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

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 bo th by stacking on to a tyrosine side chain and by hydrogen bonding to an as paragine side chain. The RNA consensus sequence derived from coat protein b inding studies with natural sequence variants suggested that the -5 base ne eds 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 Angstrom resolution, which is the highest to date for any MS2 RNA-protein c omplex. All the complexes presented here show very similar conformations, d espite variation in affinity in solution. The results suggest that the stac king of the -5 base on to the tyrosine side chain is the most important dri ving force for complex formation. A number of hydrogen bonds that are prese nt in the wild-type complex are not crucial for binding, as- they are missi ng 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.