3QGK

3.0 A Model of Iron Containing Urease UreA2B2 from Helicobacter mustelae (refined w/ no ordered solvent)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Iron-containing urease in a pathogenic bacterium.

Carter, E.L.Tronrud, D.E.Taber, S.R.Karplus, P.A.Hausinger, R.P.

(2011) Proc.Natl.Acad.Sci.USA 108: 13095-13099

  • DOI: 10.1073/pnas.1106915108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Helicobacter mustelae, a gastric pathogen of ferrets, synthesizes a distinct iron-dependent urease in addition to its archetypical nickel-containing enzyme. The iron-urease is oxygen-labile, with the inactive protein exhibiting a methemerythrin-like ...

    Helicobacter mustelae, a gastric pathogen of ferrets, synthesizes a distinct iron-dependent urease in addition to its archetypical nickel-containing enzyme. The iron-urease is oxygen-labile, with the inactive protein exhibiting a methemerythrin-like electronic spectrum. Significantly, incubation of the oxidized protein with dithionite under anaerobic conditions leads to restoration of activity and bleaching of the spectrum. Structural analysis of the oxidized species reveals a dinuclear iron metallocenter bridged by a lysine carbamate, closely resembling the traditional nickel-urease active site. Although the iron-urease is less active than the nickel-enzyme, its activity allows H. mustelae to survive the carnivore's low-nickel gastric environment.


    Organizational Affiliation

    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fusion of urease beta and gamma subunits
A, D, G, J, M, P
225Helicobacter mustelae (strain ATCC 43772 / LMG 18044 / NCTC 12198 / 12198)Mutation(s): 0 
Gene Names: ureA2
EC: 3.5.1.5
Find proteins for D3UJ81 (Helicobacter mustelae (strain ATCC 43772 / LMG 18044 / NCTC 12198 / 12198))
Go to UniProtKB:  D3UJ81
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Urease subunit beta 2
C, F, I, L, O, R
568Helicobacter mustelae (strain ATCC 43772 / LMG 18044 / NCTC 12198 / 12198)Mutation(s): 0 
Gene Names: ureB (ureB2)
EC: 3.5.1.5
Find proteins for D3UJ80 (Helicobacter mustelae (strain ATCC 43772 / LMG 18044 / NCTC 12198 / 12198))
Go to UniProtKB:  D3UJ80
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
C, F, I, L, O, R
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
C, F, I, L, O, R
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
FME
Query on FME
A, D, G, J, M, P
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.177 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 166.980α = 90.00
b = 223.940β = 90.00
c = 395.870γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
BOSdata collection
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-08-24
    Type: Database references