1I3Y

SOLUTION STRUCTURE OF THE A LOOP OF 23S RIBOSOMAL RNA.

Summary for 1I3Y

• Entry DOI: 10.2210/pdb1i3y/pdb
• Related: 1I3X
• Descriptor: 5'-R(*GP*GP*CP*UP*GP*GP*CP*(OMU)P*GP*UP*UP*CP*GP*CP*CP*AP*GP*CP*C)-3' (1 entity in total)
• Functional Keywords: a loop, a site, 23s rrna, rna
• Total number of polymer chains: 1
• Total formula weight: 6075.65

Authors

Puglisi, J.D.,Blanchard, S.C. (deposition date: 2001-02-17, release date: 2001-04-04, Last modification date: 2024-05-22)

Primary citation

Blanchard, S.C.,Puglisi, J.D.
Solution structure of the A loop of 23S ribosomal RNA.
Proc.Natl.Acad.Sci.USA, 98:3720-3725, 2001

PubMed Abstract: 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.

PubMed: 11259644
DOI: 10.1073/pnas.051608498

Experimental method

SOLUTION NMR