3QIM

Histidine 416 of the periplamsic binding protein NikA is essential for nickel uptake in Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Histidine 416 of the periplasmic binding protein NikA is essential for nickel uptake in Escherichia coli

Cavazza, C.Martin, L.Laffly, E.Lebrette, H.Cherrier, M.V.Zeppieri, L.Richaud, P.Carriere, M.Fontecilla-Camps, J.C.

(2011) Febs Lett. 585: 711-715

  • DOI: 10.1016/j.febslet.2011.01.038

  • PubMed Abstract: 
  • Escherichia coli require nickel for the synthesis of [NiFe] hydrogenases under anaerobic growth conditions. Nickel import depends on the specific ABC-transporter NikABCDE encoded by the nik operon, which deletion causes the complete abolition of hydr ...

    Escherichia coli require nickel for the synthesis of [NiFe] hydrogenases under anaerobic growth conditions. Nickel import depends on the specific ABC-transporter NikABCDE encoded by the nik operon, which deletion causes the complete abolition of hydrogenase activity. We have previously postulated that the periplasmic binding protein NikA binds a natural metallophore containing three carboxylate functions that coordinate a Ni(II) ion, the fourth ligand being His416, the only direct metal-protein contact, completing a square-planar coordination for the metal. The crystal structure of the H416I mutant showed no electron density corresponding to a metal-chelator complex. In vivo experiments indicate that the mutation causes a significant decrease in nickel uptake and hydrogenase activity. These results confirm the essential role of His416 in nickel transport by NikA.


    Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, CEA, CNRS, Université Joseph Fourier-Grenoble 1, Grenoble, France. christine.cavazza@ibs.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nickel-binding periplasmic protein
A, B
502Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: nikA
Find proteins for P33590 (Escherichia coli (strain K12))
Go to UniProtKB:  P33590
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.731α = 90.00
b = 94.005β = 90.00
c = 124.330γ = 90.00
Software Package:
Software NamePurpose
MXdata collection
PHASERphasing
XDSdata reduction
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance