DNA Recognition by a σ54 Transcriptional Activator from Aquifex aeolicus

JOURNAL OF MOLECULAR BIOLOGY

卷:426

Article

Vidangos, Natasha K.¹  Heideker, Johanna¹  Lyubimov, Artem¹  Lamers, Meindert¹  Huo, Yixin^3,4  Pelton, Jeffrey G.²  Ton, Jimmy¹  Gralla, Jay^3,4  Berger, James¹  Wemmer, David E.^1,2 

[1] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA

[2] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA

[3] Univ Calif Los Angeles, Dept Chem & Biochem, Los Angeles, CA 90095 USA

[4] Univ Calif Los Angeles, Inst Mol Biol, Los Angeles, CA 90095 USA

关键词: DNA complex;    DNA-binding domain;    sequence-specific recognition;    NtrC;    Fis;   

DOI  :  10.1016/j.jmb.2014.08.009

来源: Elsevier

【 摘 要 】

Transcription initiation by bacterial sigma(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 sigma(54) activators. Two NtrC4-binding sites were identified upstream (-145 and -85 bp) from the start of the IpxC gene, which is responsible for the first committed step in lipid A biosynthesis. This is the first experimental evidence for sigma(54) regulation in IpxC 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. (C) 2014 Elsevier Ltd. All rights reserved.

【 授权许可】

Free