Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA.
New York Structural Biology Center, New York, NY 10027, USA.
Nucleic Acids Res. 2018 Jan 9;46(1):403-420. doi: 10.1093/nar/gkx1148.
Mycobacterium tuberculosis (Mtb) encodes two CRP/FNR family transcription factors (TF) that contribute to virulence, Cmr (Rv1675c) and CRPMt (Rv3676). Prior studies identified distinct chromosomal binding profiles for each TF despite their recognizing overlapping DNA motifs. The present study shows that Cmr binding specificity is determined by discriminator nucleotides at motif positions 4 and 13. X-ray crystallography and targeted mutational analyses identified an arginine-rich loop that expands Cmr's DNA interactions beyond the classical helix-turn-helix contacts common to all CRP/FNR family members and facilitates binding to imperfect DNA sequences. Cmr binding to DNA results in a pronounced asymmetric bending of the DNA and its high level of cooperativity is consistent with DNA-facilitated dimerization. A unique N-terminal extension inserts between the DNA binding and dimerization domains, partially occluding the site where the canonical cAMP binding pocket is found. However, an unstructured region of this N-terminus may help modulate Cmr activity in response to cellular signals. Cmr's multiple levels of DNA interaction likely enhance its ability to integrate diverse gene regulatory signals, while its novel structural features establish Cmr as an atypical CRP/FNR family member.
结核分枝杆菌（Mtb）编码两种 CRP/FNR 家族转录因子（TF），它们有助于毒力，分别是 Cmr（Rv1675c）和 CRPMt（Rv3676）。尽管它们识别重叠的 DNA 基序，但先前的研究确定了每个 TF 的独特染色体结合图谱。本研究表明，Cmr 的结合特异性由基序位置 4 和 13 的判别核苷酸决定。X 射线晶体学和靶向突变分析确定了一个富含精氨酸的环，该环扩展了 Cmr 的 DNA 相互作用，超出了所有 CRP/FNR 家族成员共有的经典螺旋-转角-螺旋接触，并促进与非完美 DNA 序列的结合。Cmr 与 DNA 的结合导致 DNA 明显的不对称弯曲，其高水平的协同性与 DNA 介导的二聚化一致。独特的 N 端延伸插入 DNA 结合和二聚化结构域之间，部分掩盖了经典 cAMP 结合口袋所在的位置。然而，这个 N 端的无结构区域可能有助于调节 Cmr 活性以响应细胞信号。Cmr 的多层次 DNA 相互作用可能增强了其整合多种基因调控信号的能力，而其新颖的结构特征使 Cmr 成为一种非典型的 CRP/FNR 家族成员。
