Structural Basis of the Versatile DNA Recognition Ability of the Methyl-CpG Binding Domain of Methyl-CpG Binding Domain Protein 4
Structural Basis of the Versatile DNA Recognition Ability of the Methyl-CpG Binding Domain of Methyl-CpG Binding Domain Protein 4
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DOI：
10.1074/jbc.m112.431098
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发表时间：
2013-03-01
影响因子：
4.8
通讯作者：
Shirakawa, Masahiro
中科院分区：
文献类型：
--
作者：
Otani, Junji;Arita, Kyohei;Shirakawa, Masahiro
甲基-CpG结合结构域（MBD）蛋白MBD 4作为糖基化酶参与DNA修复，其切除CpG位点中错配的胸腺嘧啶碱基，并且还在转录抑制中起作用。与其他MBD蛋白不同，MBD 4不仅识别甲基化的CpG二核苷酸（（5 m）CG/（5 m）CG），而且识别由5-甲基胞嘧啶自发脱氨基产生的T/G错配位点（（5 m）CG/TG）。MBD 4的糖基化酶活性还涉及由脱氨酶催化的5-甲基胞嘧啶转化为胸腺嘧啶引发的活性DNA去甲基化。本文报道了MBD_4（MBDMBD_4）与（5 m）CG/（5 m）CG和（5 m）CG/TG复合物的晶体结构。晶体结构表明，MBD 4的DNA界面具有灵活的结构特征，并拥有广泛的水网络，支持其双碱基特异性。结合生化分析的结果，MBD 4结合5-羟甲基胞嘧啶的晶体结构进一步证明MBDMBD 4能够通过独特的水网络识别广泛的5-甲基胞嘧啶修饰。MBDMBD 4的多功能碱基识别能力意味着MBD 4在调节动态DNA甲基化模式中的多功能作用，该模式与5-甲基胞嘧啶的脱氨基和/或氧化偶联。
The methyl-CpG binding domain (MBD) protein MBD4 participates in DNA repair as a glycosylase that excises mismatched thymine bases in CpG sites and also functions in transcriptional repression. Unlike other MBD proteins, MBD4 recognizes not only methylated CpG dinucleotides ((5m)CG/(5m)CG) but also T/G mismatched sites generated by spontaneous deamination of 5-methylcytosine ((5m)CG/TG). The glycosylase activity of MBD4 is also implicated in active DNA demethylation initiated by the deaminase-catalyzed conversion of 5-methylcytosine to thymine. Here, we report the crystal structures of the MBD of MBD4(MBDMBD4) complexed with (5m)CG/(5m)CG and (5m)CG/TG. The crystal structures show that the DNA interface of MBD4 has flexible structural features and harbors an extensive water network that supports its dual base specificities. Combined with the results of biochemical analyses, the crystal structure of MBD4 bound to 5-hydroxymethylcytosine further demonstrates that MBDMBD4 is able to recognize a wide range of 5-methylcytosine modifications through the unique water network. The versatile base recognition ability of MBDMBD4 implies multifunctional roles for MBD4 in the regulation of dynamic DNA methylation patterns coupled with deamination and/or oxidation of 5-methylcytosine.