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Nucleic Acids Research 2005 33(8):2464-2474; doi:10.1093/nar/gki540
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Published online 2 May 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Studies on Escherichia coli RNase P RNA with Zn2+ as the catalytic cofactor

Simona Cuzic and Roland K. Hartmann*

Philipps-Universität Marburg, Institut für Pharmazeutische Chemie Marbacher Weg 6, D-35037 Marburg, Germany

*To whom correspondence should be addressed. Tel: +49 6421 28 25827; Fax: +49 6421 28 25854; Email: roland.hartmann{at}staff.uni-marburg.de

Received February 18, 2005. Revised April 11, 2005. Accepted April 11, 2005.

We demonstrate, for the first time, catalysis by Escherichia coli ribonuclease P (RNase P) RNA with Zn2+ as the sole divalent metal ion cofactor in the presence of ammonium, but not sodium or potassium salts. Hill analysis suggests a role for two or more Zn2+ ions in catalysis. Whereas Zn2+ destabilizes substrate ground state binding to an extent that precludes reliable Kd determination, and Sr2+ in particular, both unable to support catalysis by themselves, promote high-substrate affinity. Zn2+ and substantially reduce the fraction of precursor tRNA molecules capable of binding to RNase P RNA. Stimulating and inhibitory effects of Sr2+ on the ribozyme reaction with Zn2+ as cofactor could be rationalized by a model involving two Sr2+ ions (or two classes of Sr2+ ions). Both ions improve substrate affinity in a cooperative manner, but one of the two inhibits substrate conversion in a non-competitive mode with respect to the substrate and the Zn2+. A single 2'-fluoro modification at nt –1 of the substrate substantially weakened the inhibitory effect of Sr2+. Our results demonstrate that the studies on RNase P RNA with metal cofactors other than Mg2+ entail complex effects on structural equilibria of ribozyme and substrate RNAs as well as E·S formation apart from the catalytic performance.


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