Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA

Modesto Redrejo-Rodríguez, Armelle Vigouroux, Aibek Mursalimov, Inga Grin, Doria Alili, Zhanat Koshenov, Zhiger Akishev, Andrei Maksimenko, Amangeldy K. Bissenbaev, Bakhyt T. Matkarimov, Murat Saparbaev, Alexander A. Ishchenko, Solange Moréra

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Oxidatively damaged DNA bases are substrates for two overlapping repair pathways: DNA glycosylase-initiated base excision repair (BER) and apurinic/apyrimidinic (AP) endonuclease-initiated nucleotide incision repair (NIR). In the BER pathway, an AP endonuclease cleaves DNA at AP sites and 3′-blocking moieties generated by DNA glycosylases, whereas in the NIR pathway, the same AP endonuclease incises DNA 5′ to an oxidized base. The majority of characterized AP endonucleases possess classic BER activities, and approximately a half of them can also have a NIR activity. At present, the molecular mechanism underlying DNA substrate specificity of AP endonucleases remains unclear mainly due to the absence of a published structure of the enzyme in complex with a damaged base. To identify critical residues involved in the NIR function, we performed biochemical and structural characterization of Bacillus subtilis AP endonuclease ExoA and compared its crystal structure with the structures of other AP endonucleases: Escherichia coli exonuclease III (Xth), human APE1, and archaeal Mth212. We found conserved amino acid residues in the NIR-specific enzymes APE1, Mth212, and ExoA. Four of these positions were studied by means of point mutations in APE1: we applied substitution with the corresponding residue found in NIR-deficient E. coli Xth (Y128H, N174Q, G231S, and T268D). The APE1-T268D mutant showed a drastically decreased NIR activity and an inverted Mg2+ dependence of the AP site cleavage activity, which is in line with the presence of an aspartic residue at the equivalent position among other known NIR-deficient AP endonucleases. Taken together, these data show that NIR is an evolutionarily conserved function in the Xth family of AP endonucleases.

Original languageEnglish
Pages (from-to)20-33
Number of pages14
JournalBiochimie
Volume128-129
DOIs
Publication statusPublished - Sep 1 2016

Fingerprint

Endonucleases
Repair
Nucleotides
Amino Acids
DNA
DNA Repair
DNA Glycosylases
Deoxyribonuclease I
DNA-(Apurinic or Apyrimidinic Site) Lyase
Escherichia coli
exodeoxyribonuclease III
Enzymes
Substrate Specificity
Bacillus subtilis
Point Mutation
Bacilli
Substrates
Substitution reactions
Crystal structure

Keywords

  • AP endonuclease
  • Base excision repair
  • Crystal structure
  • Nucleotide incision repair
  • Oxidative DNA damage

ASJC Scopus subject areas

  • Biochemistry

Cite this

Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA. / Redrejo-Rodríguez, Modesto; Vigouroux, Armelle; Mursalimov, Aibek; Grin, Inga; Alili, Doria; Koshenov, Zhanat; Akishev, Zhiger; Maksimenko, Andrei; Bissenbaev, Amangeldy K.; Matkarimov, Bakhyt T.; Saparbaev, Murat; Ishchenko, Alexander A.; Moréra, Solange.

In: Biochimie, Vol. 128-129, 01.09.2016, p. 20-33.

Research output: Contribution to journalArticle

Redrejo-Rodríguez, M, Vigouroux, A, Mursalimov, A, Grin, I, Alili, D, Koshenov, Z, Akishev, Z, Maksimenko, A, Bissenbaev, AK, Matkarimov, BT, Saparbaev, M, Ishchenko, AA & Moréra, S 2016, 'Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA', Biochimie, vol. 128-129, pp. 20-33. https://doi.org/10.1016/j.biochi.2016.06.011
Redrejo-Rodríguez, Modesto ; Vigouroux, Armelle ; Mursalimov, Aibek ; Grin, Inga ; Alili, Doria ; Koshenov, Zhanat ; Akishev, Zhiger ; Maksimenko, Andrei ; Bissenbaev, Amangeldy K. ; Matkarimov, Bakhyt T. ; Saparbaev, Murat ; Ishchenko, Alexander A. ; Moréra, Solange. / Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA. In: Biochimie. 2016 ; Vol. 128-129. pp. 20-33.
@article{93dc6dcf3cbc4ea4bc12510d4df83ccd,
title = "Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA",
abstract = "Oxidatively damaged DNA bases are substrates for two overlapping repair pathways: DNA glycosylase-initiated base excision repair (BER) and apurinic/apyrimidinic (AP) endonuclease-initiated nucleotide incision repair (NIR). In the BER pathway, an AP endonuclease cleaves DNA at AP sites and 3′-blocking moieties generated by DNA glycosylases, whereas in the NIR pathway, the same AP endonuclease incises DNA 5′ to an oxidized base. The majority of characterized AP endonucleases possess classic BER activities, and approximately a half of them can also have a NIR activity. At present, the molecular mechanism underlying DNA substrate specificity of AP endonucleases remains unclear mainly due to the absence of a published structure of the enzyme in complex with a damaged base. To identify critical residues involved in the NIR function, we performed biochemical and structural characterization of Bacillus subtilis AP endonuclease ExoA and compared its crystal structure with the structures of other AP endonucleases: Escherichia coli exonuclease III (Xth), human APE1, and archaeal Mth212. We found conserved amino acid residues in the NIR-specific enzymes APE1, Mth212, and ExoA. Four of these positions were studied by means of point mutations in APE1: we applied substitution with the corresponding residue found in NIR-deficient E. coli Xth (Y128H, N174Q, G231S, and T268D). The APE1-T268D mutant showed a drastically decreased NIR activity and an inverted Mg2+ dependence of the AP site cleavage activity, which is in line with the presence of an aspartic residue at the equivalent position among other known NIR-deficient AP endonucleases. Taken together, these data show that NIR is an evolutionarily conserved function in the Xth family of AP endonucleases.",
keywords = "AP endonuclease, Base excision repair, Crystal structure, Nucleotide incision repair, Oxidative DNA damage",
author = "Modesto Redrejo-Rodr{\'i}guez and Armelle Vigouroux and Aibek Mursalimov and Inga Grin and Doria Alili and Zhanat Koshenov and Zhiger Akishev and Andrei Maksimenko and Bissenbaev, {Amangeldy K.} and Matkarimov, {Bakhyt T.} and Murat Saparbaev and Ishchenko, {Alexander A.} and Solange Mor{\'e}ra",
year = "2016",
month = "9",
day = "1",
doi = "10.1016/j.biochi.2016.06.011",
language = "English",
volume = "128-129",
pages = "20--33",
journal = "Biochimie",
issn = "0300-9084",
publisher = "Elsevier",

