The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

Abstract

The bacterial nucleoid-associated protein Fis regulates diverse reactions by bending DNA and through DNAdependent interactions with other control proteins and enzymes. In addition to dynamic nonspecific binding to DNA, Fis forms stable complexes with DNA segments that share little sequence conservation. Here we report the first crystal structures of Fis bound to high-and low-affinity 27-base-pair DNA sites. These 11 structures reveal that Fis selects targets primarily through indirect recognition mechanisms involving the shape of the minor groove and sequence-dependent induced fits over adjacent major groove interfaces. The DNA shows an overall curvature of 65°, and the unprecedented close spacing between helix-turn-helix motifs present in the apodimer is accommodated by severe compression of the central minor groove. In silico DNA structure models show that only the roll, twist, and slide parameters are sufficient to reproduce the changes in minor groove widths and recreate the curved Fis-bound DNA structure. Models based on naked DNA structures suggest that Fis initially selects DNA targets with intrinsically narrow minor grooves using the separation between helix-turn-helix motifs in the Fis dimer as a ruler. Then Fis further compresses the minor groove and bends the DNA to generate the bound structure.[Keywords: DNA structure; protein-DNA recognition; DNA bending; nucleoid protein; X-ray crystallography] Supplemental material is available at http://www.genesdev.org.

Nucleoprotein architectures regulating the directionality of viral integration and excision

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“…2C), compatible with their occurrence along one helix face opposite the bound protein. Phased hyperactive DNase I sites are evident in some LytTR protein-DNA interactions (25,41) as well as other classes of well-characterized protein-DNA interactions where protein binding to one DNA face induces significant bending, including DNA bound by cyclic AMP receptor protein (33), factor of inversion (44,48), and MerR family regulators (36). Significant RcoM Bx -1-induced DNA bending is also consistent with the surprisingly poor activity of the UQ6148 reporter (Table 2), where the separately functional "a ϩ b ϩ c" and "d ϩ e ϩ f" binding regions were merged with a two-turn "c"-to-"d" interval.…”

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