Chivers Peter T, Tahirov Tahir H
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
J Mol Biol. 2005 May 6;348(3):597-607. doi: 10.1016/j.jmb.2005.03.017.
The Pyrococcus horikoshii OT3 genome contains a gene (PH0601 or nikR) encoding a protein (PhNikR) that shares 33.8% amino acid sequence identity with Escherichia coli nickel responsive repressor NikR (EcNikR), including many residues that are functionally important in the E.coli ortholog. We succeeded in crystallization and structural characterization of PhNikR in the apo form and two nickel bound forms that exhibit different conformations, open and closed. Moreover, we have identified a putative "low-affinity" nickel-binding pocket in the closed form. This binding site has unusual nickel coordination and exhibits high sensitivity to phosphate in the crystal structure. Analysis of the PhNikR structures and structure-based mutational studies with EcNikR reveals a plausible mechanism of nickel-dependent promoter recognition by the NikR family of proteins.
嗜热栖热菌OT3基因组包含一个基因（PH0601或nikR），该基因编码一种蛋白质（PhNikR），其与大肠杆菌镍响应阻遏蛋白NikR（EcNikR）的氨基酸序列同一性为33.8%，包括许多在大肠杆菌直系同源物中具有功能重要性的残基。我们成功获得了无配体形式以及两种具有不同构象（开放和闭合）的镍结合形式的PhNikR的晶体并对其进行了结构表征。此外，我们在闭合形式中鉴定出一个假定的“低亲和力”镍结合口袋。该结合位点具有不寻常的镍配位，并且在晶体结构中对磷酸盐表现出高敏感性。对PhNikR结构的分析以及基于结构的EcNikR突变研究揭示了NikR家族蛋白质对镍依赖性启动子识别的一种合理机制。
