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Nucleic Acids Research Advance Access originally published online on June 9, 2009
Nucleic Acids Research 2009 37(14):4723-4735; doi:10.1093/nar/gkp496
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Nucleic Acids Research, 2009, Vol. 37, No. 14 4723-4735
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

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

Thirumananseri Kumarevel1,*, Tomoyuki Tanaka1, Takashi Umehara2 and Shigeyuki Yokoyama2,3

1RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, 2Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 and 3Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan

*To whom correspondence should be addressed. Tel: +81 791 58 2838 (ext 7894); Fax: +81 791 58 2826; Email: tskvel{at}spring8.or.jp

Received April 24, 2009. Revised May 21, 2009. Accepted May 21, 2009.

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 Å 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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