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J. Biol. Chem., Vol. 278, Issue 20, 17752-17759, May 16, 2003

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Structural Analysis of the DNA-binding Domain of the Erwinia amylovora RcsB Protein and Its Interaction with the RcsAB Box^*

Primo Pristovek^§, Kaushik Sengupta^¶, Frank Löhr^¶, Birgit Schäfer^¶, Markus Wehland von Trebra, Heinz Rüterjans^¶, and Frank Bernhard^¶**

From the  Kemijski Institute, National Institute of Chemistry, Hajdrihova 19, P. O. Box 660, SI-1001 Ljubljana, Slovenia, the ^¶ Universität Frankfurt/Main, Institut für Biophysikalische Chemie, Marie Curie Str. 9, D-60439 Frankfurt, Germany, and the  Freie Universität Berlin, Institut für Kristallographie, Takustr.6, D-14195 Berlin, Germany

The transcriptional regulator RcsB interacts with other coactivators to control the expression of biosynthetic operons in enterobacteria. While in a heterodimer complex with the regulator RcsA the RcsAB box consensus is recognized, DNA binding sites for RcsB without RcsA have also been identified. The conformation of RcsB might therefore be modulated upon interaction with various coactivators, resulting in the recognition of different DNA targets. We report the solution structure of the C-terminal DNA-binding domain of the RcsB protein from Erwinia amylovora spanning amino acid residues 129-215 solved by heteronuclear magnetic resonance (NMR) spectroscopy. The C-terminal domain is composed of four -helices where two central helices form a helix-turn-helix motif similar to the structures of the regulatory proteins GerE, NarL, and TraR. Amino acid residues involved in the RcsA independent DNA binding of RcsB were identified by titration studies with a RcsAB box consensus fragment. Data obtained from NMR spectroscopy together with surface plasmon resonance measurements demonstrate that the RcsAB box is specifically recognized by the RcsAB heterodimer as well as by RcsB alone. However, the binding constant of RcsB alone at target promoters from Escherichia coli, E. amylovora, and Pantoea stewartii was approximately 1 order of magnitude higher compared with that of the RcsAB heterodimer. We present evidence that the obvious role of RcsA is not to alter the DNA binding specificity of RcsB but to stabilize RcsB-DNA complexes.

The atomic coordinates and the structure factors (code 1NRL) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

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