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A Conserved Phenylalanine of Motif IV in Superfamily 2 Helicases Is Required for Cooperative, ATP-Dependent Binding of RNA Substrates in DEAD-Box Proteins ^,

Josette Banroques,^1,2 Olivier Cordin,^1,2, Monique Doère,¹ Patrick Linder,^1* and N. Kyle Tanner^1*

Départemente de Microbiologie et Médecine Moléculaire, Centre Médical Universitaire, Geneva, Switzerland,¹ Centre de Génétique Moléculaire, CNRS, Gif-sur-Yvette, France²

Received 24 August 2007/ Returned for modification 23 October 2007/ Accepted 26 February 2008

We have identified a highly conserved phenylalanine in motif IV of the DEAD-box helicases that is important for their enzymatic activities. In vivo analyses of essential proteins in yeast showed that mutants of this residue had severe growth phenotypes. Most of the mutants also were temperature sensitive, which suggested that the mutations altered the conformational stability. Intragenic suppressors of the F405L mutation in yeast Ded1 mapped close to regions of the protein involved in ATP or RNA binding in DEAD-box crystal structures, which implicated a defect at this level. In vitro experiments showed that these mutations affected ATP binding and hydrolysis as well as strand displacement activity. However, the most pronounced effect was the loss of the ATP-dependent cooperative binding of the RNA substrates. Sequence analyses and an examination of the Protein Data Bank showed that the motif IV phenylalanine is conserved among superfamily 2 helicases. The phenylalanine appears to be an anchor that maintains the rigidity of the RecA-like domain. For DEAD-box proteins, the phenylalanine also aligns a highly conserved arginine of motif VI through van der Waals and cation- interactions, thereby helping to maintain the network of interactions that exist between the different motifs involved in ATP and RNA binding.

Published ahead of print on 10 March 2008.

Supplemental material for this article may be found at http://mcb.asm.org/.

Present address: Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom.