Pyramidalization of the Glycosidic Nitrogen Provides the Way for Efficient Cleavage of the N-Glycosidic Bond of 8-OxoG with the hOGG1 DNA Repair Protein

Abstract

A mechanistic pathway for cleavage of the N-glycosidic bond of 8-oxo-2'-deoxyguanosine (oxoG) catalyzed with the human 8-oxoguanine glycosylase 1 DNA repair protein (hOGG1) is proposed in this theoretical study. The reaction scheme suggests direct proton addition to the glycosidic nitrogen N9 of oxoG from the Nε-ammonium of Lys249 residue of hOGG1 that is enabled owing to the N9 pyramidal geometry. The N9-pyramidalization of oxoG is induced within hOGG1 active site. The coordination of N9 nitrogen to the Nε-ammonium of Lys249 unveiled by available crystal structures enables concerted, synchronous substitution of the N9-C1' bond by the N9-H bond. The reaction is compared with other pathways already proposed by means of calculated activation energies. The ΔG(#) energy for the newly proposed reaction mechanism calculated with the B3LYP/6-31G(d,p) method 17.0 kcal mol(-1) is significantly lower than ΔG(#) energies for other reactions employing attack of the Nε-amino group to the anomeric carbon C1' of oxoG and attack of the Nε-ammonium to the N3 nitrogen of oxoG base. Moreover, activation energy for the oxoG cleavage proceeding via N9-pyramidalization is lower than energy calculated for normal G because the electronic state of the five-membered aromatic ring of oxoG is better suited for the reaction. The modification of aromatic character introduced by oxidation to the nucleobase thus seems to be the factor that is checked by hOGG1 to achieve base-specific cleavage.

The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine

“…Under this assumption, Lys249 presumably compensates for the negative charge on the leaving oxoG base and Asp268 compensates for the incipient charge on the ribose oxocarbenium. The σ-bond substitution reaction that complies with these assumptions was proposed previously, assuming only the effect of Lys249 (46). In the current work, the base-excision reaction with hOGG1 will be illustrated within a complete catalytic core by employing the QM/MM calculation method.…”

“…Similar pKa values were also calculated for Lys249 and Asp268 in both the original and geometry-optimized 2NOZ structure (Supplementary Table S1). These pKa values implicate the prevalence of the NH 3 + (Lys249) and CO 2 − (Asp268) forms that are prerequisites for the σ-bond substitution base-excision reaction (46). …”

“…The initial attack of lone-pair electrons at the N9(oxoG) to the ammonium NεH 3 + group of Lys249 triggers the σ-bond substitution reaction (46). The distance between the N9(oxoG) and Nε(Lys249) atoms in 2NOZ and in the QM/MM-optimized reactant was 3.027 and 2.969 Å, respectively.…”

“…The π–cation interaction between the aromatic ring of the oxoG base and NH 3 + (Lys249) initiated proton transfer from NH 3 + (Lys249) to N3(oxoG), which activated the base-excision reaction (44,45). Lastly, the abstraction of the proton from NH 3 + (Lys249) with the N9(oxoG) atom triggered substitution of the N-glycosidic bond of oxoG with the N9-H bond in a concerted synchronous manner (the σ-bond substitution mechanism) (46). …”

Recognition and Excision Properties of 8‐Halogenated‐7‐Deaza‐2′‐Deoxyguanosine as 8‐Oxo‐2′‐Deoxyguanosine Analogues and Fpg and hOGG1 Inhibitors

“…[44] Interestingly,t he experimental resultsa nd Figure 5B indicatet hat Cl-deaza-dG can be found in the hOGG1 pocket, although hOGG1 possesses am ore rigid active site. Notably,C l-deaza-dG demonstrates as trong binding affinity for hOGG1, relative to the various 8-oxo-dG analogues.…”