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结核分枝杆菌应答调节因子PhoP的DNA结合结构域结构

Structure of the DNA-binding domain of the response regulator PhoP from Mycobacterium tuberculosis.

作者信息

Wang Shuishu, Engohang-Ndong Jean, Smith Issar

机构信息

Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA.

出版信息

Biochemistry. 2007 Dec 25;46(51):14751-61. doi: 10.1021/bi700970a. Epub 2007 Dec 1.

Abstract

The PhoP-PhoR two-component signaling system from Mycobacterium tuberculosis is essential for the virulence of the tubercle bacillus. The response regulator, PhoP, regulates expression of over 110 genes. In order to elucidate the regulatory mechanism of PhoP, we determined the crystal structure of its DNA-binding domain (PhoPC). PhoPC exhibits a typical fold of the winged helix-turn-helix subfamily of response regulators. The structure starts with a four-stranded antiparallel beta-sheet, followed by a three-helical bundle of alpha-helices, and then a C-terminal beta-hairpin, which together with a short beta-strand between the first and second helices forms a three-stranded antiparallel beta-sheet. Structural elements are packed through a hydrophobic core, with the first helix providing a scaffold for the rest of the domain to pack. The second and third helices and the long, flexible loop between them form the helix-turn-helix motif, with the third helix being the recognition helix. The C-terminal beta-hairpin turn forms the wing motif. The molecular surfaces around the recognition helix and the wing residues show strong positive electrostatic potential, consistent with their roles in DNA binding and nucleotide sequence recognition. The crystal packing of PhoPC gives a hexamer ring, with neighboring molecules interacting in a head-to-tail fashion. This packing interface suggests that PhoPC could bind DNA in a tandem association. However, this mode of DNA binding is likely to be nonspecific because the recognition helix is partially blocked and would be prevented from inserting into the major groove of DNA. Detailed structural analysis and implications with respect to DNA binding are discussed.

摘要

结核分枝杆菌的PhoP-PhoR双组分信号系统对结核杆菌的毒力至关重要。应答调节因子PhoP调控超过110个基因的表达。为了阐明PhoP的调控机制,我们确定了其DNA结合结构域(PhoPC)的晶体结构。PhoPC呈现出应答调节因子中典型的带翼螺旋-转角-螺旋亚家族折叠。该结构起始于一个四链反平行β折叠,接着是一个由三个α螺旋组成的螺旋束,然后是一个C端β发夹结构,它与第一和第二个螺旋之间的一条短β链共同形成一个三链反平行β折叠。结构元件通过一个疏水核心堆积在一起,第一个螺旋为结构域的其余部分提供了堆积的支架。第二和第三个螺旋以及它们之间的长而灵活的环形成螺旋-转角-螺旋基序,第三个螺旋为识别螺旋。C端β发夹转折形成翼状基序。识别螺旋和翼状残基周围的分子表面显示出很强的正静电势,这与其在DNA结合和核苷酸序列识别中的作用一致。PhoPC的晶体堆积形成一个六聚体环,相邻分子以头对尾的方式相互作用。这种堆积界面表明PhoPC可能以串联结合的方式结合DNA。然而,这种DNA结合模式可能是非特异性的,因为识别螺旋部分受阻,无法插入DNA的大沟中。文中讨论了关于DNA结合的详细结构分析及意义。

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