Structure of the most conserved internal loop in SRP RNA

The signal recognition particle (SRP) directs translating ribosomes to the protein translocation apparatus of endoplasmic reticulum (ER) membrane or t he bacterial plasma membrane. The SRP is universally conserved, and in prok aryotes consists of two essential subunits, SRP RNA and SRP54, the latter o f which binds to signal sequences on the nascent protein chains. Here we de scribe the solution NMR structure of a 28-mer RNA composing the most conser ved part of SRP RNA to which SRP54 binds. Central to this function is a six -nucleotide internal loop that assumes a novel Mg2+-dependent structure wit h unusual cross-strand interactions; besides a cross-strand A/A stack, two guanines form hydrogen bonds with opposite-strand phosphates, The structure completely explains the phylogenetic conservation of the loop bases, under lining its importance for SRP54 binding and SRP function.