Lee Choongdeok, Kim Meong Il, Hong Minsun
Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea.
Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea.
Biochem Biophys Res Commun. 2017 Jan 29;483(1):264-270. doi: 10.1016/j.bbrc.2016.12.155. Epub 2016 Dec 24.
A phenolic acid decarboxylase (padC) regulator, PadR and its homologs proteins belong to the PadR family. Despite the growing numbers of the PadR family members and their various roles in bacteria, such as detoxifications, drug transports and circadian rhythms, biochemical and biophysical studies of the PadR family are very limited. Thus, a ligand-induced regulatory mechanism of the PadR family transcription factors remains to be elucidated. Here, we report a crystal structure of a Bacteroides fragilis PadR-like protein, BF2549 and revealed its interaction with putative operator DNA and ligand molecules. Comparative structural and primary sequence analyses provide a PadR-specific motif that is conserved in the PadR family but deviated from the MarR family. Furthermore, putative ligand binding sites are observed in the BF2549 structure. Finally, a homology-based structure model of BF2549 and 29-mer dsDNA propose regulatory mechanisms of the PadR family in transcriptional derepression.
一种酚酸脱羧酶（padC）调节因子PadR及其同源蛋白属于PadR家族。尽管PadR家族成员数量不断增加，且在细菌中发挥着各种作用，如解毒、药物转运和昼夜节律，但对PadR家族的生化和生物物理研究非常有限。因此，PadR家族转录因子的配体诱导调节机制仍有待阐明。在此，我们报道了脆弱拟杆菌PadR样蛋白BF2549的晶体结构，并揭示了其与假定的操纵子DNA和配体分子的相互作用。比较结构和一级序列分析提供了一个PadR特异性基序，该基序在PadR家族中保守，但与MarR家族不同。此外，在BF2549结构中观察到了假定的配体结合位点。最后，基于同源性的BF2549和29聚体双链DNA结构模型提出了PadR家族在转录去抑制中的调节机制。
