Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I.

Richard N A Martin, John E McGeehan, Neil J Ball, Simon D Streeter, Sarah-Jane Thresh, G G Kneale
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Abstract

The controller protein of the type II restriction-modification (RM) system Esp1396I binds to three distinct DNA operator sequences upstream of the methyltransferase and endonuclease genes in order to regulate their expression. Previous biophysical and crystallographic studies have shown molecular details of how the controller protein binds to the operator sites with very different affinities. Here, two protein-DNA co-crystal structures containing portions of unbound DNA from native operator sites are reported. The DNA in both complexes shows significant distortion in the region between the conserved symmetric sequences, similar to that of a DNA duplex when bound by the controller protein (C-protein), indicating that the naked DNA has an intrinsic tendency to bend when not bound to the C-protein. Moreover, the width of the major groove of the DNA adjacent to a bound C-protein dimer is observed to be significantly increased, supporting the idea that this DNA distortion contributes to the substantial cooperativity found when a second C-protein dimer binds to the operator to form the tetrameric repression complex.

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调控限制性修饰系统 Esp1396I 的 DNA 蛋白复合物结构分析。
II 型限制性修饰(RM)系统的控制蛋白 Esp1396I 与甲基转移酶和内切酶基因上游的三个不同 DNA 操作序列结合,以调控它们的表达。先前的生物物理和晶体学研究显示了控制蛋白如何以非常不同的亲和力与操作者位点结合的分子细节。本文报告了两种蛋白质-DNA 共晶体结构,其中包含来自原生操作者位点的未结合 DNA 部分。这两种复合物中的 DNA 在保守对称序列之间的区域显示出明显的扭曲,类似于 DNA 双链与控制蛋白(C 蛋白)结合时的扭曲,表明裸 DNA 在未与 C 蛋白结合时具有内在的弯曲趋势。此外,还观察到与结合的 C 蛋白二聚体相邻的 DNA 主沟宽度明显增加,这支持了这样一种观点,即当第二个 C 蛋白二聚体与操作者结合形成四聚体抑制复合物时,DNA 的这种扭曲会产生巨大的合作作用。
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期刊介绍: Acta Crystallographica Section F is a rapid structural biology communications journal. Articles on any aspect of structural biology, including structures determined using high-throughput methods or from iterative studies such as those used in the pharmaceutical industry, are welcomed by the journal. The journal offers the option of open access, and all communications benefit from unlimited free use of colour illustrations and no page charges. Authors are encouraged to submit multimedia content for publication with their articles. Acta Cryst. F has a dedicated online tool called publBio that is designed to make the preparation and submission of articles easier for authors.
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