title: Structural polymorphism in the major groove of a 5S RNA gene complements the zinc finger domains of transcription factor IIIA.
abstract: Metal complexes that bind to DNA on the basis of shape-selection have been used to map the conformational features of the DNA binding site for transcription factor IIIA. Conformationally distinct segments are detected on the 5S rRNA gene that correspond closely to the binding sites identified for the individual zinc finger domains of the protein. The local conformations are characterized by a major groove opened because of a change in base pair inclination and/or displacement at a central 5'-pyrimidine-purine-3' step, flanked by a widened minor groove, as would arise at the junctions between alternating B- and A-like DNA segments. Docking experiments with a consensus structure of a zinc finger reveal that the mixed A-B binding site accommodates the peptide domain better than either canonical B- or A-DNA helices. The close structural matching of the conformational variations in the 5S rDNA both to the proposed sites of zinc finger binding and to the shape of an individual zinc finger domain points to DNA structural polymorphism as providing an important determinant in recognition. In particular, shape selection in the 5' half of the internal control region may orient the multiple finger domains.
authors.affiliation: Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556.
authors.forename: P W
authors.initials: PW
authors.lastname: Huber
authors.forename: T
authors.initials: T
authors.lastname: Morii
authors.forename: H Y
authors.initials: HY
authors.lastname: Mei
authors.forename: J K
authors.initials: JK
authors.lastname: Barton
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D005796:Genes; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010957:Plasmids; D011110:Polymorphism, Genetic; D011487:Protein Conformation; D012341:RNA, Ribosomal, 5S / Q000235:genetics*; D015183:Restriction Mapping; D035582:Transcription Factor TFIIIA; D014157:Transcription Factors / Q000378:metabolism*; D014981:Xenopus; D016335:Zinc Fingers / Q000235:genetics*
chemical_list: D012341:RNA, Ribosomal, 5S; D035582:Transcription Factor TFIIIA; D014157:Transcription Factors