2MI0

NMR structure of the I-V kissing-loop interaction of the Neurospora VS ribozyme

Summary for 2MI0

• Entry DOI: 10.2210/pdb2mi0/pdb
• NMR Information: BMRB: 19662
• Descriptor: 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3' (2 entities in total)
• Functional Keywords: neurospora vs ribozyme, kissing-loop interaction, substrate recognition, u-turn, nmr structural studies, rna
• Biological source: Neurospora; More
• Total number of polymer chains: 2
• Total formula weight: 13770.26

Authors

Bouchard, P.,Legault, P. (deposition date: 2013-12-05, release date: 2014-01-15, Last modification date: 2024-05-01)

Primary citation

Bouchard, P.,Legault, P.
Structural insights into substrate recognition by the neurospora varkud satellite ribozyme: importance of u-turns at the kissing-loop junction.
Biochemistry, 53:258-269, 2014

PubMed Abstract: Substrate recognition by the Neurospora Varkud satellite ribozyme depends on the formation of a magnesium-dependent kissing-loop interaction between the stem-loop I (SLI) substrate and stem-loop V (SLV) of the catalytic domain. From mutagenesis studies, it has been established that this I/V kissing-loop interaction involves three Watson-Crick base pairs and is associated with a structural rearrangement of the SLI substrate that facilitates catalysis. Here, we report the NMR structural characterization of this I/V kissing-loop using isolated stem-loops. NMR studies were performed on different SLI/SLV complexes containing a common SLV and shiftable, preshifted, or double-stranded SLI variants. These studies confirm the presence of three Watson-Crick base pairs at the kissing-loop junction and provide evidence for the structural rearrangement of shiftable SLI variants upon SLV binding. NMR structure determination of an SLI/SLV complex demonstrates that both the SLI and SLV loops adopt U-turn structures, which facilitates intermolecular Watson-Crick base pairing. Several other interactions at the I/V interface, including base triples and base stacking, help create a continuously stacked structure. These NMR studies provide a structural basis to understand the stability of the I/V kissing-loop interaction and lead us to propose a kinetic model for substrate activation in the VS ribozyme.

PubMed: 24325625
DOI: 10.1021/bi401491g

Experimental method

SOLUTION NMR