6T3S

Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon

Summary for 6T3S

• Entry DOI: 10.2210/pdb6t3s/pdb
• Related: 6T3K 6T3N 6T3R
• Descriptor: Group IIC Intron Ribozyme, MAGNESIUM ION, SODIUM ION, ... (5 entities in total)
• Functional Keywords: ribozyme, self-splicing, retrotransposition, spliceosome, rna
• Biological source: Oceanobacillus iheyensis
• Total number of polymer chains: 1
• Total formula weight: 130610.42

Authors

Marcia, M.,Pyle, A.M. (deposition date: 2019-10-11, release date: 2020-05-13, Last modification date: 2024-01-24)

Primary citation

Manigrasso, J.,Chillon, I.,Genna, V.,Vidossich, P.,Somarowthu, S.,Pyle, A.M.,De Vivo, M.,Marcia, M.
Visualizing group II intron dynamics between the first and second steps of splicing.
Nat Commun, 11:2837-2837, 2020

PubMed Abstract: Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5'-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy.

PubMed: 32503992
DOI: 10.1038/s41467-020-16741-4

Experimental method

X-RAY DIFFRACTION (3.28 Å)