Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase

doi:10.1073/pnas.0705488105

Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase

^†Department of Biophysical Chemistry, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland; and
^‡Department of Experimental Physics IV, University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany

Edited by Vincent Croquette, École Normale Supérieure, Paris, France, and accepted by the Editorial Board November 19, 2007 (received for review June 12, 2007)

Abstract

RNA helicases couple the energy from ATP hydrolysis with structural changes of their RNA substrates. DEAD box helicases form the largest class of RNA helicases and share a helicase core comprising two RecA-like domains. An opening and closing of the interdomain cleft during RNA unwinding has been postulated but not shown experimentally. Single-molecule FRET experiments with the Bacillus subtilis DEAD box helicase YxiN carrying donor and acceptor fluorophores on different sides of the interdomain cleft reveal an open helicase conformation in the absence of nucleotides, or in the presence of ATP, or ADP, or RNA. In the presence of ADP and RNA, the open conformation is retained. By contrast, cooperative binding of ATP and RNA leads to a compact helicase structure, proving that the ATP- and ADP-bound states of RNA helicases display substantially different structures only when the RNA substrate is bound. These results establish a closure of the interdomain cleft in the helicase core at the beginning of the unwinding reaction, and suggest a conserved mechanism of energy conversion among DEAD box helicases across kingdoms.

Footnotes

^¶To whom correspondence should be addressed. E-mail: dagmar.klostermeier{at}unibas.ch
Author contributions: B.T., A.R.K., and D.K. designed research; B.T. and A.R.K. performed research; B.T., A.R.K., J.K., A.G., and D.K. contributed new reagents/analytic tools; B.T., A.R.K., A.G., and D.K. analyzed data; and B.T. and D.K. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission. V.C. is a guest editor invited by the Editorial Board.
This article contains supporting information online at www.pnas.org/cgi/content/full/0705488105/DC1.