Structural Basis of Pyrimidine Specificity in the MS2 RNA Hairpin-Coat-Protein Complex.Grahn, E., Moss, T., Helgstrand, C., Fridborg, K., Sundaram, M., Tars, K., Lago, H., Stonehouse, N.J., Davis, D.R., Stockley, P.G., Liljas, L.
(2001) RNA 7: 1616
- PubMed: 11720290
- Primary Citation of Related Structures:  2BU1, 2C4Q, 2C4Y, 2C4Z, 2C51
- PubMed 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 ty ...
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 A 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.
Department of Cell and Molecular Biology, Uppsala University, Sweden.