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: 3.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.261 

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

  • 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 ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alginate and motility regulator Z
A, B, C, D
69Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: amrZ
Find proteins for G3XCY4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  G3XCY4
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*TP*GP*GP*CP*AP*AP*AP*AP*CP*GP*CP*CP*GP*GP*CP*A)-3')E18N/A
Entity ID: 3
MoleculeChainsLengthOrganism
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, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.261 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 129.465α = 90.00
b = 129.465β = 90.00
c = 152.554γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
RESOLVEphasing
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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