title: Structural basis of RXR-DNA interactions.
abstract: 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.
authors.affiliation: Department of Pharmacology X-ray Crystallography Laboratory, University of Virginia, Charlottesville, VA, 22908, USA.
authors.forename: Q
authors.initials: Q
authors.lastname: Zhao
authors.forename: S A
authors.initials: SA
authors.lastname: Chasse
authors.forename: S
authors.initials: S
authors.lastname: Devarakonda
authors.forename: M L
authors.initials: ML
authors.lastname: Sierk
authors.forename: B
authors.initials: B
authors.lastname: Ahvazi
authors.forename: F
authors.initials: F
authors.lastname: Rastinejad
mesh_terms: D000494:Allosteric Regulation; D000595:Amino Acid Sequence; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D016384:Consensus Sequence / Q000235:genetics; D003460:Crystallization; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D019281:Dimerization; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D018160:Receptors, Cytoplasmic and Nuclear / Q000737:chemistry / Q000378:metabolism; D018168:Receptors, Retinoic Acid / Q000737:chemistry* / Q000378:metabolism*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D020218:Response Elements / Q000235:genetics; D047488:Retinoid X Receptors; D013379:Substrate Specificity; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D018160:Receptors, Cytoplasmic and Nuclear; D018168:Receptors, Retinoic Acid; D047488:Retinoid X Receptors; D014157:Transcription Factors; D004247:DNA