title: The carboxy-terminal domain of the DExDH protein YxiN is sufficient to confer specificity for 23S rRNA.
abstract: DE x DH proteins are believed to modulate the structures of RNAs and ribonucleoprotein complexes by disrupting RNA helices and RNA-protein interactions. All DE x DH proteins contain a two-domain catalytic core that enables their RNA-dependent ATPase and RNA helicase activities. The catalytic core may be flanked by ancillary domains that are proposed to confer substrate specificity and facilitate the unique functions of individual proteins. The Escherichia coli DE x DH protein DbpA and its Bacillus subtilis ortholog YxiN have similar 75aa carboxy-terminal domains, and both proteins are specifically targeted to 23S rRNA. Here we demonstrate that the carboxy-terminal domain of YxiN is sufficient to confer RNA specificity by characterizing a chimera in which this domain is appended to the core domains of E.coli SrmB, a DE x DH protein with no apparent substrate specificity. Both the RNA-dependent ATPase and RNA helicase activities of the chimera are specifically activated by 23S rRNA and abolished by sequence changes within hairpin 92, a critical recognition element for Y x iN. These data support a model in which the carboxy-terminal domain binds hairpin 92 to target the protein to 23S rRNA.
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado, Campus Box 215, Boulder, CO 80309-0215, USA.
authors.forename: Karl
authors.initials: K
authors.lastname: Kossen
authors.forename: Fedor V
authors.initials: FV
authors.lastname: Karginov
authors.forename: Olke C
authors.initials: OC
authors.lastname: Uhlenbeck
mesh_terms: D000251:Adenosine Triphosphatases / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D020134:Catalytic Domain; D017124:Conserved Sequence; D053487:DEAD-box RNA Helicases; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D007700:Kinetics; D008954:Models, Biological; D011189:Potassium Chloride / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D020365:RNA Helicases / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D012338:RNA, Ribosomal, 23S / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D011993:Recombinant Fusion Proteins / Q000378:metabolism; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D013696:Temperature
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S; D016601:RNA-Binding Proteins; D011993:Recombinant Fusion Proteins; D011189:Potassium Chloride; D000255:Adenosine Triphosphate; C401542:yxiN protein, Bacillus subtilis; D000251:Adenosine Triphosphatases; C027900:RNA-dependent ATPase; D053487:DEAD-box RNA Helicases; D020365:RNA Helicases