Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
Nucleic Acids Res. 2019 Nov 4;47(19):10388-10399. doi: 10.1093/nar/gkz744.
HMCES and yedK were recently identified as sensors of abasic sites in ssDNA. In this study, we present multiple crystal structures captured in the apo-, nonspecific-substrate-binding, specific-substrate-binding, and product-binding states of yedK. In combination with biochemical data, we unveil the molecular basis of AP site sensing in ssDNA by yedK. Our results indicate that yedK has a strong preference for AP site-containing ssDNA over native ssDNA and that the conserved Glu105 residue is important for identifying AP sites in ssDNA. Moreover, our results reveal that a thiazolidine linkage is formed between yedK and AP sites in ssDNA, with the residues that stabilize the thiazolidine linkage important for the formation of DNA-protein crosslinks between yedK and the AP sites. We propose that our findings offer a unique platform to develop yedK and other SRAP domain-containing proteins as tools for detecting abasic sites in vitro and in vivo.
HMCES 和 yedK 最近被鉴定为 ssDNA 中无碱基位点的传感器。在这项研究中，我们呈现了 yedK 的apo、非特异性底物结合、特异性底物结合和产物结合状态的多个晶体结构。结合生化数据，我们揭示了 yedK 通过 ssDNA 进行 AP 位点感应的分子基础。我们的结果表明，yedK 对含有 AP 位点的 ssDNA 有很强的偏好，而保守的 Glu105 残基对于识别 ssDNA 中的 AP 位点很重要。此外，我们的结果揭示了 yedK 与 ssDNA 中的 AP 位点之间形成了噻唑烷键，稳定噻唑烷键的残基对于 yedK 与 AP 位点之间形成 DNA-蛋白质交联很重要。我们提出，我们的发现为开发 yedK 和其他含有 SRAP 结构域的蛋白质作为体外和体内检测无碱基位点的工具提供了一个独特的平台。
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