Structural and biophysical characterization of PadR family protein Rv0047c of Mycobacterium tuberculosis H37Rv

The members of the PadR family of transcriptional regulators are important for cell survival in toxic environments and play an important role in detoxification, pathogenicity, and multi-drug resistance. Rv0047c of Mycobacterium tuberculosis H37Rv is annotated as a PadR family protein. We have characterized the stability and structure of Rv0047c. Rv0047c forms a stable dimer in solution. Its stability is characterized by a thermal melting transition temperature (Tm) of 55.3 degrees C. The crystal structure of Rv0047c was determined at a resolution of 3.15 & Aring;. The structure indicates the biological unit to be a dimer with each monomer having a characteristic N-terminal winged-helix-turn-helix DNA binding domain and a C-terminal dimerization domain. The N-terminal domain is composed of four helices, alpha 1, alpha 2, alpha 3, and alpha 4 and two beta strands beta 1 and beta 2. The C-terminal dimerization domain (CTD) consists two long helices alpha 6 and alpha 7. The two domains are connected by helix alpha 5. A short helical turn (helix alpha a, residue 89-92), leads to compaction of the alpha 4-alpha 5 loop. Rv0047c exhibits specificity in binding to an upstream region having an inverted repeat sequence. This binding is dependent upon Y18 and Y40 residue of Rv0047c, which are highly conserved among the PadR family. Overall, our results suggest a transcription regulatory role for Rv0047c, similar to other PadR family proteins.