Chemistry

Cleavage (geology)

Gene

Nucleotide

Biology

Pseudoknot

Fracture (geology)

VS ribozyme

Stereochemistry

Paleontology

Ribozyme

Biochemistry

Deoxyribozyme

Nature Chemical Biology

Structural and biochemical analysis of the recently discovered env25 pistol ribozyme reveal an active site containing a pseudoknot that enforces in-line nucleophilic attack at the scissile phosphate and positions nucleotides for general acid and general base catalysis.                                                                 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 cl...

Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage