Computational clues for a new mechanism in the glycosylase activity of the human DNA repair protein hOGG1. A generalized paradigm for purine-repairing systems?
A theoretical density functional theory (DFT, B3LYP) investigation has been carried out on the catalytic cycle responsible for the glycosylase activity of the human DNA repair protein hOGG1: enzyme activation, cleavage of the glycosidic bond, and expulsion of the damaged base. An unprecedented large quantum mechanics (QM) model system has been used, which includes a complete oxoG molecule, the deoxyribose ring bonded to the phosphate groups, and most of the surrounding residues that simulate the protein binding pocket. It has been found that Asp268 does not play any role in Lys249 activation and that the oxoG basis acts as a coenzyme, triggering nucleophile activation by Lys249 deprotonation. An SN2 nucleophilic attack by Lys249 on the anomeric carbon then follows. This is the rate-determining step of the process with an activation barrier of 16.7 kcal mol(-1) in good agreement with the experimental value of 17.1 kcal mol(-1). The expelled oxoG plays again as an enzyme cofactor at the end of the process by activating (via proton transfer) ribose ring opening and Schiff base formation. This study suggests a recurring catalytic strategy in the enzymatic cleavage of purine nucleoside where the activation of the leaving group by protonation of the nucleoside base (via an enzymatic general acid) triggers the cleavage of the glycosidic bond.
Calvaresi
Matteo
M
Dipartimento di Chimica G. Ciamician, Universita' di Bologna, via Selmi 2, 40126 Bologna, Italy.
Bottoni
Andrea
A
Garavelli
Marco
M
D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D045647:DNA Glycosylases / Q000737:chemistry / Q000378:metabolism*; D004260:DNA Repair; D006147:Guanine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D009699:N-Glycosyl Hydrolases / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation; D011687:Purines / Q000737:chemistry*
D011687:Purines; C024829:8-hydroxyguanine; D006147:Guanine; D045647:DNA Glycosylases; D009699:N-Glycosyl Hydrolases; C479058:oxoguanine glycosylase 1, human; C030985:purine