DNA-binding Domain of E.coli Positive Regulator OmpR

The structure of the C-terminal DNA-binding domain of OmpR was determined by the X-ray crystallography at 2.0A resolution. OmpR is a positive regulator involved in osmoregulation expression of the ompF and ompC genes in Escherichia coli. The C-terminal half domain of OmpR, consisting of about 120 residues, exhibits an inherent DNA-binding ability specific to the cognate promoters. The molecule consists of a four-stranded beta-sheet and a three-helix bundle with a C-terminal beta-hairpin. Well-conserved hydrophobic residues cluster between the N-terminal four-stranded beta-sheet and the C-terminal three-helix bundle, thus demonstrating the importance of the four-stranded beta-sheet for the integrity of the DNA-binding domain. Two helices, alpha2 and alpha3, and loop between them create a structure somewhat similar to the helix-turn-helix motif. The 'turn' region, consisting of 11 residues, forms an RNA polymerase contact site.

References

• Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site
  Hidemasa Kondo, Atsushi Nakagawa, Jun Nishihira, Yoshifumi Nishimura Takeshi Mizuno and Isao Tanaka
  Nature Struct. Biol., 4, 28-31 (1997)

• Crystallization and X-ray diffraction studies of the DNA-binding domain of OmpR protein, a positive regulator involved in activation of osmoregulatory genes in Escherichia coli
  Hidemasa Kondo, Taka-aki Miyaji, Mamoru Suzuki, Shin-ichi Tate, Takeshi Mizuno, Yoshifumi Nishimura and Isao Tanaka
  J. Mol. Biol., 235, 780-782 (1994)