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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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Structural comparison of the Cα backbones of VicRc (red), PhoB (green) and OmpR (blue). The α-loops and the loops linking α3 to the C-terminal β-hairpin are labelled.
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fig2: Structural comparison of the Cα backbones of VicRc (red), PhoB (green) and OmpR (blue). The α-loops and the loops linking α3 to the C-terminal β-hairpin are labelled.

Mentions: VicRc superimposes closely on representative members of the OmpR/PhoB family, OmpR, PhoB, PrrA, DrrB and DrrD (Buckler et al., 2002 ▶; PDB code 1kgs), with r.m.s.d. values of 1.5, 1.1, 1.2, 1.3 and 1.4 Å, respectively, when using Cα atoms only. Fig. 2 ▶ only shows the superposition of VicRc on OmpR and PhoB, with the other structures omitted for clarity. Although the sequence identities of VicRc with OmpR and PhoB are low (25 and 32%, respectively), the overall structures are almost identical. This is perhaps not surprising as the conserved residues play a key role in linking the secondary-structure elements responsible for DNA recognition (Blanco et al., 2002 ▶). The differences arise mainly for two loop regions: the α-loop and the loop region following α3 and linking it to the C-terminal β-hairpin (Fig. 2 ▶). Both these loops were removed when the ensemble model was prepared for molecular replacement.


Structure of the response regulator VicR DNA-binding domain.

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

Structural comparison of the Cα backbones of VicRc (red), PhoB (green) and OmpR (blue). The α-loops and the loops linking α3 to the C-terminal β-hairpin are labelled.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Structural comparison of the Cα backbones of VicRc (red), PhoB (green) and OmpR (blue). The α-loops and the loops linking α3 to the C-terminal β-hairpin are labelled.
Mentions: VicRc superimposes closely on representative members of the OmpR/PhoB family, OmpR, PhoB, PrrA, DrrB and DrrD (Buckler et al., 2002 ▶; PDB code 1kgs), with r.m.s.d. values of 1.5, 1.1, 1.2, 1.3 and 1.4 Å, respectively, when using Cα atoms only. Fig. 2 ▶ only shows the superposition of VicRc on OmpR and PhoB, with the other structures omitted for clarity. Although the sequence identities of VicRc with OmpR and PhoB are low (25 and 32%, respectively), the overall structures are almost identical. This is perhaps not surprising as the conserved residues play a key role in linking the secondary-structure elements responsible for DNA recognition (Blanco et al., 2002 ▶). The differences arise mainly for two loop regions: the α-loop and the loop region following α3 and linking it to the C-terminal β-hairpin (Fig. 2 ▶). Both these loops were removed when the ensemble model was prepared for molecular replacement.

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