8HCN

CryoEM Structure of Klebsiella pneumoniae UreD/urease complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urease subunit gamma
A, E, I
100Klebsiella pneumoniaeMutation(s): 0 
EC: 3.5.1.5
UniProt
Find proteins for Q02943 (Klebsiella pneumoniae)
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Go to UniProtKB:  Q02943
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UniProt GroupQ02943
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Urease subunit beta
B, F, J
106Klebsiella pneumoniaeMutation(s): 0 
EC: 3.5.1.5
UniProt
Find proteins for W9BBU3 (Klebsiella pneumoniae)
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UniProt GroupW9BBU3
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Urease subunit alpha
C, G, K
567Klebsiella pneumoniaeMutation(s): 0 
Gene Names: ureCureC_1DDJ63_24795NCTC13443_06457NCTC5052_03970SAMEA3649733_03670SAMEA3727643_03166
EC: 3.5.1.5
UniProt
Find proteins for A0A060VJP5 (Klebsiella pneumoniae)
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UniProt GroupA0A060VJP5
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Urease accessory protein UreD
D, H, L
282Klebsiella pneumoniaeMutation(s): 0 
Gene Names: ureDDDJ63_24810
UniProt
Find proteins for A0A9Q6A135 (Klebsiella pneumoniae)
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UniProt GroupA0A9Q6A135
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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