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Structural polymorphism in the major groove of a 5S RNA gene complements the zinc finger domains of transcription factor IIIA

Huber, Paul W. and Morii, Takashi and Mei, Houng-Yau and Barton, Jacqueline K. (1991) Structural polymorphism in the major groove of a 5S RNA gene complements the zinc finger domains of transcription factor IIIA. Proceedings of the National Academy of Sciences of the United States of America, 88 (23). pp. 10801-10805. ISSN 0027-8424. http://resolver.caltech.edu/CaltechAUTHORS:HUBpnas91

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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 ringer 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 ringer 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.


Item Type:Article
Additional Information:Copyright © 1991 by the National Academy of Sciences. Communicated by Nicholas J. Turro, July 17, 1991 (received for review May 14, 1991). We thank Prof. J. Berg for supplying the coordinates of his consensus zinc finger domain. We are grateful for the financial support of the National Institutes of Health (GM33309 and CA33620 to J.K.B.; GM38200 to P.W.H.), the American Heart Association, Indiana Affiliate (Grant in Aid to P.W.H.), and for a Jesse H. Jones Faculty Research Award (to P.W.H.). The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.
Subject Keywords:internal control region, repressor operator complex, binding-site, B-form, crystal-structure, metal-complexes, chiral probe, 5S-RNA gene, DNA, xenopus
Record Number:CaltechAUTHORS:HUBpnas91
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:HUBpnas91
Alternative URL:http://www.pnas.org/cgi/content/abstract/88/23/10801
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:1012
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:01 Dec 2005
Last Modified:14 Nov 2014 19:18

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