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 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.
Grahn
E
E
Department of Cell and Molecular Biology, Uppsala University, Sweden.
Moss
T
T
Helgstrand
C
C
Fridborg
K
K
Sundaram
M
M
Tars
K
K
Lago
H
H
Stonehouse
N J
NJ
Davis
D R
DR
Stockley
P G
PG
Liljas
L
L
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
D036022:Capsid Proteins; D011743:Pyrimidines; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D001976:Bromouracil; D013889:Thiouracil; D006147:Guanine; D000225:Adenine; C030986:pyrimidine