4OER

Crystal structure of NikA from Brucella suis, unliganded form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Promiscuous nickel import in human pathogens: structure, thermodynamics, and evolution of extracytoplasmic nickel-binding proteins.

Lebrette, H.Brochier-Armanet, C.Zambelli, B.de Reuse, H.Borezee-Durant, E.Ciurli, S.Cavazza, C.

(2014) Structure 22: 1421-1432

  • DOI: 10.1016/j.str.2014.07.012
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In human pathogenic bacteria, nickel is required for the activation of two enzymes, urease and [NiFe]-hydrogenase, necessary for host infection. Acquisition of Ni(II) is mediated by either permeases or ABC-importers, the latter including a subclass t ...

    In human pathogenic bacteria, nickel is required for the activation of two enzymes, urease and [NiFe]-hydrogenase, necessary for host infection. Acquisition of Ni(II) is mediated by either permeases or ABC-importers, the latter including a subclass that involves an extracytoplasmic nickel-binding protein, Ni-BP. This study reports on the structure of three Ni-BPs from a diversity of human pathogens and on the existence of three new nickel-binding motifs. These are different from that previously described for Escherichia coli Ni-BP NikA, known to bind nickel via a nickelophore, and indicate a variegated ligand selectivity for Ni-BPs. The structures are consistent with ligand affinities measured in solution by calorimetry and challenge the hypothesis of a general requirement of nickelophores for nickel uptake by canonical ABC importers. Phylogenetic analyses showed that Ni-BPs have different evolutionary origins and emerged independently from peptide-binding proteins, possibly explaining the promiscuous behavior of this class of Ni(II) carriers.


    Organizational Affiliation

    University Grenoble Alpes, LCBM, 17, Avenue des Martyrs, 38054 Grenoble Cedex 09, France. Electronic address: christine.cavazza@cea.fr.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NikA protein
A, B
500Brucella suisMutation(s): 0 
Gene Names: nikAE4658_07960
Find proteins for Q9AL82 (Brucella suis)
Go to UniProtKB:  Q9AL82
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.02α = 90
b = 62.231β = 105.3
c = 114.483γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Database references