title: Structural and functional analysis of BF2549, a PadR-like transcription factor from Bacteroides fragilis.
abstract: 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.
authors.affiliation: Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea.
authors.forename: Choongdeok
authors.initials: C
authors.lastname: Lee
authors.affiliation: Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea.
authors.forename: Meong Il
authors.initials: MI
authors.lastname: Kim
authors.affiliation: Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea. Electronic address: minsunhong@yonsei.ac.kr.
authors.forename: Minsun
authors.initials: M
authors.lastname: Hong
mesh_terms: D020816:Amino Acid Motifs; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001441:Bacteroides fragilis / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D002262:Carboxy-Lyases / Q000378:metabolism*; D018360:Crystallography, X-Ray; D004269:DNA, Bacterial / Q000737:chemistry; D004591:Electrophoresis, Polyacrylamide Gel; D015964:Gene Expression Regulation, Bacterial; D008024:Ligands; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014961:X-Ray Diffraction
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D008024:Ligands; D014157:Transcription Factors; D002262:Carboxy-Lyases; C417714:phenolic acid decarboxylase
keywords: BF2549; Bacteroides fragilis; Crystal structure; Phenolic acid decarboxylase regulator (PadR)