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ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.

Kumarevel T, Tanaka T, Umehara T, Yokoyama S - Nucleic Acids Res. (2009)

Bottom Line: Significantly large conformational changes occurred upon DNA binding and in each of the dimeric monomers in the asymmetric unit of the ST1710-DNA complex.Conserved wHtH loop residues interacting with the bound DNA and mutagenic analysis indicated that R89, R90 and K91 were important for DNA recognition.Significantly, the bound DNA exhibited a new binding mechanism.

View Article: PubMed Central - PubMed

Affiliation: RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan. tskvel@spring8.or.jp

ABSTRACT
ST1710, a member of the multiple antibiotic resistance regulator (MarR) family of regulatory proteins in bacteria and archaea, plays important roles in development of antibiotic resistance, a global health problem. Here, we present the crystal structure of ST1710 from Sulfolobus tokodaii strain 7 complexed with salicylate, a well-known inhibitor of MarR proteins and the ST1710 complex with its promoter DNA, refined to 1.8 and 2.10 A resolutions, respectively. The ST1710-DNA complex shares the topology of apo-ST1710 and MarR proteins, with each subunit containing a winged helix-turn-helix (wHtH) DNA binding motif. Significantly large conformational changes occurred upon DNA binding and in each of the dimeric monomers in the asymmetric unit of the ST1710-DNA complex. Conserved wHtH loop residues interacting with the bound DNA and mutagenic analysis indicated that R89, R90 and K91 were important for DNA recognition. Significantly, the bound DNA exhibited a new binding mechanism.

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Structural comparison of ST1710–DNA complex monomers with its native structure and salicylate complex. (A) Superimposition of ST1710–DNA complex monomers. As shown in Figure 2C one monomer of the complex is shown in cyan and the other monomer is in red. (B) The ST1710–DNA complex monomers superimposed with the ST1710 native structure and salicylate complex. The native structure and salicylate complex are represented by orange and green, respectively.
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Figure 5: Structural comparison of ST1710–DNA complex monomers with its native structure and salicylate complex. (A) Superimposition of ST1710–DNA complex monomers. As shown in Figure 2C one monomer of the complex is shown in cyan and the other monomer is in red. (B) The ST1710–DNA complex monomers superimposed with the ST1710 native structure and salicylate complex. The native structure and salicylate complex are represented by orange and green, respectively.

Mentions: In our recent report, we noticed a small change only at the loop region connecting strands β1 and β2 in the protein conformers crystallized in two different space groups and the overall structure was identical with an rmsd of 0.519 Å for 141 Cα atoms (13). In a similar way, when we compared the present ST1710–salicylate complex and native structure crystallized under the same conditions, a similar structural conformation was revealed with an rmsd of 0.11 Å for superposition of 141 Cα atoms. Additionally, the subunits in the dimer were identical. In contrast, the superimposition of the ST1710–DNA complex subunits (A and B chains) on one another revealed a large local conformational change all along the structure, excluding the helices α1 and α5 with an rmsd of 2.85 Å for 142 Cα atoms; however, the overall structural topology was similar (Figure 5A). A displacement of ∼3.5–5.5 Å was seen all along the winged HtH motif region and the C-terminal helix showed the displacement of around 2–3 Å. The winged HtH motif of A-chain where the DNA is recognized was elevated up compared to the B-chain, while the C-terminal helix α6 was shifted down.Figure 5.


ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.

Kumarevel T, Tanaka T, Umehara T, Yokoyama S - Nucleic Acids Res. (2009)

Structural comparison of ST1710–DNA complex monomers with its native structure and salicylate complex. (A) Superimposition of ST1710–DNA complex monomers. As shown in Figure 2C one monomer of the complex is shown in cyan and the other monomer is in red. (B) The ST1710–DNA complex monomers superimposed with the ST1710 native structure and salicylate complex. The native structure and salicylate complex are represented by orange and green, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2724296&req=5

Figure 5: Structural comparison of ST1710–DNA complex monomers with its native structure and salicylate complex. (A) Superimposition of ST1710–DNA complex monomers. As shown in Figure 2C one monomer of the complex is shown in cyan and the other monomer is in red. (B) The ST1710–DNA complex monomers superimposed with the ST1710 native structure and salicylate complex. The native structure and salicylate complex are represented by orange and green, respectively.
Mentions: In our recent report, we noticed a small change only at the loop region connecting strands β1 and β2 in the protein conformers crystallized in two different space groups and the overall structure was identical with an rmsd of 0.519 Å for 141 Cα atoms (13). In a similar way, when we compared the present ST1710–salicylate complex and native structure crystallized under the same conditions, a similar structural conformation was revealed with an rmsd of 0.11 Å for superposition of 141 Cα atoms. Additionally, the subunits in the dimer were identical. In contrast, the superimposition of the ST1710–DNA complex subunits (A and B chains) on one another revealed a large local conformational change all along the structure, excluding the helices α1 and α5 with an rmsd of 2.85 Å for 142 Cα atoms; however, the overall structural topology was similar (Figure 5A). A displacement of ∼3.5–5.5 Å was seen all along the winged HtH motif region and the C-terminal helix showed the displacement of around 2–3 Å. The winged HtH motif of A-chain where the DNA is recognized was elevated up compared to the B-chain, while the C-terminal helix α6 was shifted down.Figure 5.

Bottom Line: Significantly large conformational changes occurred upon DNA binding and in each of the dimeric monomers in the asymmetric unit of the ST1710-DNA complex.Conserved wHtH loop residues interacting with the bound DNA and mutagenic analysis indicated that R89, R90 and K91 were important for DNA recognition.Significantly, the bound DNA exhibited a new binding mechanism.

View Article: PubMed Central - PubMed

Affiliation: RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan. tskvel@spring8.or.jp

ABSTRACT
ST1710, a member of the multiple antibiotic resistance regulator (MarR) family of regulatory proteins in bacteria and archaea, plays important roles in development of antibiotic resistance, a global health problem. Here, we present the crystal structure of ST1710 from Sulfolobus tokodaii strain 7 complexed with salicylate, a well-known inhibitor of MarR proteins and the ST1710 complex with its promoter DNA, refined to 1.8 and 2.10 A resolutions, respectively. The ST1710-DNA complex shares the topology of apo-ST1710 and MarR proteins, with each subunit containing a winged helix-turn-helix (wHtH) DNA binding motif. Significantly large conformational changes occurred upon DNA binding and in each of the dimeric monomers in the asymmetric unit of the ST1710-DNA complex. Conserved wHtH loop residues interacting with the bound DNA and mutagenic analysis indicated that R89, R90 and K91 were important for DNA recognition. Significantly, the bound DNA exhibited a new binding mechanism.

Show MeSH
Related in: MedlinePlus