Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain
Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain
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DOI：
10.1093/nar/gkz113
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发表时间：
2019-05-07
影响因子：
14.9
通讯作者：
Liu, Junfeng
中科院分区：
文献类型：
--
作者：
Cheng, Xiankun;Zhao, Yanxiang;Liu, Junfeng
在水稻中，水杨酸信号传导途径的关键调节因子是OsWRKY 45，其是WRKY TF家族的转录因子（TF），通过与基因启动子的W盒结合来发挥功能，但OsWRKY 45/W盒DNA识别的结构基础尚不清楚。在这里，我们显示了OsWRKY 45的DNA结合结构域（OsWRKY 45-DBD，即WRKY和锌指结构域）与W盒DNA复合的晶体结构。令人惊讶的是，两个OsWRKY 4 - 5-DBD分子交换β 4-5链以形成二聚体。结构域交换发生在β 3和β 4链之间的铰链区，并且通过来自不同链的配位残基被锌离子桥接和稳定。二聚体含有两个相同的DNA结合结构域，它们与W盒DNA的大沟相互作用。除了疏水氢键和直接氢键外，水介导的氢键也参与蛋白质和DNA之间的碱基特异性相互作用。最后，我们讨论了OsWRKY 45-DBD结构域交换的原因和后果，并在我们的工作和前人研究的基础上，提出了WRKY转录因子识别W盒的详细机制。这项工作揭示了一种新的二聚化和DNA结合的WRKY TF的模式，和WRKY/W-box DNA识别的复杂图片。
In rice, the critical regulator of the salicylic acid signalling pathway is OsWRKY45, a transcription factor (TF) of the WRKY TF family that functions by binding to the W-box of gene promoters, but the structural basis of OsWRKY45/W-box DNA recognition is unknown. Here, we show the crystal structure of the DNA binding domain of OsWRKY45 (OsWRKY45-DBD, i.e. the WRKY and zinc finger domain) in complex with a W-box DNA. Surprisingly, two OsWRKY45-DBD molecules exchange beta 4-5 strands to form a dimer. The domain swapping occurs at the hinge region between the beta 3 and beta 4 strands, and is bridged and stabilized by zinc ion via coordinating residues from different chains. The dimer contains two identical DNA binding domains that interact with the major groove of W-box DNA. In addition to hydrophobic and direct hydrogen bonds, water mediated hydrogen bonds are also involved in base-specific interaction between protein and DNA. Finally, we discussed the cause and consequence of domain swapping of OsWRKY45-DBD, and based on our work and that of previous studies present a detailed mechanism of W-box recognition by WRKY TFs. This work reveals a novel dimerization and DNA-binding mode of WRKY TFs, and an intricate picture of the WRKY/W-box DNA recognition.