}

TY - JOUR

T1 - Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA

AU - Redrejo-Rodríguez, Modesto

AU - Vigouroux, Armelle

AU - Mursalimov, Aibek

AU - Grin, Inga

AU - Alili, Doria

AU - Koshenov, Zhanat

AU - Akishev, Zhiger

AU - Maksimenko, Andrei

AU - Bissenbaev, Amangeldy K.

AU - Matkarimov, Bakhyt T.

AU - Saparbaev, Murat

AU - Ishchenko, Alexander A.

AU - Moréra, Solange

PY - 2016/9/1

Y1 - 2016/9/1

N2 - Oxidatively damaged DNA bases are substrates for two overlapping repair pathways: DNA glycosylase-initiated base excision repair (BER) and apurinic/apyrimidinic (AP) endonuclease-initiated nucleotide incision repair (NIR). In the BER pathway, an AP endonuclease cleaves DNA at AP sites and 3′-blocking moieties generated by DNA glycosylases, whereas in the NIR pathway, the same AP endonuclease incises DNA 5′ to an oxidized base. The majority of characterized AP endonucleases possess classic BER activities, and approximately a half of them can also have a NIR activity. At present, the molecular mechanism underlying DNA substrate specificity of AP endonucleases remains unclear mainly due to the absence of a published structure of the enzyme in complex with a damaged base. To identify critical residues involved in the NIR function, we performed biochemical and structural characterization of Bacillus subtilis AP endonuclease ExoA and compared its crystal structure with the structures of other AP endonucleases: Escherichia coli exonuclease III (Xth), human APE1, and archaeal Mth212. We found conserved amino acid residues in the NIR-specific enzymes APE1, Mth212, and ExoA. Four of these positions were studied by means of point mutations in APE1: we applied substitution with the corresponding residue found in NIR-deficient E. coli Xth (Y128H, N174Q, G231S, and T268D). The APE1-T268D mutant showed a drastically decreased NIR activity and an inverted Mg2+ dependence of the AP site cleavage activity, which is in line with the presence of an aspartic residue at the equivalent position among other known NIR-deficient AP endonucleases. Taken together, these data show that NIR is an evolutionarily conserved function in the Xth family of AP endonucleases.

AB - Oxidatively damaged DNA bases are substrates for two overlapping repair pathways: DNA glycosylase-initiated base excision repair (BER) and apurinic/apyrimidinic (AP) endonuclease-initiated nucleotide incision repair (NIR). In the BER pathway, an AP endonuclease cleaves DNA at AP sites and 3′-blocking moieties generated by DNA glycosylases, whereas in the NIR pathway, the same AP endonuclease incises DNA 5′ to an oxidized base. The majority of characterized AP endonucleases possess classic BER activities, and approximately a half of them can also have a NIR activity. At present, the molecular mechanism underlying DNA substrate specificity of AP endonucleases remains unclear mainly due to the absence of a published structure of the enzyme in complex with a damaged base. To identify critical residues involved in the NIR function, we performed biochemical and structural characterization of Bacillus subtilis AP endonuclease ExoA and compared its crystal structure with the structures of other AP endonucleases: Escherichia coli exonuclease III (Xth), human APE1, and archaeal Mth212. We found conserved amino acid residues in the NIR-specific enzymes APE1, Mth212, and ExoA. Four of these positions were studied by means of point mutations in APE1: we applied substitution with the corresponding residue found in NIR-deficient E. coli Xth (Y128H, N174Q, G231S, and T268D). The APE1-T268D mutant showed a drastically decreased NIR activity and an inverted Mg2+ dependence of the AP site cleavage activity, which is in line with the presence of an aspartic residue at the equivalent position among other known NIR-deficient AP endonucleases. Taken together, these data show that NIR is an evolutionarily conserved function in the Xth family of AP endonucleases.

KW - AP endonuclease

KW - Base excision repair

KW - Crystal structure

KW - Nucleotide incision repair

KW - Oxidative DNA damage

UR - http://www.scopus.com/inward/record.url?scp=84978153667&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84978153667&partnerID=8YFLogxK

U2 - 10.1016/j.biochi.2016.06.011

DO - 10.1016/j.biochi.2016.06.011

M3 - Article

VL - 128-129

SP - 20

EP - 33

JO - Biochimie

JF - Biochimie

SN - 0300-9084

ER -