6P0U

Crystal structure of ternary DNA complex " FX(1-2)-2Xis" containing E. coli Fis and phage lambda Xis

Summary for 6P0U

• Entry DOI: 10.2210/pdb6p0u/pdb
• Descriptor: DNA-binding protein Fis, DNA (27-MER), FX1-2, Excisionase, ... (4 entities in total)
• Functional Keywords: protein-dna ternary complex, dna shape, cooperative binding, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 6
• Total formula weight: 52680.22

Authors

Hancock, S.P.,Cascio, D.,Johnson, R.C. (deposition date: 2019-05-17, release date: 2019-06-19, Last modification date: 2023-10-11)

Primary citation

Hancock, S.P.,Cascio, D.,Johnson, R.C.
Cooperative DNA binding by proteins through DNA shape complementarity.
Nucleic Acids Res., 47:8874-8887, 2019

PubMed Abstract: 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.

PubMed: 31616952
DOI: 10.1093/nar/gkz642

Experimental method

X-RAY DIFFRACTION (3.3 Å)