Variable Structures of Fis-DNA Complexes Determined by Flanking DNA – Protein Contacts

• Published in: Journal of molecular biology 1996-12, Vol.264 (4), p.675-695
• Main Authors: Pan, Clark Q., Finkel, Steven E., Cramton, Sarah E., Feng, Jin-An, Sigman, David S., Johnson, Reid C.
• Format: Article
• Language: English
• Subjects: 1,10-phenanthroline copper; Base Sequence; Binding Sites; Carrier Proteins - chemistry; Carrier Proteins - metabolism; Dimerization; DNA - chemistry; DNA - metabolism; DNA bending; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - metabolism; Electrophoresis, Polyacrylamide Gel; Escherichia coli; Factor For Inversion Stimulation Protein; Fis; Helix-Turn-Helix Motifs; Hydrogen Bonding; Integration Host Factors; Models, Molecular; molecular modeling; Nucleic Acid Conformation; Oligodeoxyribonucleotides - chemistry; Oligodeoxyribonucleotides - metabolism; Phenanthrolines; Protein Conformation; protein-DNA interactions; Salmonella typhimurium
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1006/jmbi.1996.0669

The Fis protein from Escherichia coliand Salmonella typhimuriumregulates 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 ≤50° to ≥90°. 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.