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: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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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
  • Primary Citation of Related Structures:  
    3QIM

  • 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 hydrogenase activity ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nickel-binding periplasmic proteinA, B502Escherichia coli K-12Mutation(s): 1 
Gene Names: b3476, JW3441, nikA
UniProt
Find proteins for P33590 (Escherichia coli (strain K12))
Explore P33590 
Go to UniProtKB:  P33590
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33590
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth B],
Q [auth A],
R [auth A],
S [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth A],
J [auth A],
O [auth A],
T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
G [auth A],
I [auth A],
K [auth A],
L [auth A],
M [auth A],
G [auth A],
I [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
P [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.731α = 90
b = 94.005β = 90
c = 124.33γ = 90
Software Package:
Software NamePurpose
MXdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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