3QOQ

Crystal Structure of the Transcription Factor AmrZ in Complex with the 18 Base Pair amrZ1 Binding Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Transcription Factor AmrZ Utilizes Multiple DNA Binding Modes to Recognize Activator and Repressor Sequences of Pseudomonas aeruginosa Virulence Genes.

Pryor Jr., E.E.Waligora, E.A.Xu, B.Dellos-Nolan, S.Wozniak, D.J.Hollis, T.

(2012) PLoS Pathog 8: e1002648-e1002648

  • DOI: 10.1371/journal.ppat.1002648
  • Primary Citation of Related Structures:  
    3QOQ

  • PubMed Abstract: 
  • AmrZ, a member of the Ribbon-Helix-Helix family of DNA binding proteins, functions as both a transcriptional activator and repressor of multiple genes encoding Pseudomonas aeruginosa virulence factors. The expression of these virulence factors leads to chronic and sustained infections associated with worsening prognosis ...

    AmrZ, a member of the Ribbon-Helix-Helix family of DNA binding proteins, functions as both a transcriptional activator and repressor of multiple genes encoding Pseudomonas aeruginosa virulence factors. The expression of these virulence factors leads to chronic and sustained infections associated with worsening prognosis. In this study, we present the X-ray crystal structure of AmrZ in complex with DNA containing the repressor site, amrZ1. Binding of AmrZ to this site leads to auto-repression. AmrZ binds this DNA sequence as a dimer-of-dimers, and makes specific base contacts to two half sites, separated by a five base pair linker region. Analysis of the linker region shows a narrowing of the minor groove, causing significant distortions. AmrZ binding assays utilizing sequences containing variations in this linker region reveals that secondary structure of the DNA, conferred by the sequence of this region, is an important determinant in binding affinity. The results from these experiments allow for the creation of a model where both intrinsic structure of the DNA and specific nucleotide recognition are absolutely necessary for binding of the protein. We also examined AmrZ binding to the algD promoter, which results in activation of the alginate exopolysaccharide biosynthetic operon, and found the protein utilizes different interactions with this site. Finally, we tested the in vivo effects of this differential binding by switching the AmrZ binding site at algD, where it acts as an activator, for a repressor binding sequence and show that differences in binding alone do not affect transcriptional regulation.


    Organizational Affiliation

    Department of Biochemistry and Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alginate and motility regulator ZA, B, C, D69Pseudomonas aeruginosaMutation(s): 0 
Gene Names: algZamrZPA3385
Find proteins for G3XCY4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XCY4 
Go to UniProtKB:  G3XCY4
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*CP*TP*GP*GP*CP*AP*AP*AP*AP*CP*GP*CP*CP*GP*GP*CP*A)-3')E18N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*GP*CP*CP*GP*GP*CP*GP*TP*TP*TP*TP*GP*CP*CP*AP*GP*T)-3')F18N/A
      Small Molecules
      Modified Residues  1 Unique
      IDChainsTypeFormula2D DiagramParent
      MSE
      Query on MSE
      A, B, C, DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.10 Å
      • R-Value Free: 0.295 
      • R-Value Work: 0.261 
      • R-Value Observed: 0.263 
      • Space Group: I 4 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 129.465α = 90
      b = 129.465β = 90
      c = 152.554γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      SOLVEphasing
      RESOLVEphasing
      REFMACrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2012-02-15
        Type: Initial release
      • Version 1.1: 2012-05-02
        Changes: Database references
      • Version 1.2: 2012-10-17
        Changes: Structure summary
      • Version 1.3: 2017-11-08
        Changes: Refinement description