Format

Send to

Choose Destination
J Mol Biol. 2014 Oct 23;426(21):3553-68. doi: 10.1016/j.jmb.2014.08.009. Epub 2014 Aug 23.

DNA recognition by a σ(54) transcriptional activator from Aquifex aeolicus.

Author information

1
Department of Chemistry, University of California, MC-1460, Berkeley, CA 94720, USA.
2
Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Box 951569, Los Angeles, CA 90095, USA.
3
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
4
Department of Chemistry, University of California, MC-1460, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: dewemmer@berkeley.edu.

Abstract

Transcription initiation by bacterial σ(54)-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 σ(54) activators. Two NtrC4-binding sites were identified upstream (-145 and -85bp) 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 σ(54) 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.

KEYWORDS:

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

PMID:
25158097
PMCID:
PMC4188747
DOI:
10.1016/j.jmb.2014.08.009
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Elsevier Science Icon for PubMed Central
Loading ...
Support Center