Šebera Jakub, Hattori Yoshikazu, Sato Daichi, Reha David, Nencka Radim, Kohno Takashi, Kojima Chojiro, Tanaka Yoshiyuki, Sychrovský Vladimír
The Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo námestí 2, 166 10 Praha, Czech Republic.
Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama-Boji 180, Yamashiro-cho, Tokushima 770 8514, Japan.
Nucleic Acids Res. 2017 May 19;45(9):5231-5242. doi: 10.1093/nar/gkx157.
The excision of 8-oxoguanine (oxoG) by the human 8-oxoguanine DNA glycosylase 1 (hOGG1) base-excision repair enzyme was studied by using the QM/MM (M06-2X/6-31G(d,p):OPLS2005) calculation method and nuclear magnetic resonance (NMR) spectroscopy. The calculated glycosylase reaction included excision of the oxoG base, formation of Lys249-ribose enzyme-substrate covalent adduct and formation of a Schiff base. The formation of a Schiff base with ΔG# = 17.7 kcal/mol was the rate-limiting step of the reaction. The excision of the oxoG base with ΔG# = 16.1 kcal/mol proceeded via substitution of the C1΄-N9 N-glycosidic bond with an H-N9 bond where the negative charge on the oxoG base and the positive charge on the ribose were compensated in a concerted manner by NH3+(Lys249) and CO2-(Asp268), respectively. The effect of Asp268 on the oxoG excision was demonstrated with 1H NMR for WT hOGG1 and the hOGG1(D268N) mutant: the excision of oxoG was notably suppressed when Asp268 was mutated to Asn. The loss of the base-excision function was rationalized with QM/MM calculations and Asp268 was confirmed as the electrostatic stabilizer of ribose oxocarbenium through the initial base-excision step of DNA repair. The NMR experiments and QM/MM calculations consistently illustrated the base-excision reaction operated by hOGG1.
采用量子力学/分子力学(QM/MM,M06 - 2X/6 - 31G(d,p):OPLS2005)计算方法和核磁共振(NMR)光谱,研究了人类8 - 氧代鸟嘌呤DNA糖基化酶1(hOGG1)碱基切除修复酶对8 - 氧代鸟嘌呤(oxoG)的切除作用。计算得到的糖基化酶反应包括oxoG碱基的切除、Lys249 - 核糖酶 - 底物共价加合物的形成以及席夫碱的形成。形成席夫碱(ΔG# = 17.7 kcal/mol)是该反应的限速步骤。oxoG碱基的切除(ΔG# = 16.1 kcal/mol)是通过用H - N9键取代C1΄ - N9 N - 糖苷键进行的,其中oxoG碱基上带负电荷,核糖上带正电荷,分别由NH3+(Lys249)和CO2-(Asp268)协同补偿。通过1H NMR对野生型hOGG1和hOGG1(D268N)突变体进行研究,证实了Asp268对oxoG切除的影响:当Asp268突变为Asn时,oxoG的切除明显受到抑制。通过QM/MM计算对碱基切除功能的丧失进行了合理解释,并且通过DNA修复的初始碱基切除步骤,证实Asp268是核糖氧化碳正离子的静电稳定剂。NMR实验和QM/MM计算一致说明了hOGG1所进行的碱基切除反应。