1ZLQ

Crystallographic and spectroscopic evidence for high affinity binding of Fe EDTA (H2O)- to the periplasmic nickel transporter NikA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic and Spectroscopic Evidence for High Affinity Binding of FeEDTA(H(2)O)(-) to the Periplasmic Nickel Transporter NikA

Cherrier, M.V.Martin, L.Cavazza, C.Jacquamet, L.Lemaire, D.Gaillard, J.Fontecilla Camps, J.C.

(2005) J.Am.Chem.Soc. 127: 10075-10082

  • DOI: 10.1021/ja0518530

  • PubMed Abstract: 
  • Because nickel is both essential and toxic to a great variety of organisms, its detection and transport is highly regulated. In Escherichia coli and other related Gram-negative bacteria, high affinity nickel transport depends on proteins expressed by ...

    Because nickel is both essential and toxic to a great variety of organisms, its detection and transport is highly regulated. In Escherichia coli and other related Gram-negative bacteria, high affinity nickel transport depends on proteins expressed by the nik operon. A central actor of this process is the periplasmic NikA transport protein. A previous structural report has proposed that nickel binds to NikA as a pentahydrate species. However, both stereochemical considerations and X-ray absorption spectroscopic results are incompatible with that interpretation. Here, we report the 1.8 A resolution structure of NikA and show that it binds FeEDTA(H2O)- with very high affinity. In addition, we provide crystallographic evidence that a metal-EDTA complex was also bound to the previously reported NikA structure. Our observations strongly suggest that nickel transport in E. coli requires the binding of this metal ion to a metallophore that bears significant resemblance to EDTA. They also provide a basis for the potential use of NikA in the bioremediation of toxic transition metals and the design of artificial metalloenzymes.


    Organizational Affiliation

    Laboratoire de Cristallographie et de Cristallogenèse des Protéines and Laboratoire de Spectroscopie de Masse des Protéines, Institut de Biologie Structurale J.P. Ebel (CEA-CNRS-UJF), 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nickel-binding periplasmic protein
A, B
502Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nikA
Find proteins for P33590 (Escherichia coli (strain K12))
Go to UniProtKB:  P33590
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDT
Query on EDT

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A, B
{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
C10 H16 N2 O8
KCXVZYZYPLLWCC-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
DTT
Query on DTT

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A
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.830α = 90.00
b = 93.870β = 90.00
c = 124.490γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
AMoREphasing
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance