3TJA

Crystal structure of Helicobacter pylori UreE in the apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallographic and X-ray absorption spectroscopic characterization of Helicobacter pylori UreE bound to Ni2+ and Zn2+ reveals a role for the disordered C-terminal arm in metal trafficking.

Banaszak, K.Martin-Diaconescu, V.Bellucci, M.Zambelli, B.Rypniewski, W.Maroney, M.J.Ciurli, S.

(2012) Biochem.J. 441: 1017-1026

  • DOI: 10.1042/BJ20111659
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The survival and growth of the pathogen Helicobacter pylori in the gastric acidic environment is ensured by the activity of urease, an enzyme containing two essential Ni²⁺ ions in the active site. The metallo-chaperone UreE facilitates in vivo Ni²⁺ i ...

    The survival and growth of the pathogen Helicobacter pylori in the gastric acidic environment is ensured by the activity of urease, an enzyme containing two essential Ni²⁺ ions in the active site. The metallo-chaperone UreE facilitates in vivo Ni²⁺ insertion into the apoenzyme. Crystals of apo-HpUreE (H. pylori UreE) and its Ni⁺- and Zn⁺-bound forms were obtained from protein solutions in the absence and presence of the metal ions. The crystal structures of the homodimeric protein, determined at 2.00 Å (apo), 1.59 Å (Ni²⁺) and 2.52 Å (Zn²⁺) resolution, show the conserved proximal and solvent-exposed His¹⁰² residues from two adjacent monomers invariably involved in metal binding. The C-terminal regions of the apoprotein are disordered in the crystal, but acquire significant ordering in the presence of the metal ions due to the binding of His¹⁵². The analysis of X-ray absorption spectral data obtained using solutions of Ni²⁺- and Zn²⁺-bound HpUreE provided accurate information of the metal-ion environment in the absence of solid-state effects. These results reveal the role of the histidine residues at the protein C-terminus in metal-ion binding, and the mutual influence of protein framework and metal-ion stereo-electronic properties in establishing co-ordination number and geometry leading to metal selectivity.


    Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Urease accessory protein ureE
A, B, C, D
170Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: ureE
Find proteins for Q09064 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  Q09064
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.999α = 90.00
b = 70.468β = 90.00
c = 123.340γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PHASERphasing
HKL-2000data reduction
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2012-02-01
    Type: Database references