Ball N, Streeter S D, Kneale G G, McGeehan J E
Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, UK.
Acta Crystallogr D Biol Crystallogr. 2009 Sep;65(Pt 9):900-5. doi: 10.1107/S0907444909020514. Epub 2009 Aug 6.
The controller protein of the Esp1396I restriction-modification (R-M) system binds differentially to three distinct operator sequences upstream of the methyltransferase (M) and endonuclease (R) genes to regulate the timing of gene expression. The crystal structure of a complex of the protein with two adjacent operator DNA sequences has been reported; however, the structure of the free protein has not yet been determined. Here, the crystal structure of the free protein is reported, with seven dimers in the asymmetric unit. Two of the 14 monomers show an alternative conformation to the major conformer in which the side chains of residues 43-46 in the loop region flanking the DNA-recognition helix are displaced by up to 10 A. It is proposed that the adoption of these two conformational states may play a role in DNA-sequence promiscuity. The two alternative conformations are also found in the R35A mutant structure, which is otherwise identical to the native protein. Comparison of the free and bound protein structures shows a 1.4 A displacement of the recognition helices when the dimer is bound to its DNA target.
Esp1396I 限制修饰（R-M）系统的调控蛋白与甲基转移酶（M）基因和核酸内切酶（R）基因上游的三个不同操纵序列存在差异结合，以调控基因表达的时间。该蛋白与两个相邻操纵子DNA序列形成复合物的晶体结构已见报道；然而，游离蛋白的结构尚未确定。本文报道了游离蛋白的晶体结构，其不对称单元中有七个二聚体。14个单体中的两个呈现出与主要构象不同的构象，在DNA识别螺旋侧翼的环区中，43-46位残基的侧链位移高达10 Å。有人提出，这两种构象状态的采用可能在DNA序列混杂中起作用。在R35A突变体结构中也发现了这两种不同的构象，该突变体结构在其他方面与天然蛋白相同。游离蛋白和结合蛋白结构的比较表明，当二聚体与其DNA靶点结合时，识别螺旋会发生1.4 Å的位移。
