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J. Biol. Chem., Vol. 280, Issue 24, 23157-23164, June 17, 2005

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Cooperative Mechanism of RNA Packaging Motor^*

Jií Lísal and Roman Tuma

From the Department of Biological and Environmental Sciences and Institute of Biotechnology, University of Helsinki, Helsinki FIN-00014, Finland

P4 is a hexameric ATPase that serves as the RNA packaging motor in double-stranded RNA bacteriophages from the Cystoviridae family. P4 shares sequence and structural similarities with hexameric helicases. A structure-based mechanism for mechano-chemical coupling has recently been proposed for P4 from bacteriophage 12. However, coordination of ATP hydrolysis among the subunits and coupling with RNA translocation remains elusive. Here we present detailed kinetic study of nucleotide binding, hydrolysis, and product release by 12 P4 in the presence of different RNA and DNA substrates. Whereas binding affinities for ATP and ADP are not affected by RNA binding, the hydrolysis step is accelerated and the apparent cooperativity is increased. No nucleotide binding cooperativity is observed. We propose a stochastic-sequential cooperativity model to describe the coordination of ATP hydrolysis within the hexamer. In this model the apparent cooperativity is a result of hydrolysis stimulation by ATP and RNA binding to neighboring subunits rather than cooperative nucleotide binding. The translocation step appears coupled to hydrolysis, which is coordinated among three neighboring subunits. Simultaneous interaction of neighboring subunits with RNA makes the otherwise random hydrolysis sequential and processive.

Received for publication, March 10, 2005 , and in revised form, April 12, 2005.

^* This work was supported in part by the Academy of Finland (Finnish Centre of Excellence Program 2000–2005) and Academy of Finland Grant 206926 (to R. T.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Supported by the Viikki Graduate School in Biosciences.

To whom correspondence should be addressed: Viikki Biocenter, P. O. Box 65, Viikinkaari 1, FIN-00014, University of Helsinki, Helsinki 00014, Finland. Tel.: 358-9-191-59577; Fax: 358-9-191-59930; E-mail: roman.tuma{at}helsinki.fi.

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