Mycobacterium tuberculosis (Mtb) encodes two CRP/FNR family transcription factors (TF) that contribute to virulence, Cmr (Rv1675c) and CRP_Mt (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.

中文翻译：

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新型结构特征驱动TB复合分枝杆菌中CRP家族蛋白Cmr的DNA结合特性

结核分枝杆菌（Mtb）编码两种有助于毒力的CRP / FNR家族转录因子（TF），即Cmr（Rv1675c）和CRP _Mt（Rv3676）。先前的研究为每个TF识别了独特的染色体结合图谱，尽管它们识别出重叠的DNA基序。本研究表明，Cmr结合特异性是由基序位置4和13处的鉴别核苷酸决定的。X射线晶体学和定向突变分析确定了一个富含精氨酸的环，该环扩大了Cmr的DNA相互作用，超越了常见的经典螺旋-转-螺旋接触。所有CRP / FNR家族成员，并有助于与不完整的DNA序列结合。Cmr与DNA的结合导致DNA明显的不对称弯曲，其高水平的协同作用与DNA促进的二聚化相一致。独特的N末端延伸片段插入DNA结合域和二聚化域之间，部分遮盖了发现典型cAMP结合口袋的位点。然而，这个N末端的非结构化区域可能有助于调节Cmr活性以响应细胞信号。Cmr的DNA相互作用的多个水平可能增强其整合各种基因调控信号的能力，而其新颖的结构特征使Cmr成为非典型的CRP / FNR家族成员。