Structural rearrangement accompanying ligand binding in the GAF domain of CodY from Bacillus subtilis.
Structural rearrangement accompanying ligand binding in the GAF domain of CodY from Bacillus subtilis.
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DOI：
10.1016/j.jmb.2009.05.077
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发表时间：
2009-07-31
影响因子：
5.6
通讯作者：
Wilkinson, Anthony J.
中科院分区：
文献类型：
--
作者：
Levdikov, Vladimir M.;Blagova, Elena;Colledge, Vicki L.;Lebedev, Andrey A.;Williamson, David C.;Sonenshein, Abraham L.;Wilkinson, Anthony J.
关键词：
GAF结构域是一个简单的模块，广泛存在于各种功能的蛋白质中，包括细胞信号蛋白和转录因子。它的结构通常跨越150个残基，具有三层;两个或更多个α-螺旋的基底层，β-折叠片层的中间层和由连接β-片层链的多肽片段形成的顶层。在与其效应物复合的GAF结构域的结构中，这些多肽区段将配体包封在空腔中，该空腔的基部由β-折叠形成，使得配体结合和释放必须伴随着结构的远端部分的构象重排。结合的描述目前受到缺乏GAF结构域的限制，GAF结构域的配体和非配体结构都是已知的。早些时候，我们解决了CodY的GAF结构域的晶体结构，CodY是芽孢杆菌中稳定期和毒力基因转录的支链氨基酸和GTP响应性调节剂，与异亮氨酸和缬氨酸复合。在这里，我们报告的结构域在其unliganded形式，允许定义的结构变化伴随配体结合。的核心的蛋白质和它的二聚化界面基本上是不变的，与圆二色光谱实验表明，二级结构组成是不受干扰的配体结合。然而，结合位点环存在广泛的重折叠，连接β3和β4的卷曲片段移动高达15 μ m，使得在不存在配体的情况下，不形成结合口袋。这些结构重排的配体的亲和力和特异性的影响进行了讨论。最后，饱和转移差核磁共振光谱显示结合异亮氨酸，但不是GTP，GAF域表明这两个辅因子没有一个共同的结合位点。
The GAF domain is a simple module widespread in proteins of diverse function including cell signalling proteins and transcription factors. Its structure, typically spanning 150 residues, has three tiers; a basal layer of two or more α-helices, a middle layer of β-pleated sheet and a top layer formed by segments of the polypeptide that connect strands of the β-sheet. In structures of GAF domains in complex with their effectors, these polypeptide segments envelop the ligand enclosing it in a cavity whose base is formed by the β-sheet, so that ligand binding and release must be accompanied by conformational rearrangements of the distal portion of the structure. Descriptions of binding are presently limited by the absence of a GAF domain for which both liganded and unliganded structures are known. Earlier, we solved the crystal structure of the GAF domain of CodY, a branched chain amino acid and GTP responsive regulator of the transcription of stationary phase and virulence genes in Bacillus, in complexes with isoleucine and valine. Here, we report the structure of this domain in its unliganded form, allowing definition of the structural changes accompanying ligand binding. The core of the protein and its dimerisation interface are essentially unchanged in agreement with circular dichroism spectroscopy experiments that show that the secondary structure composition is unperturbed by ligand binding. There is however, extensive refolding of the binding site loops, with up to 15 Å movements of the coiled segment linking β3 and β4, such that in the absence of the ligand, the binding pocket is not formed. The implications of these structural rearrangements for ligand affinity and specificity are discussed. Finally, saturation transfer difference NMR spectroscopy showed binding of isoleucine, but not GTP, to the GAF domain suggesting that the two cofactors do not have a common binding site.
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DOI：
10.1107/s0907444904019158
发表时间：
2004-12-01
影响因子：
2.2
作者：
Emsley, P;Cowtan, K
通讯作者：
Cowtan, K
影响因子：
4.8
作者：
Heikaus, Clemens C.;Stout, Joseph R.;Klevit, Rachel E.
通讯作者：
Klevit, Rachel E.
DOI：
10.1073/pnas.0409913102
发表时间：
2005-02-22
影响因子：
11.1
作者：
Martinez, SE;Bruder, S;Linder, JU
通讯作者：
Linder, JU
DOI：
10.1107/s0907444998003254
发表时间：
1998-09-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Brunger, AT;Adams, PD;Warren, GL
通讯作者：
Warren, GL
DOI：
10.1073/pnas.0703774104
发表时间：
2007-06-05
影响因子：
11.1
作者：
Lin, Zhidong;Johnson, Lynnette C.;Lowther, W. Todd
通讯作者：
Lowther, W. Todd