State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
Cell Res. 2010 Feb;20(2):166-73. doi: 10.1038/cr.2010.8. Epub 2010 Jan 26.
Dynamic regulation of histone methylation/demethylation plays an important role during development. Mutations and truncations in human plant homeodomain (PHD) finger protein 8 (PHF8) are associated with X-linked mental retardation and facial anomalies, such as a long face, broad nasal tip, cleft lip/cleft palate and large hands, yet its molecular function and structural basis remain unclear. Here, we report the crystal structures of the catalytic core of PHF8 with or without alpha-ketoglutarate (alpha-KG) at high resolution. Biochemical and structural studies reveal that PHF8 is a novel histone demethylase specific for di- and mono-methylated histone H3 lysine 9 (H3K9me2/1), but not for H3K9me3. Our analyses also reveal how human PHF8 discriminates between methylation states and achieves sequence specificity for methylated H3K9. The in vitro demethylation assay also showed that the F279S mutant observed in clinical patients possesses no demethylation activity, suggesting that loss of enzymatic activity is crucial for pathogenesis of PHF8 patients. Taken together, these results will shed light on the molecular mechanism underlying PHF8-associated developmental and neurological diseases.
动态调节组蛋白甲基化/去甲基化在发育过程中起着重要作用。人类植物同源结构域（PHD）手指蛋白 8（PHF8）中的突变和截短与 X 连锁智力低下和面部异常有关，如长脸、宽鼻尖、唇裂/腭裂和大手，但它的分子功能和结构基础仍不清楚。在这里，我们报告了高分辨率下含有或不含有α-酮戊二酸（α-KG）的 PHF8 催化核心的晶体结构。生化和结构研究表明，PHF8 是一种新型的组蛋白去甲基酶，特异性识别二甲基和单甲基化的组蛋白 H3 赖氨酸 9（H3K9me2/1），但不识别 H3K9me3。我们的分析还揭示了人类 PHF8 如何区分甲基化状态并实现对甲基化 H3K9 的序列特异性。体外去甲基化实验也表明，在临床患者中观察到的 F279S 突变体没有去甲基化活性，这表明酶活性的丧失对 PHF8 患者的发病机制至关重要。总之，这些结果将为 PHF8 相关发育和神经疾病的分子机制提供线索。
