YxiN is a modular protein combining a DExD/H core and a specific RNA-binding domain

Fedor V. Karginov, Jonathan M. Caruthers, Yao Xiong Hu, David B. McKay, Olke C. Uhlenbeck*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

59 Scopus citations


DExD/H proteins, typically described as RNA helicases, participate in rearrangement of RNA-RNA and possibly RNA-protein complexes in the cell. Aside from the conserved DExD/H core, members of this protein family often contain N- and C-terminal extensions that are responsible for additional functions. The Bacillus subtilis DEx D/H-box protein YxiN and its Escherichia coli ortholog DbpA contain an ∼80 amino acid C-terminal extension that has been proposed to specifically interact with a region of 23 S ribosomal RNA including hairpin 92. In this study, the DExD/H-box core and the C-terminal domain of YxiN were expressed and characterized as separate proteins. The isolated DExD/H-box core, YxCat, had weak, nonspecific RNA binding activity and showed RNA-stimulated ATPase activity with a K m(ATP) that resembled several non-specific DExD/ H proteins. The isolated C-terminal domain, YxRBD, bound RNA with the high affinity and specificity seen with full-length YxiN. Thus, YxiN is a modular protein combining the activities of the YxCat and YxRBD domains. Footprinting of YxiN and YxRBD on a 172-nucleotide fragment of 23 S rRNA was used to identify the sites of interaction of the C-terminal and helicase domains with the RNA.

Original languageEnglish (US)
Pages (from-to)35499-35505
Number of pages7
JournalJournal of Biological Chemistry
Issue number42
StatePublished - Oct 21 2005

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology


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