DSSR-PyMOL cartoon-block schematics: PDB entry 4qjd

PDB-id

4qjd; SNAP-derived features in text and JSON formats

Class

RNA

Method

X-ray (3.1 Å)

Summary

Crystal structure of twister with the nucleotide 5'- to the cleavage site disordered at 3.1 Å resolution

Reference

Eiler D, Wang J, Steitz TA (2014): "Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme." Proc.Natl.Acad.Sci.USA, 111, 13028-13033. doi: 10.1073/pnas.1414571111.

Abstract

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 crystal structure of twister from Orzyza sativa determined at 3.1-Å resolution exhibits a disordered scissile phosphate and nucleotide 5' to the cleavage site. The core of twister is stabilized by base pairing, a large network of stacking interactions, and two pseudoknots. We observe three nucleotides that appear to mediate catalysis: a guanosine that we propose deprotonates the 2'-hydroxyl of the nucleotide 5' to the cleavage site and a conserved adenosine. We suggest the adenosine neutralizes the negative charge on a nonbridging phosphate oxygen atom at the cleavage site. The active site also positions the labile linkage for in-line nucleophilic attack, and thus twister appears to simultaneously use three strategies proposed for small self-cleaving ribozymes. The twister crystal structures (i) show its global structure, (ii) demonstrate the significance of the double pseudoknot fold, (iii) provide a possible hypothesis for enhanced catalysis, and (iv) illuminate the roles of all 10 highly conserved nucleotides of twister that participate in the formation of its small and stable catalytic pocket.