Common Kinetic Mechanism of Abasic Site Recognition by Structurally Different Apurinic/Apyrimidinic Endonucleases

• Published in: International journal of molecular sciences 2021-08, Vol.22 (16), p.8874
• Main Authors: Kuznetsova, Alexandra A, Senchurova, Svetlana I, Ishchenko, Alexander A, Saparbaev, Murat, Fedorova, Olga S, Kuznetsov, Nikita A
• Format: Article
• Language: English
• Subjects: abasic site; Amino acids; apurinic/apyrimidinic endonuclease; Base excision repair; Binding Sites; Biochemistry, Molecular Biology; Catalysis; Catalytic Domain; Complex formation; conformational dynamics; damaged DNA; Deoxyribonucleic acid; DNA; DNA Cleavage; DNA Damage; DNA Repair; DNA-(Apurinic or Apyrimidinic Site) Lyase - chemistry; DNA-(Apurinic or Apyrimidinic Site) Lyase - metabolism; Enzymes; Escherichia coli; Extrusion; Flexibility; Fluorescence; Humans; Kinetics; Life Sciences; Metal ions; Molecular Dynamics Simulation; Nucleic Acid Conformation; Nucleotides; Nucleotides - chemistry; Nucleotides - metabolism; Protein Conformation; Proteins; Recognition; Stability analysis; stopped-flow enzyme kinetics; Structural Biology; Substrate Specificity
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms22168874

Apurinic/apyrimidinic (AP) endonucleases Nfo ( ) and APE1 (human) represent two conserved structural families of enzymes that cleave AP-site-containing DNA in base excision repair. Nfo and APE1 have completely different structures of the DNA-binding site, catalytically active amino acid residues and catalytic metal ions. Nonetheless, both enzymes induce DNA bending, AP-site backbone eversion into the active-site pocket and extrusion of the nucleotide located opposite the damage. All these stages may depend on local stability of the DNA duplex near the lesion. Here, we analysed effects of natural nucleotides located opposite a lesion on catalytic-complex formation stages and DNA cleavage efficacy. Several model DNA substrates that contain an AP-site analogue [F-site, i.e., (2 ,3 )-2-(hydroxymethyl)-3-hydroxytetrahydrofuran] opposite G, A, T or C were used to monitor real-time conformational changes of the tested enzymes during interaction with DNA using changes in the enzymes' intrinsic fluorescence intensity mainly caused by Trp fluorescence. The extrusion of the nucleotide located opposite F-site was recorded via fluorescence intensity changes of two base analogues. The catalytic rate constant slightly depended on the opposite-nucleotide nature. Thus, structurally different AP endonucleases Nfo and APE1 utilise a common strategy of damage recognition controlled by enzyme conformational transitions after initial DNA binding.