Pseudoknot Formation Seeds the Twister Ribozyme Cleavage Reaction Coordinate
نویسندگان
چکیده
منابع مشابه
Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme.
Twister is a recently discovered RNA motif that is estimated to have one of the fastest known catalytic rates of any naturally occurring small self-cleaving ribozyme. We determined the 4.1-Å resolution crystal structure of a twister sequence from an organism that has not been cultured in isolation, and it shows an ordered scissile phosphate and nucleotide 5' to the cleavage site. A second cryst...
متن کاملActive participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme.
We report results from combined quantum mechanical/molecular mechanical (QM/MM) free energy simulations to explore metal-assisted phosphoryl transfer and general acid catalysis in the extended hammerhead ribozyme. The mechanisms considered here assume that the 2′OH group of C17 has already been activated (i.e., is deprotonated) and acts as a nucleophile to go on an inline attack to the adjacent...
متن کاملPistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage
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...
متن کاملCore requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure
The glmS ribozyme is a self-cleaving RNA catalyst that resides in the 5'-untranslated region of glmS mRNA in certain bacteria. The ribozyme is specifically activated by glucosamine-6-phosphate (GlcN6P), the metabolic product of the GlmS protein, and is thus proposed to provide a feedback mechanism of riboswitch regulation. Both phylogenetic and biochemical analyses of the glmS ribozyme have est...
متن کاملMetals induce transient folding and activation of the Twister ribozyme
Twister is a small ribozyme present in almost all kingdoms of life that rapidly self-cleaves in variety of divalent metal ions. We used activity assays, bulk FRET and single-molecule FRET (smFRET) to understand how different metal ions promote folding and self-cleavage of the Oryza sativa twister ribozyme. Although most ribozymes require additional Mg2+ for catalysis, twister inverts this expec...
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ژورنال
عنوان ژورنال: Journal of the American Chemical Society
سال: 2017
ISSN: 0002-7863,1520-5126
DOI: 10.1021/jacs.7b01549