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PROSITE documentation PDOC51755 [for PROSITE entry PS51755]

OmpR/PhoB-type DNA-binding domain profile





Description

Bacteria and plants frequently use two-components signal transduction systems (TCSs) to adapt to environmental changes and to survive under stress conditions. Typical TCSs couple a transmembrane histidine protein kinase (HK) (see <PDOC50109>), which detects changes in the environmnent, to a cytosolic response regulator (RR), which often alters gene expression. Most RRs contain two distinct domains: an N-terminal receiver domain (see <PDOC50110>) and a C-terminal effector domain. The OmpR/PhoB subfamily is the largest subfamily of RRs. Members of the OmpR/PhoB subfamily include such diverse transcriptional regulators as Escherichia coli PhoB (of the phosphate assimilation pathway), Enterococcus faecium VanR (which controls resistance to the antibiotic vancomycin), and Agrobacterium tumefaciens VirG (involved in the establishment of crown gall tumors in plant. The C-terminal effector domain of the OmpR/PhoB subfamily RRs binds DNA. This DNA-binding domain is also found in proteins other than response regulators, such as Vibrio cholerea ToxR, a transmembrane protein involved in cholera toxin expression [1,2,3,4,5].

The OmpR/PhoB-type DNA-binding domain has the typical fold of the winged helix-turn-helix DNA-binding domain. The structure of the OmpR/PhoB-type DNA-binding domain consists of three α helices packed against two antiparallel β sheets, an N-terminal four-stranded antiparallel β sheet and a C-terminal hairpin (see <PDB:1OPC>). The hairpin interacts with a short stretch of β strand, that connects helices α1 and α2, to generate a three-stranded antiparallel β sheet. The topology for the domain is β1-β2-β3-β4-α1-β5-α2-α3-β6-β7. The hydrophobic core of the domain is formed by sidechains contributed by each of the seven β strands and three α helices [1,2,3,4,5].

The profile we developed covers the entire OmpR/PhoB-type DNA-binding domain.

Last update:

May 2015 / First entry.

Technical section

PROSITE method (with tools and information) covered by this documentation:

OMPR_PHOB, PS51755; OmpR/PhoB-type DNA-binding domain profile  (MATRIX)


References

1AuthorsMartinez-Hackert E. Stock A.M.
TitleThe DNA-binding domain of OmpR: crystal structures of a winged helix transcription factor.
SourceStructure 5:109-124(1997).
PubMed ID9016718

2AuthorsWang S. Engohang-Ndong J. Smith I.
TitleStructure of the DNA-binding domain of the response regulator PhoP from Mycobacterium tuberculosis.
SourceBiochemistry 46:14751-14761(2007).
PubMed ID18052041
DOI10.1021/bi700970a

3AuthorsOkajima T. Doi A. Okada A. Gotoh Y. Tanizawa K. Utsumi R.
TitleResponse regulator YycF essential for bacterial growth: X-ray crystal structure of the DNA-binding domain and its PhoB-like DNA recognition motif.
SourceFEBS Lett. 582:3434-3438(2008).
PubMed ID18789936
DOI10.1016/j.febslet.2008.09.007

4AuthorsMenon S. Wang S.
TitleStructure of the response regulator PhoP from Mycobacterium tuberculosis reveals a dimer through the receiver domain.
SourceBiochemistry 50:5948-5957(2011).
PubMed ID21634789
DOI10.1021/bi2005575

5AuthorsLi Y.-C. Chang C.-K. Chang C.-F. Cheng Y.-H. Fang P.-J. Yu T. Chen S.-C. Li Y.-C. Hsiao C.-D. Huang T.-H.
TitleStructural dynamics of the two-component response regulator RstA in recognition of promoter DNA element.
SourceNucleic Acids Res. 42:8777-8788(2014).
PubMed ID24990372
DOI10.1093/nar/gku572



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