Induced fit and "lock and key" recognition of 5 S RNA by zinc fingers of transcription factor IIIA

Brian M. Lee, Jing Xu, Bryan K. Clarkson, Maria A. Martinez-Yamout, H. Jane Dyson, David A. Case, Joel M. Gottesfeld, Peter E. Wright

Research output: Contribution to journalArticlepeer-review

58 Scopus citations


Transcription factor IIIA (TFIIIA) is a Cys2His2 zinc finger protein that regulates expression of the 5 S ribosomal RNA gene by binding specifically to the internal control element. TFIIIA also functions in transport and storage of 5 S RNA by binding directly to the RNA transcript. To obtain insights into the mechanism by which TFIIIA recognizes 5 S RNA, we determined the solution structure of the middle three zinc fingers bound to the central core of 5 S RNA. Finger 4 utilizes "lock and key" recognition to bind in the widened major groove of the pre-structured RNA loop E motif. This interaction is mediated by direct hydrogen bonding interactions with bases. In contrast, recognition of loop A, a flexible junction of three helices, occurs by an induced fit mechanism that involves reorganization of the conserved CAUA motif and structuring of the finger 5-finger 6 interface to form a complementary RNA binding surface.

Original languageEnglish (US)
Pages (from-to)275-291
Number of pages17
JournalJournal of molecular biology
Issue number1
StatePublished - Mar 17 2006
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology


  • NMR
  • RNA binding
  • RNA structure
  • Transcription factor
  • Zinc finger


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