Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I.
Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I.
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DOI：
10.1107/s174430911302126x
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发表时间：
2013-09
期刊：
影响因子：
--
通讯作者：
Kneale GG
中科院分区：
文献类型：
--
作者：
Martin RN;McGeehan JE;Ball NJ;Streeter SD;Thresh SJ;Kneale GG
蛋白质-DNA共晶体复合物中结合和未结合的DNA的比较揭示了转录调控中的蛋白质-蛋白质结合和DNA畸变的见解。II型限制修饰（RM）系统Esp 1396 I的控制蛋白结合到甲基转移酶和核酸内切酶基因上游的三个不同的DNA操纵子序列，以调节它们的表达。先前的生物物理学和晶体学研究已经显示了控制蛋白如何以非常不同的亲和力结合到操纵位点的分子细节。在这里，报告了两种蛋白质-DNA共晶结构，包含来自天然操纵基因位点的未结合DNA部分。两种复合物中的DNA在保守对称序列之间的区域中显示出显著的变形，类似于DNA双链体在被控制蛋白（C蛋白）结合时的变形，表明裸DNA在不与C蛋白结合时具有弯曲的内在趋势。此外，观察到与结合的C-蛋白二聚体相邻的DNA的大沟的宽度显著增加，这支持了这样的观点，即当第二个C-蛋白二聚体结合到操纵基因以形成四聚体阻遏复合物时，这种DNA扭曲有助于发现的实质性协同性。
Comparison of bound and unbound DNA in protein–DNA co-crystal complexes reveals insights into controller-protein binding and DNA distortion in transcriptional regulation. 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.