3NXZ

Crystal Structure of UreE from Helicobacter pylori (Cu2+ bound form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of Apo and Metal-Bound Forms of the UreE Protein from Helicobacter pylori: Role of Multiple Metal Binding Sites

Shi, R.Munger, C.Asinas, A.Benoit, S.L.Miller, E.Matte, A.Maier, R.J.Cygler, M.

(2010) Biochemistry 49: 7080-7088

  • DOI: 10.1021/bi100372h
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of the urease maturation protein UreE from Helicobacter pylori has been determined in its apo form at 2.1 A resolution, bound to Cu(2+) at 2.7 A resolution, and bound to Ni(2+) at 3.1 A resolution. Apo UreE forms dimers, while t ...

    The crystal structure of the urease maturation protein UreE from Helicobacter pylori has been determined in its apo form at 2.1 A resolution, bound to Cu(2+) at 2.7 A resolution, and bound to Ni(2+) at 3.1 A resolution. Apo UreE forms dimers, while the metal-bound enzymes are arranged as tetramers that consist of a dimer of dimers associated around the metal ion through coordination by His102 residues from each subunit of the tetramer. Comparison of independent subunits from different crystal forms indicates changes in the relative arrangement of the N- and C-terminal domains in response to metal binding. The improved ability of engineered versions of UreE containing hexahistidine sequences at either the N-terminal or C-terminal end to provide Ni(2+) for the final metal sink (urease) is eliminated in the H102A version. Therefore, the ability of the improved Ni(2+)-binding versions to deliver more nickel is likely an effect of an increased local concentration of metal ions that can rapidly replenish transferred ions bound to His102.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6.




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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.256 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 88.829α = 90.00
b = 88.829β = 90.00
c = 203.635γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
MOLREPphasing
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description