Park Sun Cheol, Kwak Yun Mi, Song Wan Seok, Hong Minsun, Yoon Sung-Il
Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.
Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea.
Nucleic Acids Res. 2017 Dec 15;45(22):13080-13093. doi: 10.1093/nar/gkx1055.
The PadR family is a large group of transcriptional regulators that function as environmental sensors. PadR negatively controls the expression of phenolic acid decarboxylase, which detoxifies harmful phenolic acids. To identify the mechanism by which PadR regulates phenolic acid-mediated gene expression, we performed structural and mutational studies of effector and operator recognition by Bacillus subtilis PadR. PadR contains an N-terminal winged helix-turn-helix (wHTH) domain (NTD) and a C-terminal homodimerization domain (CTD) and dimerizes into a dolmen shape. The PadR dimer interacts with the palindromic sequence of the operator DNA using the NTD. Two tyrosine residues and a positively charged residue in the NTD provide major DNA-binding energy and are highly conserved in the PadR family, suggesting that these three residues represent the canonical DNA-binding motif of the PadR family. PadR directly binds a phenolic acid effector molecule using a unique interdomain pocket created between the NTD and the CTD. Although the effector-binding site of PadR is positionally segregated from the DNA-binding site, effector binding to the interdomain pocket causes PadR to be rearranged into a DNA binding-incompatible conformer through an allosteric interdomain-reorganization mechanism.
PadR家族是一大类作为环境传感器发挥作用的转录调节因子。PadR负向调控酚酸脱羧酶的表达，酚酸脱羧酶可对有害酚酸进行解毒。为了确定PadR调控酚酸介导的基因表达的机制，我们对枯草芽孢杆菌PadR的效应物和操纵子识别进行了结构和突变研究。PadR包含一个N端带翼螺旋-转角-螺旋（wHTH）结构域（NTD）和一个C端同二聚化结构域（CTD），并二聚化为拱门形状。PadR二聚体利用NTD与操纵子DNA的回文序列相互作用。NTD中的两个酪氨酸残基和一个带正电荷的残基提供主要的DNA结合能量，并且在PadR家族中高度保守，这表明这三个残基代表PadR家族的典型DNA结合基序。PadR利用在NTD和CTD之间形成的独特结构域间口袋直接结合酚酸效应分子。尽管PadR的效应物结合位点在位置上与DNA结合位点分开，但效应物与结构域间口袋的结合会通过变构结构域间重组机制使PadR重排为与DNA结合不相容的构象。
