8HC1

CryoEM structure of Helicobacter pylori UreFD/urease complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Delivering a toxic metal to the active site of urease.

Nim, Y.S.Fong, I.Y.H.Deme, J.Tsang, K.L.Caesar, J.Johnson, S.Pang, L.T.H.Yuen, N.M.H.Ng, T.L.C.Choi, T.Wong, Y.Y.H.Lea, S.M.Wong, K.B.

(2023) Sci Adv 9: eadf7790-eadf7790

  • DOI: https://doi.org/10.1126/sciadv.adf7790
  • Primary Citation of Related Structures:  
    8HC1, 8HCN

  • PubMed Abstract: 

    Urease is a nickel (Ni) enzyme that is essential for the colonization of Helicobacter pylori in the human stomach. To solve the problem of delivering the toxic Ni ion to the active site without diffusing into the cytoplasm, cells have evolved metal carrier proteins, or metallochaperones, to deliver the toxic ions to specific protein complexes. Ni delivery requires urease to form an activation complex with the urease accessory proteins UreFD and UreG. Here, we determined the cryo-electron microscopy structures of H. pylori UreFD/urease and Klebsiella pneumoniae UreD/urease complexes at 2.3- and 2.7-angstrom resolutions, respectively. Combining structural, mutagenesis, and biochemical studies, we show that the formation of the activation complex opens a 100-angstrom-long tunnel, where the Ni ion is delivered through UreFD to the active site of urease.


  • Organizational Affiliation

    School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urease subunit alpha238Helicobacter pylori 26695Mutation(s): 0 
Gene Names: ureAhpuAHP_0073
EC: 3.5.1.5
UniProt
Find proteins for P14916 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P14916 
Go to UniProtKB:  P14916
Entity Groups  
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UniProt GroupP14916
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Urease subunit beta569Helicobacter pylori 26695Mutation(s): 0 
Gene Names: ureBhpuBHP_0072
EC: 3.5.1.5
UniProt
Find proteins for P69996 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P69996 
Go to UniProtKB:  P69996
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UniProt GroupP69996
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Urease accessory protein UreH273Helicobacter pylori 26695Mutation(s): 1 
Gene Names: ureHHP_0067
UniProt
Find proteins for Q09067 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore Q09067 
Go to UniProtKB:  Q09067
Entity Groups  
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UniProt GroupQ09067
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Urease accessory protein UreF254Helicobacter pylori 26695Mutation(s): 2 
Gene Names: ureFHP_0069
UniProt
Find proteins for Q09065 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore Q09065 
Go to UniProtKB:  Q09065
Entity Groups  
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UniProt GroupQ09065
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong KongC4041-18E, C4033-19EF, C4012-16E, 14117321, AoE/M-403/16, AoE/M-05/12
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--
Wellcome TrustUnited Kingdom219477
Medical Research Council (MRC, United Kingdom)United KingdomS021264

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release