Elrod-Erickson M, Rould M A, Nekludova L, Pabo C O
Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Structure. 1996 Oct 15;4(10):1171-80. doi: 10.1016/s0969-2126(96)00125-6.
Zinc fingers of the Cys2 His2 class recognize a wide variety of different DNA sequences and are one of the most abundant DNA-binding motifs found in eukaryotes. The previously determined 2.1 A structure of a complex containing the three zinc fingers from Zif268 has served as a basis for many modeling and design studies, and Zif268 has proved to be a very useful model system for studying how TFIIIA-like zinc fingers recognize DNA.
We have refined the structure of the Zif268 protein-DNA complex at 1.6 A resolution. Our structure confirms all the basic features of the previous model and allows us to focus on some critical details at the protein-DNA interface. In particular, our refined structure helps explain the roles of several acidic residues located in the recognition helices and shows that the zinc fingers make a number of water-mediated contacts with bases and phosphates. Modeling studies suggest that the distinctive DNA conformation observed in the Zif268-DNA complex is correlated with finger-finger interactions and the length of the linkers between adjacent fingers. Circular dichroism studies indicate that at least some of the features of this distinctive DNA conformation are induced upon complex formation.
Our 1.6 A structure should provide an excellent framework for analyzing the effects of Zif268 mutations, for modeling related zinc finger-DNA complexes, and for designing and selecting Zif268 variants that will recognize other DNA sites.
Cys2 His2类锌指可识别多种不同的DNA序列，是真核生物中发现的最为丰富的DNA结合基序之一。先前确定的包含来自Zif268的三个锌指的复合物的2.1埃结构，已成为许多建模和设计研究的基础，并且Zif268已被证明是研究类TFIIIA锌指如何识别DNA的非常有用的模型系统。
我们已将Zif268蛋白-DNA复合物的结构精修至1.6埃分辨率。我们的结构证实了先前模型的所有基本特征，并使我们能够关注蛋白质-DNA界面处的一些关键细节。特别是，我们的精修结构有助于解释位于识别螺旋中的几个酸性残基的作用，并表明锌指与碱基和磷酸之间形成了许多水介导的接触。建模研究表明，在Zif268-DNA复合物中观察到的独特DNA构象与指-指相互作用以及相邻指之间的连接子长度相关。圆二色性研究表明，这种独特DNA构象的至少一些特征是在复合物形成时诱导产生的。
我们的1.6埃结构应为分析Zif268突变的影响、对相关锌指-DNA复合物进行建模以及设计和选择可识别其他DNA位点的Zif268变体提供一个出色的框架。
