The RING-type E3 ligase has been known for over two decades, yet its diverse modes of action are still the subject of active research. Plant homeodomain (PHD) finger protein 7 (PHF7) is a RING-type E3 ubiquitin ligase responsible for histone ubiquitination. PHF7 comprises three zinc finger domains: an extended PHD (ePHD), a RING domain, and a PHD. While the function of the RING domain is largely understood, the roles of the other two domains in E3 ligase activity remain elusive. Here, we present the crystal structure of PHF7 in complex with the E2 ubiquitin-conjugating enzyme (E2). Our structure shows that E2 is effectively captured between the RING domain and the C-terminal PHD, facilitating E2 recruitment through direct contact. In addition, through in vitro binding and functional assays, we demonstrate that the N-terminal ePHD recognizes the nucleosome via DNA binding, whereas the C-terminal PHD is involved in histone H3 recognition. Our results provide a molecular basis for the E3 ligase activity of PHF7 and uncover the specific yet collaborative contributions of each domain to the PHF7 ubiquitination activity.

中文翻译：

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PHF7 介导的组蛋白 H3 泛素化的分子基础

RING 型 E3 连接酶已为人所知二十多年，但其多种作用模式仍然是活跃研究的主题。植物同源结构域 (PHD) 指蛋白 7 (PHF7) 是一种负责组蛋白泛素化的 RING 型 E3 泛素连接酶。PHF7 包含三个锌指结构域：扩展 PHD (ePHD)、RING 结构域和 PHD。虽然 RING 结构域的功能已被广泛了解，但其他两个结构域在 E3 连接酶活性中的作用仍然难以捉摸。在这里，我们展示了 PHF7 与 E2 泛素结合酶 (E2) 复合物的晶体结构。我们的结构表明，E2 在 RING 结构域和 C 端 PHD 之间被有效捕获，从而通过直接接触促进 E2 招募。此外，通过体外结合和功能测定，我们证明N端ePHD通过DNA结合识别核小体，而C端PHD参与组蛋白H3识别。我们的结果为 PHF7 的 E3 连接酶活性提供了分子基础，并揭示了每个结构域对 PHF7 泛素化活性的特定但协作的贡献。