2MTK

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

Summary for 2MTK

• Entry DOI: 10.2210/pdb2mtk/pdb
• Related: 2MTJ
• NMR Information: BMRB: 25164
• Descriptor: RNA (47-MER), MAGNESIUM ION (3 entities in total)
• Functional Keywords: vs ribozyme, three-way junction, base triple, u-turn, ribose zipper, gaaa tetraloop, cuug tetraloop, rna
• Biological source: Neurospora crassa
• Total number of polymer chains: 1
• Total formula weight: 15263.79

Authors

Bonneau, E.,Legault, P. (deposition date: 2014-08-19, release date: 2014-10-22, Last modification date: 2024-05-01)

Primary citation

Bonneau, E.,Legault, P.
Nuclear Magnetic Resonance Structure of the III-IV-V Three-Way Junction from the Varkud Satellite Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement.
Biochemistry, 53:6264-6275, 2014

PubMed Abstract: The VS ribozyme is a catalytic RNA found within some natural isolates of Neurospora that is being used as a model system to improve our understanding of RNA structure, catalysis, and engineering. The catalytic domain contains five helical domains (SLII-SLVI) that are organized by two three-way junctions. The III-IV-V junction is required for high-affinity binding of the substrate domain (SLI) through formation of a kissing loop interaction with SLV. Here, we determine the high-resolution nuclear magnetic resonance (NMR) structure of a 47-nucleotide RNA containing the III-IV-V junction (J345). The J345 RNA adopts a Y-shaped fold typical of the family C three-way junctions, with coaxial stacking between stems III and IV and an acute angle between stems III and V. The NMR structure reveals that the core of the III-IV-V junction contains four stacked base triples, a U-turn motif, a cross-strand stacking interaction, an A-minor interaction, and a ribose zipper. In addition, the NMR structure shows that the cCUUGg tetraloop used to stabilize stem IV adopts a novel RNA tetraloop fold, different from the known gCUUGc tetraloop structure. Using Mn(2+)-induced paramagnetic relaxation enhancement, we identify six Mg(2+)-binding sites within J345, including one associated with the cCUUGg tetraloop and two with the junction core. The NMR structure of J345 likely represents the conformation of the III-IV-V junction in the context of the active VS ribozyme and suggests that this junction functions as a dynamic hinge that contributes to substrate recognition and catalysis. Moreover, this study highlights a new role for family C three-way junctions in long-range tertiary interactions.

PubMed: 25238589
DOI: 10.1021/bi500826n

Experimental method

SOLUTION NMR