Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38
Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38
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DOI：
10.1074/jbc.ra118.005147
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发表时间：
2018-12-21
影响因子：
4.8
通讯作者：
Buck-Koehntop, Bethany A.
中科院分区：
文献类型：
--
作者：
Hudson, Nicholas O.;Whitby, Frank G.;Buck-Koehntop, Bethany A.
甲基CpG结合蛋白(MBP)是DNA甲基化的选择性阅读器，在调节正常和疾病细胞的转录过程中发挥着重要作用。MBPS的这一生理功能引起了人们对理解这些蛋白质阅读和解释DNA甲基化信号的机制的浓厚兴趣。锌指和含BTB结构域的38(ZBTB38)代表了MBPS中锌指(ZF)家族的一个成员。我们最近在体外和细胞内证明了ZBTB38的C-末端ZF在((A/G)TmCG(G/A)(MC/T)(G/A))的背景下表现出甲基选择性的DNA结合。在这里，我们报告了前四个C-末端ZBTB38ZF(ZFS6-9)的晶体结构，它与先前确定的甲基化共识序列在1.75分辨率下形成了络合物。从结构上看，甲基选择性结合优先定位于结合DNA的5mCpG位点，这是通过ZF7和ZF8-螺旋内残基的一系列碱基特异性相互作用促进的。ZF6和ZF9主要稳定ZF7和ZF8，以促进核心碱基特异性相互作用。进一步的结构和生化分析，包括溶液核磁共振光谱和凝胶迁移率分析，表明ZBTB38的C-末端ZF利用了另一种识别mCpG的模式，而不是目前结构评估的ZF Mbps。综上所述，这些发现提供了对ZBTB38的ZF结构域选择性识别甲基化CpG位点的机制的洞察，并扩大了我们对含ZF的蛋白质如何解释这一重要表观遗传标记的理解。
Methyl-CpG-binding proteins (MBPs) are selective readers of DNA methylation that play an essential role in mediating cellular transcription processes in both normal and diseased cells. This physiological function of MBPs has generated significant interest in understanding the mechanisms by which these proteins read and interpret DNA methylation signals. Zinc finger and BTB domain-containing 38 (ZBTB38) represents one member of the zinc finger (ZF) family of MBPs. We recently demonstrated that the C-terminal ZFs of ZBTB38 exhibit methyl-selective DNA binding within the ((A/G)TmCG(G/A)(mC/T)(G/A)) context both in vitro and within cells. Here we report the crystal structure of the first four C-terminal ZBTB38 ZFs (ZFs 6-9) in complex with the previously identified methylated consensus sequence at 1.75 resolution. From the structure, methyl-selective binding is preferentially localized at the 5 mCpG site of the bound DNA, which is facilitated through a series of base-specific interactions from residues within the -helices of ZF7 and ZF8. ZF6 and ZF9 primarily stabilize ZF7 and ZF8 to facilitate the core base-specific interactions. Further structural and biochemical analyses, including solution NMR spectroscopy and electrophoretic mobility gel shift assays, revealed that the C-terminal ZFs of ZBTB38 utilize an alternative mode of mCpG recognition from the ZF MBPs structurally evaluated to date. Combined, these findings provide insight into the mechanism by which this ZF domain of ZBTB38 selectively recognizes methylated CpG sites and expands our understanding of how ZF-containing proteins can interpret this essential epigenetic mark.