{PDOC51755}
{PS51755; OMPR_PHOB}
{BEGIN}
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* OmpR/PhoB-type DNA-binding domain profile *
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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 alpha helices packed against two antiparallel
beta sheets,  an  N-terminal  four-stranded  antiparallel  beta sheet and a C-
terminal hairpin  (see <PDB:1OPC>). The hairpin interacts with a short stretch
of beta  strand, that connects helices alpha1 and alpha2, to generate a three-
stranded antiparallel  beta sheet. The topology for the domain is beta1-beta2-
beta3-beta4-alpha1-beta5-alpha2-alpha3-beta6-beta7. The  hydrophobic  core  of
the domain  is  formed  by  sidechains  contributed  by each of the seven beta
strands and three alpha helices [1,2,3,4,5].

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

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: May 2015 / First entry.

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

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