AP lyases and dRPases

Commonality of mechanism

Research output: Contribution to journalArticle

74 Citations (Scopus)

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. Copyright (C) 2000 Elsevier Science B.V.

Original languageEnglish (US)
Pages (from-to)43-53
Number of pages11
JournalMutation Research - DNA Repair
Volume459
Issue number1
DOIs
StatePublished - Feb 16 2000
Externally publishedYes

Fingerprint

Lyases
DNA
DNA Glycosylases
Deoxyribose
Escherichia coli
DNA-Formamidopyrimidine Glycosylase
Enzymes
Phosphates
Imines
Endonucleases
Deoxyribonuclease I
Reducing Agents
Substrates
DNA Repair
Amines
Rats
Catalytic Domain
Repair
DNA deoxyribophosphodiesterase

Keywords

  • AP lyase
  • Deoxyribophosphodiesterase
  • DNA repair
  • dRPase

ASJC Scopus subject areas

  • Toxicology
  • Genetics
  • Molecular Biology

Cite this

AP lyases and dRPases : Commonality of mechanism. / Piersen, Colleen E.; McCullough, Amanda; Lloyd, Robert (Stephen).

In: Mutation Research - DNA Repair, Vol. 459, No. 1, 16.02.2000, p. 43-53.

Research output: Contribution to journalArticle

@article{5b85d1185bcf456d851e94c2c2a7caa8,
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 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. Copyright (C) 2000 Elsevier Science B.V.",
keywords = "AP lyase, Deoxyribophosphodiesterase, DNA repair, dRPase",
author = "Piersen, {Colleen E.} and Amanda McCullough and Lloyd, {Robert (Stephen)}",
year = "2000",
month = "2",
day = "16",
doi = "10.1016/S0921-8777(99)00054-3",
language = "English (US)",
volume = "459",
pages = "43--53",
journal = "Mutation Research - DNA Repair",
issn = "0921-8777",
publisher = "Elsevier BV",
number = "1",

}

TY - JOUR

T1 - AP lyases and dRPases

T2 - Commonality of mechanism

AU - Piersen, Colleen E.

AU - McCullough, Amanda

AU - Lloyd, Robert (Stephen)

PY - 2000/2/16

Y1 - 2000/2/16

N2 - 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. Copyright (C) 2000 Elsevier Science B.V.

AB - 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. Copyright (C) 2000 Elsevier Science B.V.

KW - AP lyase

KW - Deoxyribophosphodiesterase

KW - DNA repair

KW - dRPase

UR - http://www.scopus.com/inward/record.url?scp=0033951831&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0033951831&partnerID=8YFLogxK

U2 - 10.1016/S0921-8777(99)00054-3

DO - 10.1016/S0921-8777(99)00054-3

M3 - Article

VL - 459

SP - 43

EP - 53

JO - Mutation Research - DNA Repair

JF - Mutation Research - DNA Repair

SN - 0921-8777

IS - 1

ER -