Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Institute for Drug Resistance, University of Massachusetts Chan Medical School, Worcester, MA, USA.
Nat Commun. 2022 Nov 19;13(1):7117. doi: 10.1038/s41467-022-34752-1.
APOBEC3 proteins (A3s) are enzymes that catalyze the deamination of cytidine to uridine in single-stranded DNA (ssDNA) substrates, thus playing a key role in innate antiviral immunity. However, the APOBEC3 family has also been linked to many mutational signatures in cancer cells, which has led to an intense interest to develop inhibitors of A3's catalytic activity as therapeutics as well as tools to study A3's biochemistry, structure, and cellular function. Recent studies have shown that ssDNA containing 2'-deoxy-zebularine (dZ-ssDNA) is an inhibitor of A3s such as A3A, A3B, and A3G, although the atomic determinants of this activity have remained unknown. To fill this knowledge gap, we determined a 1.5 Å resolution structure of a dZ-ssDNA inhibitor bound to active A3G. The crystal structure revealed that the activated dZ-HO mimics the transition state by coordinating the active site Zn and engaging in additional stabilizing interactions, such as the one with the catalytic residue E259. Therefore, this structure allowed us to capture a snapshot of the A3's transition state and suggests that developing transition-state mimicking inhibitors may provide a new opportunity to design more targeted molecules for A3s in the future.
APOBEC3 蛋白（A3s）是一类酶，能够在单链 DNA（ssDNA）底物中催化胞嘧啶脱氨酶化反应，将其转化为尿嘧啶，从而在先天抗病毒免疫中发挥关键作用。然而，APOBEC3 家族也与癌细胞中的许多突变特征有关，这促使人们强烈希望开发 A3 催化活性的抑制剂作为治疗方法，以及研究 A3 的生物化学、结构和细胞功能的工具。最近的研究表明，含有 2'-脱氧 zebularine（dZ-ssDNA）的 ssDNA 是 A3s（如 A3A、A3B 和 A3G）的抑制剂，尽管这种活性的原子决定因素仍不清楚。为了填补这一知识空白，我们确定了一个与活性 A3G 结合的 dZ-ssDNA 抑制剂的 1.5Å 分辨率结构。晶体结构显示，活化的 dZ-HO 通过与活性位点 Zn 配位并形成额外的稳定相互作用（如与催化残基 E259 的相互作用）来模拟过渡态。因此，该结构使我们能够捕获 A3 过渡态的快照，并表明开发过渡态模拟抑制剂可能为未来设计针对 A3s 的更具针对性的分子提供新机会。
