The carboxy-terminal domain of the DExD/H protein YxiN is sufficient to confer specificity for 23 S rRNA

Karl Kossen, Fedor V. Karginov, Olke C. Uhlenbeck

Research output: Contribution to journalArticlepeer-review

81 Scopus citations

Abstract

DExD/H proteins are believed to modulate the structures of RNAs and ribonucleoprotein complexes by disrupting RNA helices and RNA-protein interactions. All DExD/H 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 DExD/H 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 DExD/H 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.

Original languageEnglish (US)
Pages (from-to)625-636
Number of pages12
JournalJournal of Molecular Biology
Volume324
Issue number4
DOIs
StatePublished - Jan 1 2002

Keywords

  • DbpA
  • Fusion protein
  • Helicase
  • RNA-binding domain
  • RNA-protein interaction

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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