Freudenthal Bret D, Beard William A, Cuneo Matthew J, Dyrkheeva Nadezhda S, Wilson Samuel H
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Research Triangle Park, USA.
Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Nat Struct Mol Biol. 2015 Nov;22(11):924-31. doi: 10.1038/nsmb.3105. Epub 2015 Oct 12.
DNA apurinic-apyrimidinic (AP) sites are prevalent noncoding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA-repair intermediate that is potentially cytotoxic. The molecular events of the incision reaction remain elusive, owing in part to limited structural information. We report multiple high-resolution human APE1-DNA structures that divulge new features of the APE1 reaction, including the metal-binding site, the nucleophile and the arginine clamps that mediate product release. We also report APE1-DNA structures with a T-G mismatch 5' to the AP site, representing a clustered lesion occurring in methylated CpG dinucleotides. These structures reveal that APE1 molds the T-G mismatch into a unique Watson-Crick-like geometry that distorts the active site, thus reducing incision. These snapshots provide mechanistic clarity for APE1 while affording a rational framework to manipulate biological responses to DNA damage.
DNA脱嘌呤-脱嘧啶（AP）位点是基因组稳定性普遍存在的非编码威胁，并由AP核酸内切酶1（APE1）进行处理。APE1切割AP位点的磷酸二酯主链，产生一种可能具有细胞毒性的DNA修复中间体。切割反应的分子事件仍不清楚，部分原因是结构信息有限。我们报告了多个高分辨率的人APE1-DNA结构，这些结构揭示了APE1反应的新特征，包括金属结合位点、亲核试剂和介导产物释放的精氨酸钳。我们还报告了在AP位点5'端存在T-G错配的APE1-DNA结构，这代表了甲基化CpG二核苷酸中出现的簇状损伤。这些结构表明，APE1将T-G错配塑造成一种独特的类似沃森-克里克的几何形状，从而扭曲活性位点，进而减少切割。这些瞬间为APE1提供了机制上的清晰认识，同时为操纵对DNA损伤的生物学反应提供了一个合理的框架。
