Abstract
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.
Highlights
Apurinic/apyrimidinic sites (AP-sites) are regarded as common lesions that occur in DNA spontaneously or owing to the hydrolysis of N-glycosidic linkages by DNA glycosylases [1,2]
It is thought that the key function of this enzyme is phosphodiester bond hydrolysis on the 50 side of an AP-site in DNA, thereby causing the cleavage of the deoxyribose-phosphate backbone and forming termini carrying a
Asn212, therebywith correlating with data on reduced efficiency of cleavage of the αA-substrate in comparison with the experimental data on reduced efficiency of cleavage of the αA-substrate in comparison with the. These findings suggest that conformational instability of the loop region may be important formay the. These findings suggest that conformational instability of the loop region recognition a damaged nucleotide
Summary
Apurinic/apyrimidinic sites (AP-sites) are regarded as common lesions that occur in DNA spontaneously or owing to the hydrolysis of N-glycosidic linkages by DNA glycosylases [1,2]. The major enzyme of base excision repair (BER), human APE1 (AP endonuclease), initiates the process of removal of AP-sites from the genome [6,7]. It is thought that the key function of this enzyme is phosphodiester bond hydrolysis on the 50 side of an AP-site in DNA, thereby causing the cleavage of the deoxyribose-phosphate backbone and forming termini carrying a. On the other hand, regarding substrates, it has been shown that this enzyme can recognize various AP-sites and some types of damaged bases, for example, oxidatively damaged pyrimidines [9], bulky photoproducts [10], benzene-derived. DNA adducts [11], etheno-derivatives of DNA bases [12,13], α-anomers of 20 -deoxynucleosides [14], and 20 -deoxyuridine [15]. The APE1 enzyme has 30 -phosphodiesterase, 30 -50 -exonuclease, and 30 -phosphatase activities [16,17]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
