3O1Q | pdb_00003o1q

Native Crystal Structure of Helicobacter pylori Urease Accessory Protein UreF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.208 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3O1Q

This is version 1.4 of the entry. See complete history

Literature

Assembly of Preactivation Complex for Urease Maturation in Helicobacter pylori: CRYSTAL STRUCTURE OF UreF-UreH PROTEIN COMPLEX.

Fong, Y.H.Wong, H.C.Chuck, C.P.Chen, Y.W.Sun, H.Wong, K.B.

(2011) J Biological Chem 286: 43241-43249

  • DOI: https://doi.org/10.1074/jbc.M111.296830
  • Primary Citation Related Structures: 
    3O1Q, 3SF5

  • PubMed Abstract: 

    Colonization of Helicobacter pylori in the acidic environment of the human stomach depends on the neutralizing activity of urease. Activation of apo-urease involves carboxylation of lysine 219 and insertion of two nickel ions. In H. pylori, this maturation process involves four urease accessory proteins as follows: UreE, UreF, UreG, and UreH. It is postulated that the apo-urease interacts with UreF, UreG, and UreH to form a pre-activation complex that undergoes GTP-dependent activation of urease. The crystal structure of the UreF-UreH complex reveals conformational changes in two distinct regions of UreF upon complex formation. First, the flexible C-terminal residues of UreF become ordered, forming an extra helix α10 and a loop structure stabilized by hydrogen bonds involving Arg-250. Second, the first turn of helix α2 uncoils to expose a conserved residue, Tyr-48. Substitution of R250A or Y48A in UreF abolishes the formation of the heterotrimeric complex of UreG-UreF-UreH and abolishes urease maturation. Our results suggest that the C-terminal residues and helix α2 of UreF are essential for the recruitment of UreG for the formation of the pre-activation complex. The molecular mass of the UreF-UreH complex determined by static light scattering was 116 ± 2.3 kDa, which is consistent with the quaternary structure of a dimer of heterodimers observed in the crystal structure. Taking advantage of the unique 2-fold symmetry observed in both the crystal structures of H. pylori urease and the UreF-UreH complex, we proposed a topology model of the pre-activation complex for urease maturation.


  • Organizational Affiliation
    • Centre for Protein Science and Crystallography, School of Life Sciences, Chinese University of Hong Kong, China, Hong Kong.

Macromolecule Content 

  • Total Structure Weight: 85.96 kDa 
  • Atom Count: 5,667 
  • Modeled Residue Count: 623 
  • Deposited Residue Count: 762 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Urease accessory protein ureF
A, B, C
254Helicobacter pyloriMutation(s): 0 
Gene Names: ureFHP_0069
UniProt
Find proteins for Q09065 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore Q09065 
Go to UniProtKB:  Q09065
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09065
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.208 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.328α = 90
b = 89.997β = 94.56
c = 66.95γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-02
    Changes: Database references
  • Version 1.3: 2011-12-28
    Changes: Database references
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references