The 2 angstrom structure of helix 6 of the human signal recognition particle RNA

Background: The mammalian signal recognition particle (SRP) is an essential cytoplasmic ribonucleoprotein complex involved in targeting signal-peptide -containing proteins to the endoplasmic reticulum. Assembly csf the SRP req uires protein SRP19 to bind first to helix 6 of the SRP RNA before the sign al-peptide-recognizing protein, SRP54, can bind to helix 8 of the RNA. Heli x 6 is closed by a GGAG tetraloop, which has been shown to form part of the SRP19-binding site. Results: The high-resolution (2.0 Angstrom) structure of a fragment of huma n SRP RNA comprising 29 nucleotides of helix 6 has been determined using th e multiple anomalous dispersion (MAD) method and bromine-labelled RNA. In t he crystal the molecule forms 28-mer duplexes rather than the native monome ric hairpin structure, although two chemically equivalent 11 base pair stre tches of the duplex represent the presumed native structure. The duplex has highly distorted A-RNA geometry caused by the occurrence of several non-Wa tson-Crick base pairs. These include a 5'-GGAG-3'/3'-GAGG-5' purine bulge ( which replaces the tetraloop) and a 5'-AC-3'/3'-CA-5' tandem mismatch that, depending on the protonation state of the adenine bases, adopts a differen t conformation in the two native-like parts of the structure. The structure also shows the 2'3'-cyclic phosphate reaction product of the hammerhead ri bozyme cleavage reaction. Conclusions: The 29-mer RNA is the first RNA structure of the human SRP and provides some insight into the binding mode of SRP19. The observed strong irregularities of the RNA helix make the major groove wide enough and flat enough to possibly accommodate an alpha helix of SRP19. The variety of non- canonical base pairs observed enlarges the limited repertoire of irregular RNA folds known to date and the observed conformation of the 2'3'-cyclic ph osphate containing Ade29 is consistent with the current understanding of th e hammerhead ribozyme reaction mechanism.