title: 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 beta (beta-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 NaBH(4) as the reducing agent. These results further support the assertion that the catalytic mechanism of the AP lyases, the beta-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 beta-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.
authors.affiliation: Center for Molecular Science, University of Texas Medical Branch, Galveston, TX 77555-1071, USA.
authors.forename: C E
authors.initials: CE
authors.lastname: Piersen
authors.forename: A K
authors.initials: AK
authors.lastname: McCullough
authors.forename: R S
authors.initials: RS
authors.lastname: Lloyd
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry; D017122:Bacteriophage T4 / Q000737:chemistry; D019757:Carbon-Oxygen Lyases / Q000737:chemistry*; D004249:DNA Damage; D019951:DNA Polymerase beta / Q000737:chemistry; D004260:DNA Repair; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase; D043382:DNA-Formamidopyrimidine Glycosylase; D043224:Deoxyribonuclease (Pyrimidine Dimer); D043223:Deoxyribonuclease IV (Phage T4-Induced); D004706:Endodeoxyribonucleases / Q000737:chemistry; D004926:Escherichia coli / Q000737:chemistry; D029968:Escherichia coli Proteins; D005090:Exodeoxyribonucleases / Q000737:chemistry; D009699:N-Glycosyl Hydrolases / Q000737:chemistry; D010727:Phosphoric Diester Hydrolases / Q000737:chemistry*; D051381:Rats; D014764:Viral Proteins
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D014764:Viral Proteins; D019951:DNA Polymerase beta; D004706:Endodeoxyribonucleases; D005090:Exodeoxyribonucleases; C489467:RecJ protein, E coli; C070765:recJ protein, Bacteria; C028450:exodeoxyribonuclease I; D043223:Deoxyribonuclease IV (Phage T4-Induced); C468972:endonuclease IV, E coli; C470698:endonuclease V, phage T4; D043224:Deoxyribonuclease (Pyrimidine Dimer); C106403:NTH protein, E coli; C058246:DNA deoxyribophosphodiesterase; D010727:Phosphoric Diester Hydrolases; D009699:N-Glycosyl Hydrolases; D043382:DNA-Formamidopyrimidine Glycosylase; C468610:DNA-formamidopyrimidine glycosylase, E coli; D019757:Carbon-Oxygen Lyases; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase