Department of Biological Chemistry, 1150 West Medical Center Drive, 5301 Medical Science Research Building III, University of Michigan, Ann Arbor, MI 48109, USA.
Department of Biological Chemistry, 1150 West Medical Center Drive, 5301 Medical Science Research Building III, University of Michigan, Ann Arbor, MI 48109, USA.
Structure. 2013 Jan 8;21(1):98-108. doi: 10.1016/j.str.2012.10.018. Epub 2012 Dec 6.
JMJD2 lysine demethylases (KDMs) participate in diverse genomic processes. Most JMJD2 homologs display dual selectivity toward H3K9me3 and H3K36me3, with the exception of JMJD2D, which is specific for H3K9me3. Here, we report the crystal structures of the JMJD2D⋅2-oxoglutarate⋅H3K9me3 ternary complex and JMJD2D apoenzyme. Utilizing structural alignments with JMJD2A, molecular docking, and kinetic analysis with an array of histone peptide substrates, we elucidate the specific signatures that permit efficient recognition of H3K9me3 by JMJD2A and JMJD2D, and the residues in JMJD2D that occlude H3K36me3 demethylation. Surprisingly, these results reveal that JMJD2A and JMJD2D exhibit subtle yet important differences in H3K9me3 recognition, despite the overall similarity in the substrate-binding conformation. Further, we show that H3T11 phosphorylation abrogates demethylation by JMJD2 KDMs. Together, these studies reveal the molecular basis for JMJD2 site specificity and provide a framework for structure-based design of selective inhibitors of JMJD2 KDMs implicated in disease.
JMJD2 赖氨酸去甲基酶（KDMs）参与多种基因组过程。大多数 JMJD2 同源物对 H3K9me3 和 H3K36me3 具有双重选择性，除了 JMJD2D，它专门针对 H3K9me3。在这里，我们报告了 JMJD2D·2-氧代戊二酸·H3K9me3 三元复合物和 JMJD2D 脱辅基酶的晶体结构。利用与 JMJD2A 的结构比对、分子对接以及一系列组蛋白肽底物的动力学分析，我们阐明了允许 JMJD2A 和 JMJD2D 有效识别 H3K9me3 的特定特征，以及 JMJD2D 中阻止 H3K36me3 去甲基化的残基。令人惊讶的是，尽管底物结合构象总体相似，但这些结果表明 JMJD2A 和 JMJD2D 在 H3K9me3 识别方面存在细微但重要的差异。此外，我们表明 H3T11 磷酸化会阻止 JMJD2 KDM 对 H3 的去甲基化。总之，这些研究揭示了 JMJD2 位点特异性的分子基础，并为基于结构的设计针对与疾病相关的 JMJD2 KDMs 的选择性抑制剂提供了框架。
