New structural insights into the recognition of undamaged splayed-arm DNA with a single pair of non-complementary nucleotides by human nucleotide excision repair protein XPA
New structural insights into the recognition of undamaged splayed-arm DNA with a single pair of non-complementary nucleotides by human nucleotide excision repair protein XPA
复制标题
人核苷酸切除修复蛋白 XPA 识别具有单对非互补核苷酸的未受损八字臂 DNA 的新结构见解
DOI：
10.1016/j.ijbiomac.2020.01.169
复制
发表时间：
2020
影响因子：
8.2
通讯作者：
Qian Chengmin
中科院分区：
文献类型：
--
作者：
Lian Fu-Ming;Yang Xiangwei;Jiang Yong-Liang;Yang Feng;Li Changlin;Yang Wancai;Qian Chengmin
XPA（Xeroderma pigmentosum complementation group A）是一种核心支架蛋白，在DNA损伤验证和核苷酸切除修复（NER）途径中募集下游核酸内切酶中起重要作用。在这里，我们提出了2.81纳米分辨率的晶体结构的DNA结合结构域（DBD）的人XPA的复合物与未受损的展臂DNA基板与一对非互补的核苷酸。该结构揭示了两个XPA分子以非序列特异性方式结合到具有10-bp双链体识别基序的一个张开臂DNA。XPA分子以特征性的β-发夹结合到DNA双链体区域的两端。一个保守的色氨酸残基Trp 175与DNA双链体的最后一个碱基对包装，并稳定特征性β-发夹的构象。在DNA结合时，XPA的C-末端最后一个螺旋将朝向DNA底物的小沟移动，以更好地相互作用。值得注意的是，人XPA能够与未受损的DNA双链体结合而没有任何扭结，并且XPA-DNA结合不会明显地使DNA底物弯曲。本研究为XPA与未损伤的单对非互补DNA的结合机制提供了结构基础。
XPA (Xeroderma pigmentosum complementation group A) is a core scaffold protein that plays significant roles in DNA damage verification and recruiting downstream endonucleases in the nucleotide excision repair (NER) pathway. Here, we present the 2.81 Å resolution crystal structure of the DNA-binding domain (DBD) of human XPA in complex with an undamaged splayed-arm DNA substrate with a single pair of non-complementary nucleotides. The structure reveals that two XPA molecules bind to one splayed-arm DNA with a 10-bp duplex recognition motif in a non-sequence-specific manner. XPA molecules bind to both ends of the DNA duplex region with a characteristic β-hairpin. A conserved tryptophan residue Trp175 packs against the last base pair of DNA duplex and stabilizes the conformation of the characteristic β-hairpin. Upon DNA binding, the C-terminal last helix of XPA would shift towards the minor groove of the DNA substrate for better interaction. Notably, human XPA is able to bind to the undamaged DNA duplex without any kinks, and XPA-DNA binding does not bend the DNA substrate obviously. This study provides structural basis for the binding mechanism of XPA to the undamaged splayed-arm DNA with a single pair of non-complementary nucleotides.