RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex

Eukaryotic Sm and Sm-like proteins associate with RNA to form the core doma in of ribonucleoprotein particles involved in pre-mRNA splicing and other p rocesses. Recently, putative Sm proteins of unknown function have been iden tified in Archaea. We show by immunoprecipitation experiments that the two Sm proteins present in Archaeoglobus fulgidus (AF-Sm1 acid AF-Sm2) associat e with RNase P RNA in vivo, suggesting a role in tRNA processing. The AF-Sm 1 protein also interacts specifically with oligouridylate in vitro, We have solved the crystal structures of this protein and a complex with RNA. AF-S m1 forms a seven-membered ring, with the RNA interacting inside the central cavity on one face of the doughnut-shaped complex. The bases are bound via stacking and specific hydrogen bonding contacts in pockets lined by residu es highly conserved in archaeal and eukaryotic Sm proteins, while the phosp hates remain solvent accessible. A comparison with the structures of human Sm protein dimers reveals closely related monomer folds and intersubunit co ntacts, indicating that the architecture of the Sm core domain and RNA bind ing have been conserved during evolution.