Structural insights into SRP RNA: An induced fit mechanism for SRP assembly

Abstract

Proper assembly of large protein-RNA complexes requires sequential binding of the proteins to the RNA. The signal recognition particle (SRP) is a multiprotein-RNA complex responsible for the cotranslational targeting of proteins to biological membranes. Here we describe the crystal structure at 2.6-Å resolution of the S-domain of SRP RNA from the archeon Methanococcus jannaschii. Comparison of this structure with the SRP19-bound form reveals the nature of the SRP19-induced conformational changes, which promote subsequent SRP54 attachment. These structural changes are initiated at the SRP19 binding site and transmitted through helix 6 to looped-out adenosines, which form tertiary RNA interaction with helix 8. Displacement of these adenosines enforces a conformational change of the asymmetric loop structure in helix 8. In free RNA, the three unpaired bases A195, C196, and C197 are directed toward the helical axis, whereas upon SRP19 binding the loop backbone inverts and the bases are splayed out in a conformation that resembles the SRP54-bound form. Nucleotides adjacent to the bulged nucleotides seem to be particularly important in the regulation of this loop transition. Binding of SRP19 to 7S RNA reveals an elegant mechanism of how protein-induced changes are directed through an RNA molecule and may relate to those regulating the assembly of other RNPs.

Interaction of signal-recognition particle 54 GTPase domain and signal-recognition particle RNA in the free signal-recognition particle

“…2B. Elevated temperature factors of the nucleotides in helices 6 and 8 and helix 5 in the SRP19-RNA complex indicate intrinsic flexibility likely to be required for SRP54 recognition (30). As expected, in the ternary complex, these nucleotides are highly ordered with low-temperature factures and well defined electron densities [supporting information (SI) Fig.…”

“…The asymmetric loop and helix 6 are in direct contact via A-minor-type interactions formed between the G-C and reversed A-U base pairs flanking the 195-ACC bulge and the looped-out adenosines, A176 and A177. These tertiary contacts play an important role in communicating conformational changes from the SRP19 binding site to the asymmetric loop (27,30). Similarly, they convey the M domaininduced conformational changes from the asymmetric loop to helix 6.…”

“…It has been shown previously that the asymmetric loop in helix 8 is flexible and undergoes critical structural changes on binding of the SRP54 M domain (20,28,29). In free M. jannaschii 7S.S RNA, the three unpaired bases 195-ACC in the asymmetric loop are pointing toward the interior of the RNA helix (30). Binding Values in parentheses are for the highest-resolution shell.…”

“…Notably, in the M. jannaschii complex, the M domain and SRP19 are in direct contact by hydrogen-bonding and stacking interactions. These are located between Arg-401 in the M domain and residues His-57-Trp-58 situated in the helix-8 binding loop L3 of SRP19 and explain the detrimental effect of a His57Ala/Trp58Ala double mutant on SRP54 assembly (30).…”

Kinship in the SRP RNA family

“…37,38 In contrast to the detailed structural information of complexes containing SRP9/14, SRP19 and SRP54, high-resolution data about SRP68/72 are unavailable. [39][40][41][42][43] Assembly of SRP9/14 with the small (or Alu) SRP RNA domain is dependent on the presence of the UGU(NR) motif and might engage the loops of helices 3 and 4 in an RNA tertiary interaction (Fig. 1B).…”