4I8C

X-ray structure of NikA in complex with Ni-(L-His)2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.503 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The binding mode of Ni-((L)-His)(2) in NikA revealed by X-ray crystallography.

Lebrette, H.Iannello, M.Fontecilla-Camps, J.C.Cavazza, C.

(2012) J.Inorg.Biochem. 121C: 16-18

  • DOI: 10.1016/j.jinorgbio.2012.12.010

  • PubMed Abstract: 
  • The ABC-type importer NikABCDE mediates nickel acquisition in Escherichia coli. The periplasmic nickel-binding component NikA has a folding similar to that of the peptide transporter OppA and does not bind free nickel. Instead, we showed that the met ...

    The ABC-type importer NikABCDE mediates nickel acquisition in Escherichia coli. The periplasmic nickel-binding component NikA has a folding similar to that of the peptide transporter OppA and does not bind free nickel. Instead, we showed that the metal is tetra-coordinated by an organic tri-dentate molecule and His416. Conversely, it has been recently reported that NikA binds Ni-(L-His)2 and that addition of histidine increases the rate of nickel uptake in vivo. Here, we report the structure of NikA/Ni-(L-His)2 and show that histidine binding differs from peptide binding in OppA. The structure also confirms the central role of His416 in nickel binding.


    Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel, Metalloproteins Group, UMR 5075, CEA, CNRS, Université Joseph Fourier-Grenoble 1, 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, C
502Escherichia coli (strain K12)Gene Names: nikA
Find proteins for P33590 (Escherichia coli (strain K12))
Go to UniProtKB:  P33590
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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

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

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

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A, B, C
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A, B, C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.503 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 158.630α = 90.00
b = 158.630β = 90.00
c = 135.820γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
MXdata collection
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-30
    Type: Initial release