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The mechanism of damage recognition by apurinic/apyrimidinic endonuclease Nfo from Escherichia coli Full article

Journal Biochimica et Biophysica Acta - General Subjects
ISSN: 0304-4165
Output data Year: 2022, Volume: 1866, Number: 11, Article number : 130216, Pages count : DOI: 10.1016/j.bbagen.2022.130216
Tags 5,6-dihydro-2′-deoxyuridine; Abasic site; Apurinic/apyrimidinic endonuclease; Conformational dynamics; Damaged DNA; DEER spectroscopy; DNA repair; FRET; Stopped-flow enzyme kinetics; α-2′-deoxyadenosine
Authors Senchurova S.I. 1 , Syryamina V.N. 2 , Kuznetsova A.A. 1 , Novopashina D.S. 1 , Ishchenko A.A. 3 , Saparbaev M. 3 , Dzuba S.A. 2 , Fedorova O.S. 1 , Kuznetsov N.A. 1,4
Affiliations
1 Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad, Lavrentieva, Novosibirsk, 630090, Russian Federation
2 Voevodsky Institute of Chemical Kinetics and Combustion, SB RAS, 3 Institutskaya Str., Novosibirsk, 630090, Russian Federation
3 Group «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif Cedex, F-94805, France
4 Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk, 630090, Russian Federation

Abstract: Apurinic/apyrimidinic (AP) endonuclease Nfo from Escherichia coli recognises AP sites in DNA and catalyses phosphodiester bond cleavage on the 5′ side of AP sites and some damaged or undamaged nucleotides. Here, the mechanism of target nucleotide recognition by Nfo was analysed by pulsed electron–electron double resonance (PELDOR, also known as DEER) spectroscopy and pre–steady-state kinetic analysis with Förster resonance energy transfer detection of DNA conformational changes during DNA binding. The efficiency of endonucleolytic cleavage of a target nucleotide in model DNA substrates was ranked as (2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran [F-site] > 5,6-dihydro-2′-deoxyuridine > α-anomer of 2′-deoxyadenosine >2′-deoxyuridine > undamaged DNA. Real-time conformational changes of DNA during interaction with Nfo revealed an increase of distances between duplex ends during the formation of the initial enzyme–substrate complex. The use of rigid-linker spin-labelled DNA duplexes in DEER measurements indicated that double-helix bending and unwinding by the target nucleotide itself is one of the key factors responsible for indiscriminate recognition of a target nucleotide by Nfo. The results for the first time show that AP endonucleases from different structural families utilise a common strategy of damage recognition, which globally may be integrated with the mechanism of searching for specific sites in DNA by other enzymes. © 2022
Cite: Senchurova S.I. , Syryamina V.N. , Kuznetsova A.A. , Novopashina D.S. , Ishchenko A.A. , Saparbaev M. , Dzuba S.A. , Fedorova O.S. , Kuznetsov N.A.
The mechanism of damage recognition by apurinic/apyrimidinic endonuclease Nfo from Escherichia coli
Biochimica et Biophysica Acta - General Subjects. 2022. V.1866. N11. 130216 . DOI: 10.1016/j.bbagen.2022.130216 WOS Scopus OpenAlex
Identifiers:
Web of science: WOS:000931946200004
Scopus: 2-s2.0-85136339002
OpenAlex: W4288045478
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Scopus 5
OpenAlex 6
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