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J. Biol. Chem., Vol. 281, Issue 37, 27443-27453, September 15, 2006

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An Extended RNA Binding Site for the Yeast Branch Point-binding Protein and the Role of Its Zinc Knuckle Domains in RNA Binding^*

From the Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229

The highly conserved branch point sequence (BPS) of UACUAAC in Saccharomyces cerevisiae is initially recognized by the branch point-binding protein (BBP). Using systematic evolution of ligands by exponential enrichment we have determined that yeast BBP binds the branch point sequence UACUAAC with highest affinity and prefers an additional adenosine downstream of the BPS. Furthermore, we also found that a stem-loop upstream of the BPS enhances binding both to an artificially designed RNA (30-fold effect) and to an RNA from a yeast intron (3-fold effect). The zinc knuckles of BBP are partially responsible for the enhanced binding to the stem-loop but do not appear to have a significant role in the binding of BBP to single-strand RNA substrates. C-terminal deletions of BBP reveal that the linker regions between the two zinc knuckles and between the N-terminal RNA binding domains (KH and QUA2 domains) and the first zinc knuckle are important for binding to RNA. The lack of involvement of the second highly conserved zinc knuckle in RNA binding suggests that this zinc knuckle plays a different role in RNA processing than enhancing the binding of BBP to the BPS.

Received for publication, April 3, 2006 , and in revised form, July 10, 2006.

^* This work was supported in part by March of Dimes Grant 5-FY03-135 (to J. A. B.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ Supported by National Institutes of Health Training Grant GM-07759 (to the Institute of Molecular Biology).

² Supported by American Heart Association Postdoctoral Fellowship 4200732.

³ To whom correspondence should be addressed. Tel.: 541-346-5097; Fax: 541-346-5891; E-mail: aberglund{at}molbio.uoregon.edu.

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