Crystal structure of KorA bound to operator.pdf

Published online 3 February 2009 Nucleic Acids Research, 2009, Vol. 37, No. 6 1915–1924 doi:10.1093/nar/gkp044 Crystal structure of KorA bound to operator DNA: insight into repressor cooperation in RP4 gene regulation Bettina Ko?nig1, Ju?rgen J. Mu?ller1, Erich Lanka2 and Udo Heinemann1,3,* 1Max-Delbru?ck-Center for Molecular Medicine, Robert-Ro?ssle-Stra?e 10, 13125 Berlin, 2Max-Planck-Institute for Molecular Genetics, Ihnestra?e 73, 14195 Berlin and 3Institute for Chemistry and Biochemistry, Free University, Takustra?e 6, 14195 Berlin, Germany Received December 23, 2008; Accepted January 14, 2009 ABSTRACT KorA is a global repressor in RP4 which regulates cooperatively the expression of plasmid genes whose products are involved in replication, conjuga- tive 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 deter- mined by multiple-wavelength anomalous diffrac- tion phasing at 1.96-A? resolution. KorA is present as a symmetric dimer and contacts DNA via a helix–turn–helix motif. Each half-site of the symmet- ric 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. INTRODUCTION Plasmids of the incompatibility group IncP are capable of transfer and stable inheritance in most Gram-negative bacteria (1). Besides various bacterial hosts, they can also transfer to yeast (2) and some higher eukaryotic cells (3). IncP-1 plasmids are divided into several sub- groups, a, b, g and d (4,5). The best-studied family mem- bers share a common back