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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.

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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 representation showing two molecules of PhoB (green) in complex with DNA shown in space-filling representation (Blanco et al., 2002 ▶; PDB code 1gxp). VicRc is shown in red, superimposed onto one PhoB monomer. The consensus sequences for YycF/VicR homologues and PhoB targets are also shown, with the C to A/T substitution mentioned in the text indicated by red arrows in each repeat. The filled red arrow indicates the corresponding base pair in the model, which has been coloured magenta and lies close to the recognition helix. The loop region of PhoB does not reach the DNA, while the VicRc loop could make contact with it.
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fig3: Ribbon representation showing two molecules of PhoB (green) in complex with DNA shown in space-filling representation (Blanco et al., 2002 ▶; PDB code 1gxp). VicRc is shown in red, superimposed onto one PhoB monomer. The consensus sequences for YycF/VicR homologues and PhoB targets are also shown, with the C to A/T substitution mentioned in the text indicated by red arrows in each repeat. The filled red arrow indicates the corresponding base pair in the model, which has been coloured magenta and lies close to the recognition helix. The loop region of PhoB does not reach the DNA, while the VicRc loop could make contact with it.

Mentions: The specific DNA target sequence for PhoB, the pho box, was identified as two seven-base-pair direct repeats separated by an AT-rich region of four base pairs (Mizuno, 1997 ▶). The corresponding consensus sequence for YycF (and presumably also VicRc) is almost identical, with one base change from C in PhoB to A or T in VicRc at position 5 in the repeat (with respect to the PhoB consensus; Fig. 3 ▶). This suggests that the protein–DNA interactions made by PhoB with its consensus DNA should be very similar to those in the VicRc–DNA complex. Fig. 3 ▶ shows a model built by superimposing VicRc on the PhoB–DNA complex (Blanco et al., 2002 ▶). In PhoB, residues Trp184 (at the C-terminal end of α2) and Arg193, Thr194, His198 and Arg200 (from α3) were all shown to be involved in specific DNA recognition (Okamura et al., 2000 ▶; Blanco et al., 2002 ▶) and all except His198 are conserved in VicR. In OmpR, Val203, Ser206 and Arg210 of α3 have been shown to be important for target specificity (Mizuno & Tanaka, 1997 ▶). The equivalent residues in PhoB are Val197, which packs against the CG base pair at position 5, Arg200, which is nearby but not in contact, interacting with the phosphate backbone, and Lys204, which lies at the end of α3 but does not contact the DNA. The corresponding residues in VicRc are Val199, Arg202 and Glu206. The first two are unchanged and Glu206 is too far away from the DNA to make contact, although it is close enough to influence the conformation of Arg202, which lies near the single base pair that differs between the consensus sequences. The following loop in PhoB is too short to contact the DNA, but in VicRc and OmpR it is longer (Figs. 2 ▶ and 3 ▶) and might play a role in DNA–protein interactions, although this loop has no previously reported association with DNA and whether the positions of these loops differ upon binding to DNA is not yet known.


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 representation showing two molecules of PhoB (green) in complex with DNA shown in space-filling representation (Blanco et al., 2002 ▶; PDB code 1gxp). VicRc is shown in red, superimposed onto one PhoB monomer. The consensus sequences for YycF/VicR homologues and PhoB targets are also shown, with the C to A/T substitution mentioned in the text indicated by red arrows in each repeat. The filled red arrow indicates the corresponding base pair in the model, which has been coloured magenta and lies close to the recognition helix. The loop region of PhoB does not reach the DNA, while the VicRc loop could make contact with it.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: Ribbon representation showing two molecules of PhoB (green) in complex with DNA shown in space-filling representation (Blanco et al., 2002 ▶; PDB code 1gxp). VicRc is shown in red, superimposed onto one PhoB monomer. The consensus sequences for YycF/VicR homologues and PhoB targets are also shown, with the C to A/T substitution mentioned in the text indicated by red arrows in each repeat. The filled red arrow indicates the corresponding base pair in the model, which has been coloured magenta and lies close to the recognition helix. The loop region of PhoB does not reach the DNA, while the VicRc loop could make contact with it.
Mentions: The specific DNA target sequence for PhoB, the pho box, was identified as two seven-base-pair direct repeats separated by an AT-rich region of four base pairs (Mizuno, 1997 ▶). The corresponding consensus sequence for YycF (and presumably also VicRc) is almost identical, with one base change from C in PhoB to A or T in VicRc at position 5 in the repeat (with respect to the PhoB consensus; Fig. 3 ▶). This suggests that the protein–DNA interactions made by PhoB with its consensus DNA should be very similar to those in the VicRc–DNA complex. Fig. 3 ▶ shows a model built by superimposing VicRc on the PhoB–DNA complex (Blanco et al., 2002 ▶). In PhoB, residues Trp184 (at the C-terminal end of α2) and Arg193, Thr194, His198 and Arg200 (from α3) were all shown to be involved in specific DNA recognition (Okamura et al., 2000 ▶; Blanco et al., 2002 ▶) and all except His198 are conserved in VicR. In OmpR, Val203, Ser206 and Arg210 of α3 have been shown to be important for target specificity (Mizuno & Tanaka, 1997 ▶). The equivalent residues in PhoB are Val197, which packs against the CG base pair at position 5, Arg200, which is nearby but not in contact, interacting with the phosphate backbone, and Lys204, which lies at the end of α3 but does not contact the DNA. The corresponding residues in VicRc are Val199, Arg202 and Glu206. The first two are unchanged and Glu206 is too far away from the DNA to make contact, although it is close enough to influence the conformation of Arg202, which lies near the single base pair that differs between the consensus sequences. The following loop in PhoB is too short to contact the DNA, but in VicRc and OmpR it is longer (Figs. 2 ▶ and 3 ▶) and might play a role in DNA–protein interactions, although this loop has no previously reported association with DNA and whether the positions of these loops differ upon binding to DNA is not yet known.

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