5AQ6

Structure of E. coli ZinT at 1.79 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Roles of Escherichia Coli Zint in Cobalt, Mercury and Cadmium Resistance and Structural Insights Into the Metal Binding Mechanism

Colaco, H.G.Santo, P.E.Matias, P.Bandeiras, T.M.Vicente, J.B.

(2016) Metallomics 8: 327

  • DOI: https://doi.org/10.1039/c5mt00291e
  • Primary Citation of Related Structures:  
    5AQ6

  • PubMed Abstract: 

    Escherichia coli ZinT is a metal binding protein involved in zinc homeostasis, with additional putative functions in the resistance against other metals. Herein, a method was designed and implemented to evaluate from a structural and functional viewpoint metal binding to E. coli ZinT in 96-well microtiter plates. The isolated ZinT was mixed with several metal ions and their binding ability was determined by differential scanning fluorimetry. From the positive hits, six metal ions were evaluated in terms of their toxicity towards an E. coli strain depleted of ZinT (ΔzinT) using as control a strain deleted in the galT gene (ΔgalT). The different sensitivities of each strain to the tested metals revealed novel roles of ZinT in the resistance to cobalt, cadmium and mercury. This approach provides a valuable and reliable platform for the analysis of metal binding and its functional implications, extendable to other metal binding proteins. In combination with the developed platform, structural studies were performed with ZinT, with the zinc-loaded crystallographic structure being obtained at 1.79 Å resolution. Besides the canonical zinc-binding site located near the N-terminus, the herein reported dimeric ZinT structure unravelled extra zinc binding sites that support its role in metal loading and/or transport. Altogether, the designed experimental platform allowed revealing new roles for the ZinT protein in microbial resistance to heavy metal toxicity, as well as structural insights into the ZinT metal binding mechanism.


  • Organizational Affiliation

    Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
METAL-BINDING PROTEIN ZINT193Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
Find proteins for P76344 (Escherichia coli (strain K12))
Explore P76344 
Go to UniProtKB:  P76344
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76344
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.01α = 90
b = 62.01β = 90
c = 149.72γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
HKL2Mapphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Other, Refinement description
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary