The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1
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...
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MDPI AG
2020-08-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/25/17/3940 |
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| author | Anatoly A. Bulygin Alexandra A. Kuznetsova Yuri N. Vorobjev Olga S. Fedorova Nikita A. Kuznetsov |
| author_facet | Anatoly A. Bulygin Alexandra A. Kuznetsova Yuri N. Vorobjev Olga S. Fedorova Nikita A. Kuznetsov |
| author_sort | Anatoly A. Bulygin |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T16:44:23Z |
| format | Article |
| id | doaj.art-ea5ae82b6e054a4a97c421a1ff648bbb |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T16:44:23Z |
| publishDate | 2020-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-ea5ae82b6e054a4a97c421a1ff648bbb2023-11-20T11:45:23ZengMDPI AGMolecules1420-30492020-08-012517394010.3390/molecules25173940The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1Anatoly A. Bulygin0Alexandra A. Kuznetsova1Yuri N. Vorobjev2Olga S. Fedorova3Nikita A. Kuznetsov4Institute of Chemical Biology and Fundamental Medicine, Lavrentyev Ave. 8, 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, Lavrentyev Ave. 8, 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, Lavrentyev Ave. 8, 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, Lavrentyev Ave. 8, 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, Lavrentyev Ave. 8, 630090 Novosibirsk, RussiaHuman 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.https://www.mdpi.com/1420-3049/25/17/3940base excision repairAP endonucleaseconformational dynamicsactive site plasticityapurinic/apyrimidinic site5,6-dihydrouridine |
| spellingShingle | Anatoly A. Bulygin Alexandra A. Kuznetsova Yuri N. Vorobjev Olga S. Fedorova Nikita A. Kuznetsov The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1 Molecules base excision repair AP endonuclease conformational dynamics active site plasticity apurinic/apyrimidinic site 5,6-dihydrouridine |
| title | The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1 |
| title_full | The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1 |
| title_fullStr | The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1 |
| title_full_unstemmed | The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1 |
| title_short | The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1 |
| title_sort | role of active site plasticity in damaged nucleotide recognition by human apurinic apyrimidinic endonuclease ape1 |
| topic | base excision repair AP endonuclease conformational dynamics active site plasticity apurinic/apyrimidinic site 5,6-dihydrouridine |
| url | https://www.mdpi.com/1420-3049/25/17/3940 |
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