The prokaryotic L11 ribosomal protein (rpL12 in eukaryotes) binds directly to the GAC, and it too makes contact with ribosomal cofactors. As such, the GAC RNA is among the most highly conserved rRNA sequences in 23S/28S rRNA. coli numbering) ribosomal RNA (rRNA) domain is essential for translation initiation, elongation and release, interacting with aminoacyl-tRNA/EF-Tu, EF-G, and release factor 2 (RF2) during these steps in protein synthesis. The 58-nucleotide GTPase center (GAC nt 1051–1108, E. We propose that L11 stabilizes a specific GAC RNA tertiary state, corresponding to the crystal structure, and that this structure reflects the functionally critical conformation of the rRNA domain in the fully assembled ribosome. While L11 protein cannot bind to the GAC until the RNA has adopted its tertiary structure, new experimental data show that L11 binds to Mg 2+-dependent folded states, which we suggest lie along the folding pathway of the RNA. In solution, we find that this tertiary structure is not static, but rather is best described as an ensemble of states. This new structure demonstrates that RNA alone folds into its tertiary structure with bound divalent ions. Here, we report a new crystal structure of the free GAC that is essentially identical to the L11-bound structure, which retains many common sites of divalent ion occupation. Previous cocrystal structures of the 58-nucleotide GAC RNA bound to L11 revealed the intricate tertiary fold of the RNA domain, with one monovalent and several divalent ions located in specific sites within the structure. The GTPase Center (GAC) RNA domain in bacterial 23S rRNA is directly bound by ribosomal protein L11, and this complex is essential to ribosome function.
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