title: Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex.
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 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.
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Sweden.
authors.forename: E
authors.initials: E
authors.lastname: Grahn
authors.forename: T
authors.initials: T
authors.lastname: Moss
authors.forename: C
authors.initials: C
authors.lastname: Helgstrand
authors.forename: K
authors.initials: K
authors.lastname: Fridborg
authors.forename: M
authors.initials: M
authors.lastname: Sundaram
authors.forename: K
authors.initials: K
authors.lastname: Tars
authors.forename: H
authors.initials: H
authors.lastname: Lago
authors.forename: N J
authors.initials: NJ
authors.lastname: Stonehouse
authors.forename: D R
authors.initials: DR
authors.lastname: Davis
authors.forename: P G
authors.initials: PG
authors.lastname: Stockley
authors.forename: L
authors.initials: L
authors.lastname: Liljas
mesh_terms: D000225:Adenine / Q000737:chemistry; D001976:Bromouracil / Q000737:chemistry; D002213:Capsid / Q000737:chemistry*; D036022:Capsid Proteins; D006147:Guanine / Q000737:chemistry; D017909:Levivirus / Q000235:genetics*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D011743:Pyrimidines / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry*; D013889:Thiouracil / Q000737:chemistry
chemical_list: D036022:Capsid Proteins; D011743:Pyrimidines; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D001976:Bromouracil; D013889:Thiouracil; D006147:Guanine; D000225:Adenine; C030986:pyrimidine