ABSTRACT
Most nuclear receptors recognize the same consensus hexameric sequence, AGGTCA. An important question has been how the various members of this transcription factor family distinguish identity features in these closely related DNA sites. We determined structures from several crystal forms of the RevErb-DNA complex and analyzed the patterns of protein-DNA interactions and DNA distortions. We found a significant and consistent DNA distortion at a TA step directly preceding the first consensus 5'-AGGTCA-3' recognition sequence. Importantly, while this base-pair sequence is associated with RevErb's high-affinity sites, there are no sequence-specific contacts formed with the protein. Our study shows that RevErb relies instead on the intrinsic geometry and flexibility of this TA site to make the required fit between the proteins' independent major groove and minor groove binding interactions, which occur on both sides of the TA step. Our findings extend the description of response element discrimination to include a role for sequence-dependent DNA deformations and suggest how other monomeric members of this superfamily, such as NGFI-B, SF-1, and ROR, could also recognize unique geometric features in their DNA targets.
Subject(s)
DNA/chemistry , Response Elements , Amino Acid Sequence , Base Sequence , Binding Sites , Crystallography, X-Ray , DNA/metabolism , Dimerization , Models, Molecular , Molecular Sequence Data , Nucleic Acid Conformation , Protein Binding , Protein Structure, Tertiary , Sequence Homology, Amino Acid , Sequence Homology, Nucleic AcidABSTRACT
The 9-cis retinoic acid receptor, RXR, binds DNA effectively as a homodimer or as a heterodimer with other nuclear receptors. The DNA-binding sites for these RXR complexes are direct repeats of a consensus sequence separated by one to five base-pairs of intervening space. Here, we report the 2.1 A crystal structure of the RXR-DNA-binding domain as a homodimer in complex with its idealized direct repeat DNA target. The structure shows how a gene-regulatory site can induce conformational changes in a transcription factor that promote homo-cooperative assembly. Specifically, an alpha-helix in the T-box is disrupted to allow efficient DNA-binding and subunit dimerization. RXR displays a relaxed mode of sequence recognition, interacting with only three base-pairs in each hexameric half-site. The structure illustrates how site selection is achieved in this large eukaryotic transcription factor family through discrete protein-protein interactions and the use of tandem DNA binding sites with characteristic spacings.
