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Mol. Cell. Biol. doi:10.1128/MCB.01555-07
Copyright (c) 2008, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

A conserved phenylalanine of motif IV in superfamily 2 helicases is required for cooperative, ATP-dependent, binding of RNA substrates in DEAD-box proteins

Département de Microbiologie et Médecine Moléculaire, Centre Médical Universitaire, Geneva, Switzerland; and Centre de Génétique Moléculaire, CNRS, Gif-sur-Yvette, France

^* To whom correspondence should be addressed. Email: patrick.linder{at}medecine.unige.ch. kyle.tanner{at}medecine.unige.ch.

	Abstract

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 were also 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, and strand-displacement activity. However, the most pronounced effect was a loss of ATP-dependent cooperative binding of the RNA substrates. Sequence analyses and 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, and it thereby helps to maintain the network of interactions that exist between the different motifs involved in ATP and RNA binding.