The DNA-binding Domain of OmpR: Crystal Structures of a Winged Helix Transcription Factor

Structure. 1997 Jan 15;5(1):109-24. doi: 10.1016/s0969-2126(97)00170-6.


Background: The differential expression of the ompF and ompC genes is regulated by two proteins that belong to the two component family of signal transduction proteins: the histidine kinase, EnvZ, and the response regulator, OmpR. OmpR belongs to a subfamily of at least 50 response regulators with homologous C-terminal DNA-binding domains of approximately 98 amino acids. Sequence homology with DNA-binding proteins of known structure cannot be detected, and the lack of structural information has prevented understanding of many of this familys functional properties.

Results: We have determined the crystal structure of the Escherichia coli OmpR C-terminal domain at 1.95 A resolution. The structure consists of three alpha helices packed against two antiparallel beta sheets. Two helices, alpha2 and alpha3, and the ten residue loop connecting them constitute a variation of the helix-turn-helix (HTH) motif. Helix alpha3 and the loop connecting the two C-terminal beta strands, beta6 and beta7, are probable DNA-recognition sites. Previous mutagenesis studies indicate that the large loop connecting helices alpha2 and alpha3 is the site of interaction with the alpha subunit of RNA polymerase.

Conclusions: OmpRc belongs to the family of 'winged helix-turn-helix' DNA-binding proteins. This relationship, and the results from numerous published mutagenesis studies, have helped us to interpret the functions of most of the structural elements present in this protein domain. The structure of OmpRc could be useful in helping to define the positioning of the alpha subunit of RNA polymerase in relation to transcriptional activators that are bound to DNA.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Outer Membrane Proteins / chemistry*
  • Bacterial Proteins
  • Binding Sites
  • Carbon-Nitrogen Ligases*
  • Conserved Sequence / genetics
  • Crystallography, X-Ray
  • DNA-Binding Proteins / chemistry
  • Escherichia coli / chemistry*
  • Escherichia coli Proteins*
  • Helix-Turn-Helix Motifs
  • Molecular Sequence Data
  • Mutagenesis / genetics
  • Mutation
  • Protein Folding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Repressor Proteins / chemistry
  • Sequence Alignment
  • Transcription Factors / chemistry*
  • Transcription, Genetic / genetics


  • Bacterial Outer Membrane Proteins
  • Bacterial Proteins
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Repressor Proteins
  • Transcription Factors
  • Carbon-Nitrogen Ligases
  • birA protein, E coli

Associated data

  • PDB/1OPC