2L5Z

NMR structure of the A730 loop of the Neurospora VS ribozyme

Summary for 2L5Z

• Entry DOI: 10.2210/pdb2l5z/pdb
• NMR Information: BMRB: 17292
• Descriptor: RNA (26-MER) (1 entity in total)
• Functional Keywords: rna, internal loop, vs ribozyme
• Biological source: Neurospora
• Total number of polymer chains: 1
• Total formula weight: 8421.11

Authors

Desjardins, G.,Bonneau, E.,Girard, N.,Boisbouvier, J.,Legault, P. (deposition date: 2010-11-10, release date: 2011-02-16, Last modification date: 2024-05-15)

Primary citation

Desjardins, G.,Bonneau, E.,Girard, N.,Boisbouvier, J.,Legault, P.
NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site.
Nucleic Acids Res., 39:4427-4437, 2011

PubMed Abstract: The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme. Here, we determined the high-resolution NMR structure of a stem-loop VI fragment containing the A730 internal loop, which forms part of the active site. In the presence of magnesium ions, the A730 loop adopts a structure that is consistent with existing biochemical data and most likely reflects its conformation in the VS ribozyme prior to docking with the cleavage site internal loop. Interestingly, the A730 loop adopts an S-turn motif that is also present in loop B within the hairpin ribozyme active site. The S-turn appears necessary to expose the Watson-Crick edge of a catalytically important residue (A756) so that it can fulfill its role in catalysis. The A730 loop and the cleavage site loop of the VS ribozyme display structural similarities to internal loops found in the active site of the hairpin ribozyme. These similarities provided a rationale to build a model of the VS ribozyme active site based on the crystal structure of the hairpin ribozyme.

PubMed: 21266483
DOI: 10.1093/nar/gkq1244

Experimental method

SOLUTION NMR