1i3y
From Proteopedia
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SOLUTION STRUCTURE OF THE A LOOP OF 23S RIBOSOMAL RNA.
Overview
The A loop is an essential RNA component of the ribosome, peptidyltransferase center that directly interacts with aminoacyl (A)-site, tRNA. The A loop is highly conserved and contains a ubiquitous 2'-O-methyl, ribose modification at position U2552. Here, we present the solution, structure of a modified and unmodified A-loop RNA to define both the, A-loop fold and the structural impact of the U2552 modification. Solution, data reveal that the A-loop RNA has a compact structure that includes a, noncanonical base pair between C2556 and U2552. NMR evidence is presented, that the N3 position of C2556 has a shifted pKa and that protonation at, C2556-N3 changes the C-U pair geometry. Our data indicate that U2552, methylation modifies the A-loop fold, in particular the dynamics and, position of residues C2556 and U2555. We compare our structural data with, the structure of the A loop observed in a recent 50S crystal structure, [Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. (2000), Science 289, 905--920; Nissen, P., Hansen, J., Ban, N., Moore, P. B. &, Steitz, T. A. (2000) Science 289, 920--930]. The solution and crystal, structures of the A loop are dramatically different, suggesting that a, structural rearrangement of the A loop must occur on docking into the, peptidyltransferase center. Possible roles of this docking event, the, shifted pKa of C2556 and the U2552 2'-O-methylation in the mechanism of, translation, are discussed.
About this Structure
1I3Y is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of the A loop of 23S ribosomal RNA., Blanchard SC, Puglisi JD, Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):3720-5. Epub 2001 Mar 20. PMID:11259644
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