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Article

The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1

1
Institute of Chemical Biology and Fundamental Medicine, Lavrentyev Ave. 8, 630090 Novosibirsk, Russia
2
Department of Natural Sciences, Novosibirsk State University, Pirogova St. 2, 630090 Novosibirsk, Russia
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: James W. Gauld
Molecules 2020, 25(17), 3940; https://doi.org/10.3390/molecules25173940
Received: 4 August 2020 / Revised: 25 August 2020 / Accepted: 26 August 2020 / Published: 28 August 2020
Human apurinic/apyrimidinic (AP) endonuclease APE1 hydrolyzes phosphodiester bonds on the 5′ side of an AP-site, and some damaged nucleotides such as 1,N6-ethenoadenosine (εA), α-adenosine (αA), and 5,6-dihydrouridine (DHU). To investigate the mechanism behind the broad substrate specificity of APE1, we analyzed pre-steady-state kinetics of conformational changes in DNA and the enzyme during DNA binding and damage recognition. Molecular dynamics simulations of APE1 complexes with one of damaged DNA duplexes containing εA, αA, DHU, or an F-site (a stable analog of an AP-site) revealed the involvement of residues Asn229, Thr233, and Glu236 in the mechanism of DNA lesion recognition. The results suggested that processing of an AP-site proceeds faster in comparison with nucleotide incision repair substrates because eversion of a small abasic site and its insertion into the active site do not include any unfavorable interactions, whereas the insertion of any target nucleotide containing a damaged base into the APE1 active site is sterically hindered. Destabilization of the α-helix containing Thr233 and Glu236 via a loss of the interaction between these residues increased the plasticity of the damaged-nucleotide binding pocket and the ability to accommodate structurally different damaged nucleotides. Nonetheless, the optimal location of εA or αA in the binding pocket does not correspond to the optimal conformation of catalytic amino acid residues, thereby significantly decreasing the cleavage efficacy for these substrates. View Full-Text
Keywords: base excision repair; AP endonuclease; conformational dynamics; active site plasticity; apurinic/apyrimidinic site; 5,6-dihydrouridine base excision repair; AP endonuclease; conformational dynamics; active site plasticity; apurinic/apyrimidinic site; 5,6-dihydrouridine
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MDPI and ACS Style

Bulygin, A.A.; Kuznetsova, A.A.; Vorobjev, Y.N.; Fedorova, O.S.; A. Kuznetsov, N. The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1. Molecules 2020, 25, 3940. https://doi.org/10.3390/molecules25173940

AMA Style

Bulygin AA, Kuznetsova AA, Vorobjev YN, Fedorova OS, A. Kuznetsov N. The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1. Molecules. 2020; 25(17):3940. https://doi.org/10.3390/molecules25173940

Chicago/Turabian Style

Bulygin, Anatoly A., Alexandra A. Kuznetsova, Yuri N. Vorobjev, Olga S. Fedorova, and Nikita A. Kuznetsov. 2020. "The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1" Molecules 25, no. 17: 3940. https://doi.org/10.3390/molecules25173940

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