological significance for the β-elimination reaction of DNA glycosylase/AP lyases in that they, in concert with hydrolytic AP endonucleases, can create appropriate gapped substrates for short patch base excision repair (BER) synthesis to occur efficiently.