Nucleic Acids Research Advance Access originally published online on February 3, 2009
Nucleic Acids Research 2009 37(6):1915-1924; doi:10.1093/nar/gkp044
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Nucleic Acids Research, 2009, Vol. 37, No. 6 1915-1924
© 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 |
Crystal structure of KorA bound to operator DNA: insight into repressor cooperation in RP4 gene regulation
1Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, 2Max-Planck-Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin and 3Institute for Chemistry and Biochemistry, Free University, Takustraße 6, 14195 Berlin, Germany
To whom correspondence should be addressed. Tel: +49 30 9406 3420; Fax: +49 30 9406 2548; Email: heinemann{at}mdc-berlin.de
Received December 23, 2008. Accepted January 14, 2009.
KorA is a global repressor in RP4 which regulates cooperatively the expression of plasmid genes whose products are involved in replication, conjugative transfer and stable inheritance. The structure of KorA bound to an 18-bp DNA duplex that contains the symmetric operator sequence and incorporates 5-bromo-deoxyuridine nucleosides has been determined by multiple-wavelength anomalous diffraction phasing at 1.96-Å resolution. KorA is present as a symmetric dimer and contacts DNA via a helix–turn–helix motif. Each half-site of the symmetric operator DNA binds one copy of the protein in the major groove. As confirmed by mutagenesis, recognition specificity is based on two KorA side chains forming hydrogen bonds to four bases within each operator half-site. KorA has a unique dimerization module shared by the RP4 proteins TrbA and KlcB. We propose that these proteins cooperate with the global RP4 repressor KorB in a similar manner via this dimerization module and thus regulate RP4 inheritance.