Cq. Pan et al., VARIABLE STRUCTURES OF FIS-DNA COMPLEXES DETERMINED BY FLANKING DNA-PROTEIN CONTACTS, Journal of Molecular Biology, 264(4), 1996, pp. 675-695
The Fis protein from Escherichia coli and Salmonella typhimurium regul
ates many diverse reactions including recombination, transcription, an
d replication and is one of the most abundant DNA binding proteins pre
sent in the cell under certain physiological conditions. As a specific
regulator, Fis binds to discrete sites that are poorly related in pri
mary sequence. Analysis of DNA scission by a collection of Fis conjuga
tes to 1,10-phenanthroline-copper combined with comparative gel electr
ophoresis has shown that the structures of Fis-DNA complexes are highl
y variable, displaying overall DNA curvatures that range from less tha
n or equal to 50 degrees to greater than or equal to 90 degrees. This
variability is primarily determined by differential wrapping of flanki
ng DNA around Fis. By contrast, DNA bending within the core recognitio
n 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 hydro
gen 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 structu
re of Fis, have enabled us to generate new models for Fis-DNA complexe
s that emphasize the variability in DNA structures within the flanking
regions. (C) 1996 Academic Press Limited