Structural basis for promoter DNA recognition by the response regulator OmpR

• Published in: Journal of structural biology Vol. 213; no. 1; p. 107638
• Main Authors: Sadotra, Sushant, Lou, Yuan-Chao, Tang, Hao-Cheng, Chiu, Yi-Chih, Hsu, Chun-Hua, Chen, Chinpan
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.03.2021
• Subjects: Bacterial two-component system; protein–DNA complex; Response regulator; X-ray crystal structure; RR; PhoBc; CD; OmpRn; HK; Bacterial two-component system; TCS; DBD; Response regulator; protein–DNA complex; X-ray crystal structure; OmpR-FL; OmpRc; RD; NMR; SEC-MALS; IPTG; BLI; Ni-NTA
• ISSN: 1047-8477; 1095-8657
• DOI: 10.1016/j.jsb.2020.107638

[Display omitted] •Crystal structures of E. coli OmpR DNA-binding domain were determined in apo and DNA-bound states.•OmpR DNA-binding domain forms a unique domain-swapped dimer.•OmpR DNA-binding domain shows intermolecular interactions in solution.•Phosphorylation may only enhance but not be required for OmpR–DNA binding. OmpR, a response regulator of the EnvZ/OmpR two-component system (TCS), controls the reciprocal regulation of two porin proteins, OmpF and OmpC, in bacteria. During signal transduction, OmpR (OmpR-FL) undergoes phosphorylation at its conserved Asp residue in the N-terminal receiver domain (OmpRn) and recognizes the promoter DNA from its C-terminal DNA-binding domain (OmpRc) to elicit an adaptive response. Apart from that, OmpR regulates many genes in Escherichia coli and is important for virulence in several pathogens. However, the molecular mechanism of the regulation and the structural basis of OmpR–DNA binding is still not fully clear. In this study, we presented the crystal structure of OmpRc in complex with the F1 region of the ompF promoter DNA from E. coli. Our structural analysis suggested that OmpRc binds to its cognate DNA as a homodimer, only in a head-to-tail orientation. Also, the OmpRc apo-form showed a unique domain-swapped crystal structure under different crystallization conditions. Biophysical experimental data, such as NMR, fluorescent polarization and thermal stability, showed that inactive OmpR-FL (unphosphorylated) could bind to promoter DNA with a weaker binding affinity as compared with active OmpR-FL (phosphorylated) or OmpRc, and also confirmed that phosphorylation may only enhance DNA binding. Furthermore, the dimerization interfaces in the OmpRc–DNA complex structure identified in this study provide an opportunity to understand the regulatory role of OmpR and explore the potential for this “druggable” target.