4HI0

Crystal Structure of Helicobacter pylori Urease Accessory Protein UreF/H/G complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of UreG/UreF/UreH complex reveals how urease accessory proteins facilitate maturation of Helicobacter pylori urease.

Fong, Y.H.Wong, H.C.Yuen, M.H.Lau, P.H.Chen, Y.W.Wong, K.B.

(2013) Plos Biol. 11: e1001678-e1001678

  • DOI: 10.1371/journal.pbio.1001678

  • PubMed Abstract: 
  • Urease is a metalloenzyme essential for the survival of Helicobacter pylori in acidic gastric environment. Maturation of urease involves carbamylation of Lys219 and insertion of two nickel ions at its active site. This process requires GTP hydrolysis ...

    Urease is a metalloenzyme essential for the survival of Helicobacter pylori in acidic gastric environment. Maturation of urease involves carbamylation of Lys219 and insertion of two nickel ions at its active site. This process requires GTP hydrolysis and the formation of a preactivation complex consisting of apo-urease and urease accessory proteins UreF, UreH, and UreG. UreF and UreH form a complex to recruit UreG, which is a SIMIBI class GTPase, to the preactivation complex. We report here the crystal structure of the UreG/UreF/UreH complex, which illustrates how UreF and UreH facilitate dimerization of UreG, and assembles its metal binding site by juxtaposing two invariant Cys66-Pro67-His68 metal binding motif at the interface to form the (UreG/UreF/UreH)2 complex. Interaction studies revealed that addition of nickel and GTP to the UreG/UreF/UreH complex releases a UreG dimer that binds a nickel ion at the dimeric interface. Substitution of Cys66 and His68 with alanine abolishes the formation of the nickel-charged UreG dimer. This nickel-charged UreG dimer can activate urease in vitro in the presence of the UreF/UreH complex. Static light scattering and atomic absorption spectroscopy measurements demonstrated that the nickel-charged UreG dimer, upon GTP hydrolysis, reverts to its monomeric form and releases nickel to urease. Based on our results, we propose a mechanism on how urease accessory proteins facilitate maturation of urease.


    Organizational Affiliation

    School of Life Sciences, Center for Protein Science and Crystallography, The Chinese University of Hong Kong, Hong Kong, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Urease accessory protein UreF
A, C
254Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: ureF
Find proteins for Q09065 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  Q09065
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Urease accessory protein UreH
B, D
265Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: ureH
Find proteins for Q09067 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  Q09067
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Urease accessory protein UreG
E, F
199Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: ureG
Find proteins for Q09066 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  Q09066
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
E, F
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.124α = 90.00
b = 96.429β = 90.00
c = 237.452γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
GDAdata collection
XDSdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references