The Carboxy-terminal Domain of the DExDH Protein YxiN is Sufficient to Confer Specificity for 23 S rRNA

DExDH proteins are believed to modulate the structures of RNAs and ribonucleoprotein complexes by disrupting RNA helices and RNA–protein interactions. All DExDH 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 DExDH protein DbpA and its Bacillus subtilis ortholog YxiN have similar 75aa carboxy-terminal domains, and both proteins are specifically targeted to 23 S 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 DExDH protein with no apparent substrate specificity. Both the RNA-dependent ATPase and RNA helicase activities of the chimera are specifically activated by 23 S rRNA and abolished by sequence changes within hairpin 92, a critical recognition element for YxiN. These data support a model in which the carboxy-terminal domain binds hairpin 92 to target the protein to 23 S rRNA.