5Y87

Structure-based Insights into Self-Cleavage by a Four-way Junctional Twister-Sister Ribozyme

Summary for 5Y87

• Entry DOI: 10.2210/pdb5y87/pdb
• Descriptor: RNA (5'-R(P*AP*CP*CP*CP*GP*CP*AP*AP*GP*GP*CP*CP*GP*AP*CP*GP*GP*C)-3'), DNA/RNA (50-MER), MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: twister-sister, riboyzme, catalysis, self-cleaving, rna, mn2+ soaking
• Biological source: metagenome; More
• Total number of polymer chains: 4
• Total formula weight: 44952.87

Authors

Zheng, L.,Micura, R.L.,Ren, A. (deposition date: 2017-08-19, release date: 2017-11-22, Last modification date: 2024-03-27)

Primary citation

Zheng, L.,Mairhofer, E.,Teplova, M.,Zhang, Y.,Ma, J.,Patel, D.J.,Micura, R.,Ren, A.
Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme
Nat Commun, 8:1180-1180, 2017

PubMed Abstract: Here we report on the crystal structure and cleavage assays of a four-way junctional twister-sister self-cleaving ribozyme. Notably, 11 conserved spatially separated loop nucleotides are brought into close proximity at the ribozyme core through long-range interactions mediated by hydrated Mg cations. The C62-A63 step at the cleavage site adopts a splayed-apart orientation, with flexible C62 directed outwards, whereas A63 is directed inwards and anchored by stacking and hydrogen-bonding interactions. Structure-guided studies of key base, sugar, and phosphate mutations in the twister-sister ribozyme, suggest contributions to the cleavage chemistry from interactions between a guanine at the active site and the non-bridging oxygen of the scissile phosphate, a feature found previously also for the related twister ribozyme. Our four-way junctional pre-catalytic structure differs significantly in the alignment at the cleavage step (splayed-apart vs. base-stacked) and surrounding residues and hydrated Mg ions relative to a reported three-way junctional pre-catalytic structure of the twister-sister ribozyme.

PubMed: 29081514
DOI: 10.1038/s41467-017-01276-y

Experimental method

X-RAY DIFFRACTION (2.132 Å)