2N3R

NMR structure of the II-III-VI three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement

Summary for 2N3R

• Entry DOI: 10.2210/pdb2n3r/pdb
• NMR Information: BMRB: 25655
• Descriptor: RNA (62-MER), MAGNESIUM ION (3 entities in total)
• Functional Keywords: rna, vs ribozyme, catalysis, mg2+ ions
• Biological source: Neurospora crassa
• Total number of polymer chains: 1
• Total formula weight: 20216.42

Authors

Bonneau, E.,Girard, N.,Lemieux, S.,Legault, P. (deposition date: 2015-06-09, release date: 2015-07-15, Last modification date: 2024-05-01)

Primary citation

Bonneau, E.,Girard, N.,Lemieux, S.,Legault, P.
The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure.
Rna, 21:1621-1632, 2015

PubMed Abstract: As part of an effort to structurally characterize the complete Neurospora VS ribozyme, NMR solution structures of several subdomains have been previously determined, including the internal loops of domains I and VI, the I/V kissing-loop interaction and the III-IV-V junction. Here, we expand this work by determining the NMR structure of a 62-nucleotide RNA (J236) that encompasses the VS ribozyme II-III-VI three-way junction and its adjoining stems. In addition, we localize Mg(2+)-binding sites within this structure using Mn(2+)-induced paramagnetic relaxation enhancement. The NMR structure of the J236 RNA displays a family C topology with a compact core stabilized by continuous stacking of stems II and III, a cis WC/WC G•A base pair, two base triples and two Mg(2+) ions. Moreover, it reveals a remote tertiary interaction between the adenine bulges of stems II and VI. Additional NMR studies demonstrate that both this bulge-bulge interaction and Mg(2+) ions are critical for the stable folding of the II-III-VI junction. The NMR structure of the J236 RNA is consistent with biochemical studies on the complete VS ribozyme, but not with biophysical studies performed with a minimal II-III-VI junction that does not contain the II-VI bulge-bulge interaction. Together with previous NMR studies, our findings provide important new insights into the three-dimensional architecture of this unique ribozyme.

PubMed: 26124200
DOI: 10.1261/rna.052076.115

Experimental method

SOLUTION NMR