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Structure of the response regulator VicR DNA-binding domain.

Trinh CH, Liu Y, Phillips SE, Phillips-Jones MK - Acta Crystallogr. D Biol. Crystallogr. (2007)

Bottom Line: The alpha-loop, which links the two helices of the helix-turn-helix motif, is similar to that of PhoB, where it has been implicated in contacting the sigma subunit of RNA polymerase, but differs from that of OmpR.Conversely, the loop following the helix-turn-helix motif is similar to that of OmpR and differs from that of PhoB.YycF/VicR, PhoB and Bacillus subtilis PhoP regulators all recognize almost identical DNA sequences and although there is currently no experimental evidence linking this loop with the DNA, the structure is consistent with possible involvement in selective DNA recognition or binding.

View Article: PubMed Central - HTML - PubMed

Affiliation: Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, England.

ABSTRACT
The response regulator VicR from the Gram-positive bacterium Enterococcus faecalis forms part of the two-component signal transduction system of the YycFG subfamily. The structure of the DNA-binding domain of VicR, VicR(c), has been solved and belongs to the winged helix-turn-helix family. It is very similar to the DNA-binding domains of Escherichia coli PhoB and OmpR, despite low sequence similarity, but differs in two important loops. The alpha-loop, which links the two helices of the helix-turn-helix motif, is similar to that of PhoB, where it has been implicated in contacting the sigma subunit of RNA polymerase, but differs from that of OmpR. Conversely, the loop following the helix-turn-helix motif is similar to that of OmpR and differs from that of PhoB. YycF/VicR, PhoB and Bacillus subtilis PhoP regulators all recognize almost identical DNA sequences and although there is currently no experimental evidence linking this loop with the DNA, the structure is consistent with possible involvement in selective DNA recognition or binding.

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Ribbon diagram of VicRc. Helices α2 and α3 form the helix–turn–helix motif, linked by the α-loop. All figures were created with PyMOL (DeLano, 2002 ▶).
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fig1: Ribbon diagram of VicRc. Helices α2 and α3 form the helix–turn–helix motif, linked by the α-loop. All figures were created with PyMOL (DeLano, 2002 ▶).

Mentions: The structure of VicRc is highly similar to the DNA-binding domains of other members of the OmpR/PhoB subfamily. It comprises an N-terminal four-stranded antiparallel β-sheet (residues 134–136, 139–141, 147–150 and 153–156), a central three α-helical bundle (α1, α2 and α3; residues 159–170, 178–185 and 194–208, respectively) and a C-terminal β-hairpin turn (residues 210–215) (Fig. 1 ▶) and belongs to the winged helix–turn–helix family of DNA-binding motifs. On DNA binding, the recognition helix α3 would be expected to occupy the major groove and to interact with bases of the consensus sequence. The loop linking α2 and α3 has been designated the α-loop in OmpR and the transactivation loop in PhoB, where it probably interacts with the σ70 subunit of RNA polymerase and is essential for transcription activation (Kim et al., 1995 ▶; Makino et al., 1996 ▶).


Structure of the response regulator VicR DNA-binding domain.

Trinh CH, Liu Y, Phillips SE, Phillips-Jones MK - Acta Crystallogr. D Biol. Crystallogr. (2007)

Ribbon diagram of VicRc. Helices α2 and α3 form the helix–turn–helix motif, linked by the α-loop. All figures were created with PyMOL (DeLano, 2002 ▶).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483477&req=5

fig1: Ribbon diagram of VicRc. Helices α2 and α3 form the helix–turn–helix motif, linked by the α-loop. All figures were created with PyMOL (DeLano, 2002 ▶).
Mentions: The structure of VicRc is highly similar to the DNA-binding domains of other members of the OmpR/PhoB subfamily. It comprises an N-terminal four-stranded antiparallel β-sheet (residues 134–136, 139–141, 147–150 and 153–156), a central three α-helical bundle (α1, α2 and α3; residues 159–170, 178–185 and 194–208, respectively) and a C-terminal β-hairpin turn (residues 210–215) (Fig. 1 ▶) and belongs to the winged helix–turn–helix family of DNA-binding motifs. On DNA binding, the recognition helix α3 would be expected to occupy the major groove and to interact with bases of the consensus sequence. The loop linking α2 and α3 has been designated the α-loop in OmpR and the transactivation loop in PhoB, where it probably interacts with the σ70 subunit of RNA polymerase and is essential for transcription activation (Kim et al., 1995 ▶; Makino et al., 1996 ▶).

Bottom Line: The alpha-loop, which links the two helices of the helix-turn-helix motif, is similar to that of PhoB, where it has been implicated in contacting the sigma subunit of RNA polymerase, but differs from that of OmpR.Conversely, the loop following the helix-turn-helix motif is similar to that of OmpR and differs from that of PhoB.YycF/VicR, PhoB and Bacillus subtilis PhoP regulators all recognize almost identical DNA sequences and although there is currently no experimental evidence linking this loop with the DNA, the structure is consistent with possible involvement in selective DNA recognition or binding.

View Article: PubMed Central - HTML - PubMed

Affiliation: Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, England.

ABSTRACT
The response regulator VicR from the Gram-positive bacterium Enterococcus faecalis forms part of the two-component signal transduction system of the YycFG subfamily. The structure of the DNA-binding domain of VicR, VicR(c), has been solved and belongs to the winged helix-turn-helix family. It is very similar to the DNA-binding domains of Escherichia coli PhoB and OmpR, despite low sequence similarity, but differs in two important loops. The alpha-loop, which links the two helices of the helix-turn-helix motif, is similar to that of PhoB, where it has been implicated in contacting the sigma subunit of RNA polymerase, but differs from that of OmpR. Conversely, the loop following the helix-turn-helix motif is similar to that of OmpR and differs from that of PhoB. YycF/VicR, PhoB and Bacillus subtilis PhoP regulators all recognize almost identical DNA sequences and although there is currently no experimental evidence linking this loop with the DNA, the structure is consistent with possible involvement in selective DNA recognition or binding.

Show MeSH
Related in: MedlinePlus