Cooperative DNA binding by proteins through DNA shape complementarity

Hancock, Stephen P.; Cascio, Duilio; Johnson, Reid C.

doi:10.1093/nar/gkz642

Title: Cooperative DNA binding by proteins through DNA shape complementarity

Journal Article · 25 July 2019 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkz642 · OSTI ID:1638899

Hancock, Stephen P. ^[1]; Cascio, Duilio ^[2]; Johnson, Reid C. ^[2]

Univ. of California, Los Angeles, CA (United States); Towson Univ., MD (United States)
Univ. of California, Los Angeles, CA (United States)

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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-06CH11357; FC02-02ER63421

OSTI ID:: 1638899

Alternate ID(s):: OSTI ID: 1562718

Journal Information:: Nucleic Acids Research, Vol. 47, Issue 16; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 9 works

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