3QGA

3.0 A Model of Iron Containing Urease UreA2B2 from Helicobacter mustelae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 U S A 108: 13095-13099

  • DOI: https://doi.org/10.1073/pnas.1106915108
  • Primary Citation of Related Structures:  
    3QGA, 3QGK

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion of urease beta and gamma subunits225Helicobacter mustelae 12198Mutation(s): 0 
Gene Names: HMU13020ureA2
UniProt
Find proteins for D3UJ81 (Helicobacter mustelae (strain ATCC 43772 / LMG 18044 / NCTC 12198 / 12198))
Explore D3UJ81 
Go to UniProtKB:  D3UJ81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3UJ81
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Urease subunit beta 2568Helicobacter mustelae 12198Mutation(s): 0 
Gene Names: HMU13010ureB2
EC: 3.5.1.5
UniProt
Find proteins for D3UJ80 (Helicobacter mustelae (strain ATCC 43772 / LMG 18044 / NCTC 12198 / 12198))
Explore D3UJ80 
Go to UniProtKB:  D3UJ80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3UJ80
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
M [auth C]
N [auth C]
O [auth F]
P [auth F]
Q [auth I]
M [auth C],
N [auth C],
O [auth F],
P [auth F],
Q [auth I],
R [auth I],
S [auth L],
T [auth L],
U [auth O],
V [auth O],
W [auth R],
X [auth R]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
C [auth D]
E [auth G]
G [auth J]
I [auth M]
A,
C [auth D],
E [auth G],
G [auth J],
I [auth M],
K [auth P]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
KCX
Query on KCX
B [auth C]
D [auth F]
F [auth I]
H [auth L]
J [auth O]
B [auth C],
D [auth F],
F [auth I],
H [auth L],
J [auth O],
L [auth R]
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.98α = 90
b = 223.94β = 90
c = 395.87γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BOSdata collection
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-08-24
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection