DSSR-PyMOL cartoon-block schematics: PDB entry 2rpk

PDB-id

2rpk; DSSR-derived features in text and JSON formats

Class

RNA

Method

NMR

Summary

Solution structure of domain ii of the positive polarity cchmvd hammerhead ribozyme

Reference

Dufour D, de la Pena M, Gago S, Flores R, Gallego J (2009): "Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads." Nucleic Acids Res., 37, 368-381. doi: 10.1093/nar/gkn918.

Abstract

Loop-loop tertiary interactions play a key role in the folding and catalytic activity of natural hammerhead ribozymes. Using a combination of NMR spectroscopy, site-directed mutagenesis and kinetic and infectivity analyses, we have examined the structure and function of loops 1 and 2 of the (+) and (-) hammerheads of chrysanthemum chlorotic mottle viroid RNA. In both hammerheads, loop 1 is a heptanucleotide hairpin loop containing an exposed U at its 5' side and an extrahelical U at its 3'-side critical for the catalytic activity of the ribozyme in vitro and for viroid infectivity in vivo, whereas loop 2 has a key opened A at its 3'-side. These structural features promote a specific loop-loop interaction motif across the major groove. The essential features of this tertiary structure element, base pairing between the 5' U of loop 1 and the 3' A of loop 2, and interaction of the extrahelical pyrimidine of loop 1 with loop 2, are likely shared by a significant fraction of natural hammerheads.