4FTH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.004 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DNA Recognition by a sigma (54) Transcriptional Activator from Aquifex aeolicus.

Vidangos, N.K.Heideker, J.Lyubimov, A.Lamers, M.Huo, Y.Pelton, J.G.Ton, J.Gralla, J.Berger, J.Wemmer, D.E.

(2014) J.Mol.Biol. 426: 3553-3568

  • DOI: 10.1016/j.jmb.2014.08.009

  • 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 ch ...

    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.


    Organizational Affiliation

    Department of Chemistry, University of California, MC-1460, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional regulator (NtrC family)
A, B
69Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: ntrC4
Find proteins for O66551 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66551
Entity ID: 2
MoleculeChainsLengthOrganism
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'C22N/A
Entity ID: 3
MoleculeChainsLengthOrganism
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'D21N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.004 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.436α = 90.00
b = 28.798β = 94.55
c = 74.931γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data collection
DENZOdata reduction
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2014-10-08
    Type: Database references
  • Version 1.2: 2014-11-12
    Type: Database references