2RO2

Solution structure of domain I of the negative polarity CChMVd hammerhead ribozyme

Summary for 2RO2

• Entry DOI: 10.2210/pdb2ro2/pdb
• Descriptor: RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3') (1 entity in total)
• Functional Keywords: hammerhead ribozyme, viroid, cchmvd, heptaloop, rna
• Total number of polymer chains: 1
• Total formula weight: 7435.46

Authors

Gallego, J.,Dufour, D.,Gago, S.,de la Pena, M.,Flores, R. (deposition date: 2008-03-05, release date: 2008-12-30, Last modification date: 2024-05-29)

Primary citation

Dufour, D.,de la Pena, M.,Gago, S.,Flores, R.,Gallego, J.
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, 2009

PubMed 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.

PubMed: 19043070
DOI: 10.1093/nar/gkn918

Experimental method

SOLUTION NMR