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Pan CQ , Finkel SE , Cramton SE , Feng JA , Sigman DS , Johnson RC
Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts
Journal of Molecular Biology. 1996 Dec 13;264(4) :675-695
PMID: ISI:A1996VX92500004   
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The Fis protein from Escherichia coli and Salmonella typhimurium regulates many diverse reactions including recombination, transcription, and replication and is one of the most abundant DNA binding proteins present in the cell under certain physiological conditions. As a specific regulator, Fis binds to discrete sites that are poorly related in primary sequence. Analysis of DNA scission by a collection of Fis conjugates to 1,10-phenanthroline-copper combined with comparative gel electrophoresis has shown that the structures of Fis-DNA complexes are highly variable, displaying overall DNA curvatures that range from less than or equal to 50 degrees to greater than or equal to 90 degrees. This variability is primarily determined by differential wrapping of flanking DNA around Fis. By contrast, DNA bending within the core recognition regions appears similar among the binding sites that were analyzed. Flanking DNA contacts by Fis depend on the nucleotide sequence and are mediated by an electrostatic interaction with arginine 71 and a hydrogen bond with asparagine 73, both of which are located outside of the helix- turn-helix DNA binding motif. These contacts strongly influence the kinetics of binding. These data, combined with the crystal structure of Fis, have enabled us to generate new models for Fis-DNA complexes that emphasize the variability in DNA structures within the flanking regions. (C) 1996 Academic Press Limited
Times Cited: 40 English Article VX925 J MOL BIOL