DNA Recognition by a σ54 Transcriptional Activator from Aquifex aeolicus

Natasha K. Vidangos, Johanna Heideker, Artem Lyubimov, Meindert Lamers, Yixin Huo, Jeffrey G. Pelton, Jimmy Ton, Jay Gralla, James Berger, David E. Wemmer

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Transcription initiation by bacterial σ54-polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain (DBD). The structurally characterized DBDs from activators all belong to the Fis (factor for inversion stimulation) family of helix-turn-helix DNA-binding proteins. We report here structures of the free and DNA-bound forms of the DBD of NtrC4 (4DBD) from Aquifex aeolicus, a member of the NtrC family of σ54 activators. Two NtrC4-binding sites were identified upstream (- 145 and - 85 bp) from the start of the lpxC gene, which is responsible for the first committed step in lipid A biosynthesis. This is the first experimental evidence for σ54 regulation in lpxC expression. 4DBD was crystallized both without DNA and in complex with the - 145-binding site. The structures, together with biochemical data, indicate that NtrC4 binds to DNA in a manner that is similar to that of its close homolog, Fis. The greater sequence specificity for the binding of 4DBD relative to Fis seems to arise from a larger number of base-specific contacts contributing to affinity than for Fis.

Original languageEnglish (US)
Pages (from-to)3553-3568
Number of pages16
JournalJournal of molecular biology
Issue number21
StatePublished - Oct 23 2014
Externally publishedYes


  • DNA complex
  • DNA-binding domain
  • Fis
  • NtrC
  • sequence-specific recognition

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology


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