Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada.
Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, QC, H3A 2B4, Canada.
Sci Rep. 2019 Nov 13;9(1):16679. doi: 10.1038/s41598-019-52964-2.
GapR is a nucleoid-associated protein required for the cell cycle of Caulobacter cresentus. We have determined new crystal structures of GapR to high resolution. As in a recently published structure, a GapR monomer folds into one long N-terminal α helix and two shorter α helices, and assembles into a tetrameric ring with a closed, positively charged, central channel. In contrast to the conclusions drawn from the published structures, we observe that the central channel of the tetramer presented here could freely accommodate B-DNA. Mutation of six conserved lysine residues lining the cavity and electrophoretic mobility gel shift experiments confirmed their role in DNA binding and the channel as the site of DNA binding. Although present in our crystals, DNA could not be observed in the electron density maps, suggesting that DNA binding is non-specific, which could be important for tetramer-ring translocation along the chromosome. In conjunction with previous GapR structures we propose a model for DNA binding and translocation that explains key published observations on GapR and its biological functions.
GapR 是一种黏着菌 Crescentus 细胞周期所必需的核质相关蛋白。我们已经确定了新的 GapR 晶体结构达到了高分辨率。与最近发表的结构一样，GapR 单体折叠成一个长的 N 端α螺旋和两个较短的α螺旋，并组装成一个具有封闭的、带正电荷的中央通道的四聚体环。与从已发表结构中得出的结论相反，我们观察到这里呈现的四聚体的中央通道可以自由容纳 B-DNA。突变六个保守的赖氨酸残基排列在腔和电泳迁移凝胶移位实验证实了它们在 DNA 结合和通道中的作用，作为 DNA 结合的位点。尽管在我们的晶体中存在，但在电子密度图中无法观察到 DNA，表明 DNA 结合是非特异性的，这对于四聚体环沿着染色体的易位可能很重要。结合以前的 GapR 结构，我们提出了一个 DNA 结合和易位的模型，该模型解释了 GapR 及其生物学功能的关键已发表观察结果。
