4MTE

Zinc Uptake Regulator Complexed with Zinc and DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Mechanistic Basis of Zinc Regulation Across the E. coli Zur Regulon.

Gilston, B.A.Wang, S.Marcus, M.D.Canalizo-Hernandez, M.A.Swindell, E.P.Xue, Y.Mondragon, A.O'Halloran, T.V.

(2014) Plos Biol. 12: e1001987-e1001987

  • DOI: 10.1371/journal.pbio.1001987
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Commensal microbes, whether they are beneficial or pathogenic, are sensitive to host processes that starve or swamp the prokaryote with large fluctuations in local zinc concentration. To understand how microorganisms coordinate a dynamic response to ...

    Commensal microbes, whether they are beneficial or pathogenic, are sensitive to host processes that starve or swamp the prokaryote with large fluctuations in local zinc concentration. To understand how microorganisms coordinate a dynamic response to changes in zinc availability at the molecular level, we evaluated the molecular mechanism of the zinc-sensing zinc uptake regulator (Zur) protein at each of the known Zur-regulated genes in Escherichia coli. We solved the structure of zinc-loaded Zur bound to the P(znuABC) promoter and show that this metalloregulatory protein represses gene expression by a highly cooperative binding of two adjacent dimers to essentially encircle the core element of each of the Zur-regulated promoters. Cooperativity in these protein-DNA interactions requires a pair of asymmetric salt bridges between Arg52 and Asp49' that connect otherwise independent dimers. Analysis of the protein-DNA interface led to the discovery of a new member of the Zur-regulon: pliG. We demonstrate this gene is directly regulated by Zur in a zinc responsive manner. The pliG promoter forms stable complexes with either one or two Zur dimers with significantly less protein-DNA cooperativity than observed at other Zur regulon promoters. Comparison of the in vitro Zur-DNA binding affinity at each of four Zur-regulon promoters reveals ca. 10,000-fold variation Zur-DNA binding constants. The degree of Zur repression observed in vivo by comparison of transcript copy number in wild-type and Δzur strains parallels this trend spanning a 100-fold difference. We conclude that the number of ferric uptake regulator (Fur)-family dimers that bind within any given promoter varies significantly and that the thermodynamic profile of the Zur-DNA interactions directly correlates with the physiological response at different promoters.


    Organizational Affiliation

    Department of Chemistry and The Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America.,Department of Chemistry and The Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America; Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America.,Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zinc uptake regulation protein
A, B, C, D
171Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: zur (yjbK)
Find proteins for P0AC51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC51
Entity ID: 2
MoleculeChainsLengthOrganism
znuABC operator DNAY33N/A
Entity ID: 3
MoleculeChainsLengthOrganism
znuABC operator DNAZ33N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 193.324α = 90.00
b = 80.470β = 120.15
c = 98.770γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
XDSdata scaling
REFMACrefinement
SHARPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-11-12
    Type: Database references