In-line alignment and Mg2+ coordination at the cleavage site of the env22 twister ribozyme

Aiming Ren, Marija Košutić, Kanagalaghatta R. Rajashankar, Marina Frener, Tobias Santner, Eric Westhof, Ronald Micura () and Dinshaw J. Patel ()
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Aiming Ren: Structural Biology Program, Memorial Sloan-Kettering Cancer Center
Marija Košutić: Institute of Organic Chemistry, Leopold-Franzens University and Center of Molecular Biosciences Innsbruck CMBI
Kanagalaghatta R. Rajashankar: Cornell University, NE-CAT, Advanced Photon Source, Argonne National laboratory
Marina Frener: Institute of Organic Chemistry, Leopold-Franzens University and Center of Molecular Biosciences Innsbruck CMBI
Tobias Santner: Institute of Organic Chemistry, Leopold-Franzens University and Center of Molecular Biosciences Innsbruck CMBI
Eric Westhof: Architecture et Réactivité de l’ARN, Institute of Molecular and Cellular Biology, University of Strasbourg, CNRS
Ronald Micura: Institute of Organic Chemistry, Leopold-Franzens University and Center of Molecular Biosciences Innsbruck CMBI
Dinshaw J. Patel: Structural Biology Program, Memorial Sloan-Kettering Cancer Center

Nature Communications, 2014, vol. 5, issue 1, 1-10

Abstract: Abstract Small self-cleaving nucleolytic ribozymes contain catalytic domains that accelerate site-specific cleavage/ligation of phosphodiester backbones. We report on the 2.9-Å crystal structure of the env22 twister ribozyme, which adopts a compact tertiary fold stabilized by co-helical stacking, double-pseudoknot formation and long-range pairing interactions. The U-A cleavage site adopts a splayed-apart conformation with the modelled 2′-O of U positioned for in-line attack on the adjacent to-be-cleaved P-O5′ bond. Both an invariant guanosine and a Mg2+ are directly coordinated to the non-bridging phosphate oxygens at the U-A cleavage step, with the former positioned to contribute to catalysis and the latter to structural integrity. The impact of key mutations on cleavage activity identified an invariant guanosine that contributes to catalysis. Our structure of the in-line aligned env22 twister ribozyme is compared with two recently reported twister ribozymes structures, which adopt similar global folds, but differ in conformational features around the cleavage site.

Date: 2014
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DOI: 10.1038/ncomms6534

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