Department of Biological Chemistry, David Geffen School of Medicine at the University of California at Los Angeles, 90095-1737, USA.
Genes Dev. 2010 Apr 15;24(8):814-26. doi: 10.1101/gad.1900610.
The bacterial nucleoid-associated protein Fis regulates diverse reactions by bending DNA and through DNA-dependent interactions with other control proteins and enzymes. In addition to dynamic nonspecific binding to DNA, Fis forms stable complexes with DNA segments that share little sequence conservation. Here we report the first crystal structures of Fis bound to high- and low-affinity 27-base-pair DNA sites. These 11 structures reveal that Fis selects targets primarily through indirect recognition mechanisms involving the shape of the minor groove and sequence-dependent induced fits over adjacent major groove interfaces. The DNA shows an overall curvature of approximately 65 degrees , and the unprecedented close spacing between helix-turn-helix motifs present in the apodimer is accommodated by severe compression of the central minor groove. In silico DNA structure models show that only the roll, twist, and slide parameters are sufficient to reproduce the changes in minor groove widths and recreate the curved Fis-bound DNA structure. Models based on naked DNA structures suggest that Fis initially selects DNA targets with intrinsically narrow minor grooves using the separation between helix-turn-helix motifs in the Fis dimer as a ruler. Then Fis further compresses the minor groove and bends the DNA to generate the bound structure.
细菌核小体相关蛋白 Fis 通过弯曲 DNA 以及与其他控制蛋白和酶的 DNA 依赖性相互作用来调节多种反应。除了与 DNA 的动态非特异性结合外，Fis 还与具有很少序列保守性的 DNA 片段形成稳定的复合物。在这里，我们报告了 Fis 与高亲和力和低亲和力 27 碱基对 DNA 位点结合的第一个晶体结构。这 11 个结构表明，Fis 主要通过涉及小沟形状和序列依赖性诱导适配的间接识别机制来选择靶标，而不是通过相邻大沟界面的直接识别。DNA 显示出大约 65 度的整体曲率，并且在无柄二聚体中存在的螺旋-转角-螺旋基序之间的前所未有的紧密间隔通过中央小沟的严重压缩来适应。计算机 DNA 结构模型表明，只有滚转、扭曲和滑动参数足以复制小沟宽度的变化，并重新创建弯曲的 Fis 结合 DNA 结构。基于裸露 DNA 结构的模型表明，Fis 最初使用 Fis 二聚体中螺旋-转角-螺旋基序之间的分离作为标尺，选择具有内在狭窄小沟的 DNA 靶标。然后，Fis 进一步压缩小沟并弯曲 DNA 以产生结合结构。
