College of Life Sciences, Northwest A&F University, Yangling, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
EMBO Rep. 2022 Jul 5;23(7):e53874. doi: 10.15252/embr.202153874. Epub 2022 Jun 23.
G-quadruplexes (G4s) are unusual stable DNA structures that cause genomic instability. To overcome the potential barriers formed by G4s, cells have evolved different families of proteins that unfold G4s. Pif1 is a DNA helicase from superfamily 1 (SF1) conserved from bacteria to humans with high G4-unwinding activity. Here, we present the first X-ray crystal structure of the Thermus oshimai Pif1 (ToPif1) complexed with a G4. Our structure reveals that ToPif1 recognizes the entire native G4 via a cluster of amino acids at domains 1B/2B which constitute a G4-Recognizing Surface (GRS). The overall structure of the G4 maintains its three-layered propeller-type G4 topology, without significant reorganization of G-tetrads upon protein binding. The three G-tetrads in G4 are recognized by GRS residues mainly through electrostatic, ionic interactions, and hydrogen bonds formed between the GRS residues and the ribose-phosphate backbone. Compared with previously solved structures of SF2 helicases in complex with G4, our structure reveals how helicases from distinct superfamilies adopt different strategies for recognizing and unfolding G4s.
四链体（G4s）是一种异常稳定的 DNA 结构，会导致基因组不稳定。为了克服 G4 形成的潜在障碍，细胞进化出了不同的蛋白家族来展开 G4。Pif1 是一种从细菌到人类都高度保守的超家族 1（SF1）的 DNA 解旋酶，具有很高的 G4 解旋活性。在这里，我们呈现了第一个与 G4 结合的 Thermus oshimai Pif1（ToPif1）复合物的 X 射线晶体结构。我们的结构揭示了 ToPif1 通过位于结构域 1B/2B 的氨基酸簇识别整个天然 G4，该簇构成了 G4 识别表面（GRS）。G4 的整体结构保持其三层推进式 G4 拓扑结构，在蛋白质结合时 G-四联体没有明显的重新组织。G4 中的三个 G-四联体主要通过 GRS 残基与核糖-磷酸骨架之间的静电、离子相互作用和氢键被 GRS 残基识别。与先前解决的与 G4 结合的 SF2 解旋酶结构相比，我们的结构揭示了不同超家族的解旋酶如何采用不同的策略来识别和展开 G4。
