Cooperative DNA binding by proteins through DNA shape complementarity.
Publication Type:Journal Article
Source:Nucleic Acids Res, Volume 47, Issue 16, p.8874-8887 (2019)
Keywords:Allosteric Site, Bacteriophage lambda, Base Sequence, Binding Sites, Chromosomes, Bacterial, Cloning, Molecular, Crystallography, X-Ray, DNA Nucleotidyltransferases, DNA, Bacterial, Escherichia coli, Escherichia coli Proteins, Factor For Inversion Stimulation Protein, Gene Expression, Genetic Vectors, Kinetics, Models, Molecular, Nucleic Acid Conformation, Protein Binding, Protein Conformation, alpha-Helical, Protein Conformation, beta-Strand, Protein Interaction Domains and Motifs, Recombinant Proteins, Recombinational DNA Repair, Sequence Alignment, Thermodynamics, Viral Proteins
<p>Localized arrays of proteins cooperatively assemble onto chromosomes to control DNA activity in many contexts. Binding cooperativity is often mediated by specific protein-protein interactions, but cooperativity through DNA structure is becoming increasingly recognized as an additional mechanism. During the site-specific DNA recombination reaction that excises phage λ from the chromosome, the bacterial DNA architectural protein Fis recruits multiple λ-encoded Xis proteins to the attR recombination site. Here, we report X-ray crystal structures of DNA complexes containing Fis + Xis, which show little, if any, contacts between the two proteins. Comparisons with structures of DNA complexes containing only Fis or Xis, together with mutant protein and DNA binding studies, support a mechanism for cooperative protein binding solely by DNA allostery. Fis binding both molds the minor groove to potentiate insertion of the Xis β-hairpin wing motif and bends the DNA to facilitate Xis-DNA contacts within the major groove. The Fis-structured minor groove shape that is optimized for Xis binding requires a precisely positioned pyrimidine-purine base-pair step, whose location has been shown to modulate minor groove widths in Fis-bound complexes to different DNA targets.</p>