title: Cofactor-dependent specificity of a DEAD-box protein.
abstract: DEAD-box proteins, a large class of RNA-dependent ATPases, regulate all aspects of gene expression and RNA metabolism. They can facilitate dissociation of RNA duplexes and remodeling of RNA-protein complexes, serve as ATP-dependent RNA-binding proteins, or even anneal duplexes. These proteins have highly conserved sequence elements that are contained within two RecA-like domains; consequently, their structures are nearly identical. Furthermore, crystal structures of DEAD-box proteins with bound RNA reveal interactions exclusively between the protein and the RNA backbone. Together, these findings suggest that DEAD-box proteins interact with their substrates in a nonspecific manner, which is confirmed in biochemical experiments. Nevertheless, this contrasts with the need to target these enzymes to specific substrates in vivo. Using the DEAD-box protein Rok1 and its cofactor Rrp5, which both function during maturation of the small ribosomal subunit, we show here that Rrp5 provides specificity to the otherwise nonspecific biochemical activities of the Rok1 DEAD-domain. This finding could reconcile the need for specific substrate binding of some DEAD-box proteins with their nonspecific binding surface and expands the potential roles of cofactors to specificity factors. Identification of helicase cofactors and their RNA substrates could therefore help define the undescribed roles of the 19 DEAD-box proteins that function in ribosome assembly.
authors: Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
authors: Crystal L
authors: CL
authors: Young
authors: Sohail
authors: S
authors: Khoshnevis
authors: Katrin
authors: K
authors: Karbstein
mesh_terms: D003001:Cloning, Molecular; D053487:DEAD-box RNA Helicases / Q000235:genetics / Q000378:metabolism*; D004591:Electrophoresis, Polyacrylamide Gel; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D059748:Proteolysis; D012313:RNA / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D054679:Ribosome Subunits, Small / Q000378:metabolism*; D012394:Rosaniline Dyes; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D009687:Nuclear Proteins; D016601:RNA-Binding Proteins; C102025:RRP5 protein, S cerevisiae; D012394:Rosaniline Dyes; D029701:Saccharomyces cerevisiae Proteins; D012313:RNA; C048139:Coomassie blue; C120858:ROK1 protein, S cerevisiae; D053487:DEAD-box RNA Helicases
keywords: RNA helicases; annealing
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