Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India.
Biochemistry. 2021 Sep 7;60(35):2652-2662. doi: 10.1021/acs.biochem.1c00191. Epub 2021 Aug 18.
The PHD finger-containing VARIANT IN METHYLATION/ORTHRUS (VIM/ORTH) family of proteins in consists of functional homologues of mammalian UHRF1 and is required for the maintenance of DNA methylation. Comparison of the sequence with those of other PHD fingers implied that VIM1 and VIM3 PHD could recognize lysine 4 of histone H3 (H3K4) through interactions mediated by a conserved aspartic acid. However, our calorimetric and modified histone peptide array binding studies suggested that neither H3K4 nor other histone marks are recognized by VIM1 and VIM3 PHD fingers. Here, we report a 2.6 Å resolution crystal structure of the VIM1 PHD finger and demonstrate significant structural changes in the putative H3 recognition segments in contrast to canonical H3K4 binding PHD fingers. These changes include (i) the H3A1 binding region, (ii) strand β1 that forms an intermolecular β-sheet with the H3 peptide, and (iii) an aspartate-containing motif involved in salt bridge interaction with H3K4, which together appear to abrogate recognition of H3K4 by the VIM1 PHD finger. To understand the significance of the altered structural features in the VIM1 PHD that might prevent histone H3 recognition, we modeled a chimeric VIM1 PHD (chmVIM1 PHD) by grafting the peptide binding structural features of the BHC80 PHD onto the VIM1 PHD. Molecular dynamics simulation and metadynamics analyses revealed that the chmVIM1 PHD-H3 complex is stable and also showed a network of intermolecular interactions similar to those of the BHC80 PHD-H3 complex. Collectively, this study reveals that subtle structural changes in the peptide binding region of the VIM1 PHD abrogate histone H3 recognition.
包含 PHD 指的 VARIANT IN METHYLATION/ORTHRUS（VIM/ORTH）家族的蛋白质在 中，包含哺乳动物 UHRF1 的功能同源物，是维持 DNA 甲基化所必需的。与其他 PHD 指的序列比较表明，VIM1 和 VIM3 PHD 可以通过保守天冬氨酸介导的相互作用识别组蛋白 H3 的赖氨酸 4（H3K4）。然而，我们的量热法和修饰组蛋白肽阵列结合研究表明，VIM1 和 VIM3 PHD 指都不识别 H3K4 或其他组蛋白标记。在这里，我们报告了 VIM1 PHD 指的 2.6 Å 分辨率晶体结构，并证明了与典型的 H3K4 结合 PHD 指相比，在假定的 H3 识别片段中存在显著的结构变化。这些变化包括（i）H3A1 结合区域，（ii）与 H3 肽形成分子间β-sheet 的β1 链，以及（iii）参与与 H3K4 盐桥相互作用的天冬氨酸基序，它们共同似乎阻止了 VIM1 PHD 指识别 H3K4。为了理解 VIM1 PHD 中改变的结构特征在可能阻止组蛋白 H3 识别方面的意义，我们通过将 BHC80 PHD 的肽结合结构特征嫁接到 VIM1 PHD 上来构建嵌合 VIM1 PHD（chmVIM1 PHD）。分子动力学模拟和元动力学分析表明，chmVIM1 PHD-H3 复合物是稳定的，并且也显示出与 BHC80 PHD-H3 复合物相似的分子间相互作用网络。总的来说，这项研究表明，VIM1 PHD 肽结合区域的细微结构变化会阻止组蛋白 H3 的识别。
