Ng Stanley S, Kavanagh Kathryn L, McDonough Michael A, Butler Danica, Pilka Ewa S, Lienard Benoit M R, Bray James E, Savitsky Pavel, Gileadi Opher, von Delft Frank, Rose Nathan R, Offer John, Scheinost Johanna C, Borowski Tomasz, Sundstrom Michael, Schofield Christopher J, Oppermann Udo
Structural Genomics Consortium, Botnar Research Center, University of Oxford, Oxford OX3 7LD, UK.
Nature. 2007 Jul 5;448(7149):87-91. doi: 10.1038/nature05971. Epub 2007 Jun 24.
Post-translational histone modification has a fundamental role in chromatin biology and is proposed to constitute a 'histone code' in epigenetic regulation. Differential methylation of histone H3 and H4 lysyl residues regulates processes including heterochromatin formation, X-chromosome inactivation, genome imprinting, DNA repair and transcriptional regulation. The discovery of lysyl demethylases using flavin (amine oxidases) or Fe(II) and 2-oxoglutarate as cofactors (2OG oxygenases) has changed the view of methylation as a stable epigenetic marker. However, little is known about how the demethylases are selective for particular lysyl-containing sequences in specific methylation states, a key to understanding their functions. Here we reveal how human JMJD2A (jumonji domain containing 2A), which is selective towards tri- and dimethylated histone H3 lysyl residues 9 and 36 (H3K9me3/me2 and H3K36me3/me2), discriminates between methylation states and achieves sequence selectivity for H3K9. We report structures of JMJD2A-Ni(II)-Zn(II) inhibitor complexes bound to tri-, di- and monomethyl forms of H3K9 and the trimethyl form of H3K36. The structures reveal a lysyl-binding pocket in which substrates are bound in distinct bent conformations involving the Zn-binding site. We propose a mechanism for achieving methylation state selectivity involving the orientation of the substrate methyl groups towards a ferryl intermediate. The results suggest distinct recognition mechanisms in different demethylase subfamilies and provide a starting point to develop chemical tools for drug discovery and to study and dissect the complexity of reversible histone methylation and its role in chromatin biology.
翻译后组蛋白修饰在染色质生物学中具有重要作用，并且被认为在表观遗传调控中构成一种“组蛋白密码”。组蛋白H3和H4赖氨酸残基的差异甲基化调节着包括异染色质形成、X染色体失活、基因组印记、DNA修复和转录调控等过程。利用黄素（胺氧化酶）或Fe(II)和2-氧代戊二酸作为辅因子（2OG双加氧酶）的赖氨酸去甲基化酶的发现，改变了甲基化作为一种稳定表观遗传标记的观点。然而，对于去甲基化酶如何在特定甲基化状态下对特定含赖氨酸序列具有选择性，这一理解其功能的关键问题，人们却知之甚少。在这里，我们揭示了人类JMJD2A（含jumonji结构域2A）如何对三甲基化和二甲基化的组蛋白H3赖氨酸残基9和36（H3K9me3/me2和H3K36me3/me2）具有选择性，区分甲基化状态并实现对H3K9的序列选择性。我们报道了与H3K9的三甲基、二甲基和单甲基形式以及H3K36的三甲基形式结合的JMJD2A-Ni(II)-Zn(II)抑制剂复合物的结构。这些结构揭示了一个赖氨酸结合口袋，其中底物以涉及锌结合位点的不同弯曲构象结合。我们提出了一种实现甲基化状态选择性的机制，该机制涉及底物甲基基团朝向铁氧中间体的取向。结果表明不同去甲基化酶亚家族中存在不同的识别机制，并为开发用于药物发现的化学工具以及研究和剖析可逆组蛋白甲基化的复杂性及其在染色质生物学中的作用提供了一个起点。
