Suppr超能文献

人源8-氧鸟嘌呤DNA糖基化酶1(hOGG1)碱基切除修复酶的糖基化酶反应机制:8-氧鸟嘌呤切除过程中赖氨酸249和天冬氨酸268的协同作用

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

作者信息

Šebera Jakub, Hattori Yoshikazu, Sato Daichi, Reha David, Nencka Radim, Kohno Takashi, Kojima Chojiro, Tanaka Yoshiyuki, Sychrovský Vladimír

机构信息

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.

出版信息

Nucleic Acids Res. 2017 May 19;45(9):5231-5242. doi: 10.1093/nar/gkx157.

Abstract

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.

摘要

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。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/903c/5435939/358c29f43b67/gkx157fig1.jpg

相似文献

4
Repair activities of human 8-oxoguanine DNA glycosylase are stimulated by the interaction with human checkpoint sensor Rad9-Rad1-Hus1 complex.
DNA Repair (Amst). 2009 Oct 2;8(10):1190-200. doi: 10.1016/j.dnarep.2009.06.004. Epub 2009 Jul 16.
5
Product inhibition and magnesium modulate the dual reaction mode of hOgg1.
DNA Repair (Amst). 2005 Mar 2;4(3):381-7. doi: 10.1016/j.dnarep.2004.11.002.
7
Step-by-step mechanism of DNA damage recognition by human 8-oxoguanine DNA glycosylase.
Biochim Biophys Acta. 2014 Jan;1840(1):387-95. doi: 10.1016/j.bbagen.2013.09.035. Epub 2013 Oct 3.
8
Catalytically Competent Conformation of the Active Site of Human 8-Oxoguanine-DNA Glycosylase.
Biochemistry (Mosc). 2020 Feb;85(2):192-204. doi: 10.1134/S0006297920020066.
9
Thermodynamics of the DNA damage repair steps of human 8-oxoguanine DNA glycosylase.
PLoS One. 2014 Jun 9;9(6):e98495. doi: 10.1371/journal.pone.0098495. eCollection 2014.

引用本文的文献

2
Assessment of hOGG1 Genetic Polymorphism (rs1052133) and DNA Damage in Radiation-Exposed Workers.
Asian Pac J Cancer Prev. 2022 Dec 1;23(12):4005-4012. doi: 10.31557/APJCP.2022.23.12.4005.
3
Hexavalent chromium disrupts chromatin architecture.
Semin Cancer Biol. 2021 Nov;76:54-60. doi: 10.1016/j.semcancer.2021.07.009. Epub 2021 Jul 15.

本文引用的文献

1
Repair of 8-oxo-7,8-dihydroguanine in prokaryotic and eukaryotic cells: Properties and biological roles of the Fpg and OGG1 DNA N-glycosylases.
Free Radic Biol Med. 2017 Jun;107:179-201. doi: 10.1016/j.freeradbiomed.2016.11.042. Epub 2016 Nov 27.
2
Singlet Oxygen Attack on Guanine: Reactivity and Structural Signature within the B-DNA Helix.
Chemistry. 2016 Aug 22;22(35):12358-62. doi: 10.1002/chem.201601287. Epub 2016 Jul 21.
3
Exploring a DNA Sequence for the Three-Dimensional Structure Determination of a Silver(I)-Mediated C-C Base Pair in a DNA Duplex By (1)H NMR Spectroscopy.
Nucleosides Nucleotides Nucleic Acids. 2015;34(12):877-900. doi: 10.1080/15257770.2015.1088160. Epub 2015 Nov 17.
4
Unraveling the Base Excision Repair Mechanism of Human DNA Glycosylase.
J Am Chem Soc. 2015 Aug 12;137(31):9824-31. doi: 10.1021/jacs.5b01449. Epub 2015 Jul 30.
5
Small Molecule Inhibitors of 8-Oxoguanine DNA Glycosylase-1 (OGG1).
ACS Chem Biol. 2015 Oct 16;10(10):2334-43. doi: 10.1021/acschembio.5b00452. Epub 2015 Aug 7.
6
An ONIOM and MD Investigation of Possible Monofunctional Activity of Human 8-Oxoguanine-DNA Glycosylase (hOgg1).
J Phys Chem B. 2015 Jun 25;119(25):8013-23. doi: 10.1021/acs.jpcb.5b04051. Epub 2015 Jun 9.
8
Microscopic mechanism of DNA damage searching by hOGG1.
Nucleic Acids Res. 2014 Aug;42(14):9295-303. doi: 10.1093/nar/gku621. Epub 2014 Jul 12.
9
Thermodynamics of the DNA damage repair steps of human 8-oxoguanine DNA glycosylase.
PLoS One. 2014 Jun 9;9(6):e98495. doi: 10.1371/journal.pone.0098495. eCollection 2014.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验