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6T3R

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

Summary for 6T3R
Entry DOI10.2210/pdb6t3r/pdb
Related6T3K 6T3N
DescriptorGroup IIC Intron Ribozyme, MAGNESIUM ION, POTASSIUM ION, ... (7 entities in total)
Functional Keywordsribozyme, self-splicing, retrotransposition, spliceosome, rna
Biological sourceOceanobacillus iheyensis HTE831
More
Total number of polymer chains2
Total formula weight132248.73
Authors
Marcia, M.,Pyle, A.M. (deposition date: 2019-10-11, release date: 2020-05-13, Last modification date: 2024-01-24)
Primary citationManigrasso, 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
Cited by
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
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (3.57 Å)
Structure validation

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