PROSITE documentation PDOC51755OmpR/PhoB-type DNA-binding domain profile
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.
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PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | Martinez-Hackert E. Stock A.M. |
| Title | The DNA-binding domain of OmpR: crystal structures of a winged helix transcription factor. | |
| Source | Structure 5:109-124(1997). | |
| PubMed ID | 9016718 |
| 2 | Authors | Wang S. Engohang-Ndong J. Smith I. |
| Title | Structure of the DNA-binding domain of the response regulator PhoP from Mycobacterium tuberculosis. | |
| Source | Biochemistry 46:14751-14761(2007). | |
| PubMed ID | 18052041 | |
| DOI | 10.1021/bi700970a |
| 3 | Authors | Okajima T. Doi A. Okada A. Gotoh Y. Tanizawa K. Utsumi R. |
| Title | Response regulator YycF essential for bacterial growth: X-ray crystal structure of the DNA-binding domain and its PhoB-like DNA recognition motif. | |
| Source | FEBS Lett. 582:3434-3438(2008). | |
| PubMed ID | 18789936 | |
| DOI | 10.1016/j.febslet.2008.09.007 |
| 4 | Authors | Menon S. Wang S. |
| Title | Structure of the response regulator PhoP from Mycobacterium tuberculosis reveals a dimer through the receiver domain. | |
| Source | Biochemistry 50:5948-5957(2011). | |
| PubMed ID | 21634789 | |
| DOI | 10.1021/bi2005575 |
| 5 | Authors | Li 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. |
| Title | Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element. | |
| Source | Nucleic Acids Res. 42:8777-8788(2014). | |
| PubMed ID | 24990372 | |
| DOI | 10.1093/nar/gku572 |
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