4FTH

Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA

Summary for 4FTH

• Entry DOI: 10.2210/pdb4fth/pdb
• Related: 3E7L
• Descriptor: Transcriptional regulator (NtrC family), 5'-D(*AP*CP*TP*TP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*AP*AP*AP*TP*GP*CP*AP*T)-3', 5'-D(P*GP*AP*TP*GP*CP*AP*TP*TP*TP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*AP*A)-3', ... (4 entities in total)
• Functional Keywords: sigma-54, transcriptional activator, dna-binding domain, ntrc, fis, helix-turn-helix, dna-binding, transcription regulator-dna complex, transcription regulator/dna
• Biological source: Aquifex aeolicus
• Total number of polymer chains: 4
• Total formula weight: 30079.32

Authors

Vidangos, N.K.,Heideker, J.,Lyubimov, A.Y.,Lamers, M.,Huo, Y.,Pelton, J.G.,Ton, J.,Gralla, J.D.,Kuriyan, J.,Berger, J.M.,Wemmer, D.E. (deposition date: 2012-06-27, release date: 2012-08-29, Last modification date: 2023-09-13)

Primary citation

Vidangos, N.K.,Heideker, J.,Lyubimov, A.,Lamers, M.,Huo, Y.,Pelton, J.G.,Ton, J.,Gralla, J.,Berger, J.,Wemmer, D.E.
DNA Recognition by a sigma (54) Transcriptional Activator from Aquifex aeolicus.
J.Mol.Biol., 426:3553-3568, 2014

PubMed 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.

PubMed: 25158097
DOI: 10.1016/j.jmb.2014.08.009

Experimental method

X-RAY DIFFRACTION (3.004 Å)