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Nucleic Acids Research 2006 34(5):1450-1458; doi:10.1093/nar/gkl015
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Published online 9 March 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Structures of {omega} repressors bound to direct and inverted DNA repeats explain modulation of transcription

Wilhelm Andreas Weihofen, Aslan Cicek, Florencia Pratto1, Juan Carlos Alonso1 and Wolfram Saenger*

Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin Takustr. 6, 14195 Berlin, Germany 1Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología CSIC, 28049 Madrid, Spain

*To whom correspondence should be addressed. Tel: +49 30 838 53412; Fax: +49 30 838 56702; Email: saenger{at}chemie.fu-berlin.de

Received December 20, 2005. Revised February 14, 2006. Accepted February 14, 2006.

Repressor {omega} regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. {omega} belongs to homodimeric ribbon-helix-helix (RHH2) repressors typified by a central, antiparallel ß-sheet for DNA major groove binding. Homodimeric {omega}2 binds cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA heptad repeats (5'-A/TATCACA/T-3', symbolized by ->) in palindromic inverted, converging (-><-) or diverging (<-->) orientation and also, unique to {omega}2 and contrasting other RHH2 repressors, to non-palindromic direct (->->) repeats. Here we investigate with crystal structures how {omega}2 binds specifically to heptads in minimal operators with (->->) and (-><-) repeats. Since the pseudo-2-fold axis relating the monomers in {omega}2 passes the central C–G base pair of each heptad with ~0.3 Å downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (->->), ~0.6 Å shorter in (-><-) but would be ~0.6 Å longer in (<-->). These variations grade interactions between adjacent {omega}2 and explain modulations in cooperative binding affinity of {omega}2 to operators with different heptad orientations.

Present address: Wilhelm Andreas Weihofen, Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA


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