title: A conserved phenylalanine of motif IV in superfamily 2 helicases is required for cooperative, ATP-dependent binding of RNA substrates in DEAD-box proteins.
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 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-pi interactions, thereby helping to maintain the network of interactions that exist between the different motifs involved in ATP and RNA binding.
authors.affiliation: Départmente de Microbiologie et Médecine Moléculaire, Centre Médical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.
authors.forename: Josette
authors.initials: J
authors.lastname: Banroques
authors.forename: Olivier
authors.initials: O
authors.lastname: Cordin
authors.forename: Monique
authors.initials: M
authors.lastname: Doère
authors.forename: Patrick
authors.initials: P
authors.lastname: Linder
authors.forename: N Kyle
authors.initials: NK
authors.lastname: Tanner
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry; D001483:Base Sequence; D017124:Conserved Sequence; D053487:DEAD-box RNA Helicases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D010641:Phenotype; D010649:Phenylalanine / Q000737:chemistry; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity; D013489:Suppression, Genetic
chemical_list: D012331:RNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; D010649:Phenylalanine; D000255:Adenosine Triphosphate; D001120:Arginine; C492152:DED1 protein, S cerevisiae; D053487:DEAD-box RNA Helicases