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 

wwPDB Validation 3D Report Full Report


This is version 2.0 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: 10.1039/c5mt00291e

  • 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 viewp ...

    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

    Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal and Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal. tiagob@itqb.unl.pt jvicente@itqb.unl.pt.,Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Portugal.,Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal. tiagob@itqb.unl.pt jvicente@itqb.unl.pt.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METAL-BINDING PROTEIN ZINT
A
193Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: zinT (yodA)
Find proteins for P76344 (Escherichia coli (strain K12))
Go to UniProtKB:  P76344
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 62.010α = 90.00
b = 62.010β = 90.00
c = 149.720γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
XDSdata reduction
HKL2Mapphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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