Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea.
Department of Biomedical Laboratory Science, Yonsei University, Wonju, 26493, Republic of Korea.
Biochem Biophys Res Commun. 2020 Nov 5;532(2):251-257. doi: 10.1016/j.bbrc.2020.08.035. Epub 2020 Aug 28.
Since the first discovery of phenolic acid decarboxylase transcriptional regulator (PadR), its homologs have been identified mostly in bacterial species and constitute the PadR family. PadR family members commonly contain a winged helix-turn-helix (wHTH) motif and function as a transcription factor. However, the PadR family members are varied in terms of molecular size and structure. As a result, they are divided into PadR subfamily-1 and PadR subfamily-2. PadR subfamily-2 proteins have been reported in some pathogenic bacteria, including Listeria monocytogenes and Streptococcus pneumoniae, and implicated in drug resistance processes. Despite the growing numbers of known PadR family proteins and their critical functions in bacteria survival, biochemical and biophysical studies of the PadR subfamily-2 are limited. Here, we report the crystal structure of a PadR subfamily-2 member from Streptococcus pneumoniae (SpPadR) at a 2.40 Å resolution. SpPadR forms a dimer using its N-terminal and C-terminal helices. The two wHTH motifs of a SpPadR dimer expose their positively charged residues presumably to interact with DNA. Our structure-based mutational and biochemical study indicates that SpPadR specifically recognizes a palindromic nucleotide sequence upstream of its encoding region as a transcriptional regulator. Furthermore, comparative structural analysis of diverse PadR family members combined with a modeling study highlights the structural and regulatory features of SpPadR that are canonical to the PadR family or specific to the PadR subfamily-2.
自首次发现酚酸脱羧酶转录调节因子（PadR）以来，其同源物主要在细菌物种中被鉴定，并构成 PadR 家族。PadR 家族成员通常含有一个翼状螺旋-转角-螺旋（wHTH）基序，作为转录因子发挥作用。然而，PadR 家族成员在分子大小和结构上存在差异。因此，它们分为 PadR 亚家族-1 和 PadR 亚家族-2。PadR 亚家族-2 蛋白已在一些病原菌中被报道，包括李斯特菌和肺炎链球菌，并与耐药过程有关。尽管已知的 PadR 家族蛋白数量不断增加，并且它们在细菌生存中具有重要功能，但对 PadR 亚家族-2 的生化和生物物理研究仍然有限。在这里，我们报告了来自肺炎链球菌（SpPadR）的 PadR 亚家族-2 成员的晶体结构，分辨率为 2.40Å。SpPadR 使用其 N 端和 C 端螺旋形成二聚体。SpPadR 二聚体的两个 wHTH 基序暴露其带正电荷的残基，可能与 DNA 相互作用。我们基于结构的突变和生化研究表明，SpPadR 特异性识别其编码区域上游的回文核苷酸序列作为转录调节剂。此外，对不同 PadR 家族成员的结构比较分析结合建模研究突出了 SpPadR 的结构和调节特征，这些特征对于 PadR 家族是典型的，或者对于 PadR 亚家族-2 是特定的。
