Under conditions of oxidative stress, reactive oxygen species (ROS) continuously assault the structure of DNA resulting in oxidation and fragmentation of the nucleobases. When the nucleobase structure is altered, its base-pairing properties may also be altered, promoting mutations. Consequently, oxidative DNA damage is a major source of the mutation load that gives rise to numerous human maladies, including cancer. Base excision repair (BER) is the primary pathway tasked with removing and replacing mutagenic DNA base damage. Apurinic/apyrimidinic endonuclease 1 (APE1) is a central enzyme with AP-endonuclease and 3′ to 5′ exonuclease functions during BER, and therefore is key to maintenance of genome stability. Polymorphisms, or SNPs, in the gene encoding APE1 (APEX1) have been identified among specific human populations and result in variants of APE1 with modified function. These defects in APE1 potentially result in impaired DNA repair capabilities and consequently an increased risk of disease for individuals within these populations. In the present study, we determined the X-ray crystal structures of three prevalent disease-associated APE1 SNPs (D148E, L104R, and R237C). Each APE1 SNP results in unique localized changes in protein structure, including protein dynamics and DNA binding contacts. Combined with comprehensive biochemical characterization, including pre-steady-state kinetic and DNA binding analyses, variant APE1:DNA complex structures with both AP-endonuclease and exonuclease substrates were analyzed to elucidate how these SNPs might perturb the two major repair functions employed by APE1 during BER.

在氧化应激条件下，活性氧（ROS）不断攻击DNA的结构，导致核碱基的氧化和断裂。当核碱基结构改变时，其碱基配对特性也可能改变，从而促进突变。因此，氧化DNA损伤是导致许多人类疾病（包括癌症）的突变负荷的主要来源。碱基切除修复（BER）是去除和替代诱变DNA碱基损伤的主要途径。apurinic / apyrimidinic核酸内切酶1（APE1）是在BER期间具有AP核酸内切酶和3'至5'核酸外切酶功能的核心酶，因此是维持基因组稳定性的关键。多态性或SNP，在特定人群中已鉴定出编码APE1（APEX1）的基因中的“ APE1”，并导致APE1的变体功能得到修饰。APE1中的这些缺陷可能会导致DNA修复功能受损，并因此增加这些人群中个体的患病风险。在本研究中，我们确定了三种常见的疾病相关APE1 SNP（D148E，L104R和R237C）的X射线晶体结构。每个APE1 SNP都会导致蛋白质结构发生独特的局部变化，包括蛋白质动力学和DNA结合接触。结合全面的生化特征，包括稳态前动力学和DNA结合分析，变体APE1：