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Structural basis of pyrimidine specificity in the MS2 RNA hairpin–coat-protein complex

Published online by Cambridge University Press:  11 January 2002

ELIN GRAHN
Affiliation:
Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
TIMOTHY MOSS
Affiliation:
Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
CHARLOTTE HELGSTRAND
Affiliation:
Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
KERSTIN FRIDBORG
Affiliation:
Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
MALLIKARJUN SUNDARAM
Affiliation:
Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
KASPARS TARS
Affiliation:
Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden Present address: Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden.
HUGO LAGO
Affiliation:
Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
NICOLA J. STONEHOUSE
Affiliation:
Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
DARRELL R. DAVIS
Affiliation:
Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
PETER G. STOCKLEY
Affiliation:
Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
LARS LILJAS
Affiliation:
Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
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Abstract

We have determined the X-ray structures of six MS2 RNA hairpin–coat-protein complexes having five different substitutions at the hairpin loop base −5. This is a uracil in the wild-type hairpin and contacts the coat protein both by stacking on to a tyrosine side chain and by hydrogen bonding to an asparagine side chain. The RNA consensus sequence derived from coat protein binding studies with natural sequence variants suggested that the −5 base needs to be a pyrimidine for strong binding. The five −5 substituents used in this study were 5-bromouracil, pyrimidin-2-one, 2-thiouracil, adenine, and guanine. The structure of the 5-bromouracil complex was determined to 2.2 Å resolution, which is the highest to date for any MS2 RNA–protein complex. All the complexes presented here show very similar conformations, despite variation in affinity in solution. The results suggest that the stacking of the −5 base on to the tyrosine side chain is the most important driving force for complex formation. A number of hydrogen bonds that are present in the wild-type complex are not crucial for binding, as- they are missing in one or more of the complexes. The results also reveal the flexibility of this RNA-protein interface, with respect to functional group variation, and may be generally applicable to other RNA–protein complexes.

Type
Research Article
Information
RNA , Volume 7 , Issue 11 , November 2001 , pp. 1616 - 1627
Copyright
© 2001 RNA Society

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