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Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage
- Source :
- Nature Chemical Biology, Nature chemical biology
- Publication Year :
- 2016
-
Abstract
- The field of small self-cleaving nucleolytic ribozymes has been invigorated by the recent discovery of the twister, twister-sister, pistol and hatchet ribozymes. We report the crystal structure of a pistol ribozyme termed env25, which adopts a compact tertiary architecture stabilized by an embedded pseudoknot fold. The G-U cleavage site adopts a splayed-apart conformation with in-line alignment of the modeled 2'-O of G for attack on the adjacent to-be-cleaved P-O5' bond. Highly conserved residues G40 (N1 position) and A32 (N3 and 2'-OH positions) are aligned to act as a general base and a general acid, respectively, to accelerate cleavage chemistry, with their roles confirmed by cleavage assays on variants, and an increased pKa of 4.7 for A32. Our structure of the pistol ribozyme defined how the overall and local topologies dictate the in-line alignment at the G-U cleavage site, with cleavage assays on variants revealing key residues that participate in acid-base-catalyzed cleavage chemistry.
- Subjects :
- Models, Molecular
0301 basic medicine
RNA Folding
Magnetic Resonance Spectroscopy
Stereochemistry
010402 general chemistry
Cleavage (embryo)
01 natural sciences
Article
03 medical and health sciences
RNA, Catalytic
Molecular Biology
biology
Chemistry
Ribozyme
RNA
Cell Biology
Nuclear magnetic resonance spectroscopy
Molecular biology
0104 chemical sciences
030104 developmental biology
Mutation
Biocatalysis
biology.protein
Nucleic Acid Conformation
Mammalian CPEB3 ribozyme
Hairpin ribozyme
Pseudoknot
VS ribozyme
Subjects
Details
- Volume :
- 12
- Issue :
- 9
- Database :
- OpenAIRE
- Journal :
- Nature Chemical Biology
- Accession number :
- edsair.doi.dedup.....3f4ebec7c14dbb1c51a012eb4d3b3508
- Full Text :
- https://doi.org/10.1038/nchembio.2125