1. Role of AP-endonuclease (Ape1) active site residues in stabilization of the reactant enzyme-DNA complex
- Author
-
Petra Imhof, Jovan Dragelj, and Hossein Batebi
- Subjects
0301 basic medicine ,Stereochemistry ,Protein Conformation ,Protein-DNA complex ,Molecular Dynamics Simulation ,01 natural sciences ,Biochemistry ,AP endonuclease ,Substrate Specificity ,03 medical and health sciences ,Structural Biology ,Catalytic Domain ,0103 physical sciences ,DNA-(Apurinic or Apyrimidinic Site) Lyase ,Humans ,AP site ,Binding site ,Molecular Biology ,Binding Sites ,010304 chemical physics ,biology ,Chemistry ,Leaving group ,Active site ,Hydrogen Bonding ,Base excision repair ,DNA ,DNA-(apurinic or apyrimidinic site) lyase ,Molecular Docking Simulation ,030104 developmental biology ,biology.protein ,Protons - Abstract
Apurinic/apyrimidinic endonuclease 1 (Ape1) is an important metal-dependent enzyme in the base excision repair mechanism, responsible for the backbone cleavage of abasic DNA through a phosphate hydrolysis reaction. Molecular dynamics simulations of Ape1 complexed to its substrate DNA performed for models containing 1 or 2 Mg2+ -ions as cofactor located at different positions show a complex with 1 metal ion bound on the leaving group site of the scissile phosphate to be the most likely reaction-competent conformation. Active-site residue His309 is found to be protonated based on pKa calculations and the higher conformational stability of the Ape1-DNA substrate complex compared to scenarios with neutral His309. Simulations of the D210N mutant further support the prevalence of protonated His309 and strongly suggest Asp210 as the general base for proton acceptance by a nucleophilic water molecule.
- Published
- 2017