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.
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