Klebsiella pneumoniae UreG in complex with GMPPNP and nickel

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

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This is version 1.3 of the entry. See complete history


Structural insights into how GTP-dependent conformational changes in a metallochaperone UreG facilitate urease maturation.

Yuen, M.H.Fong, Y.H.Nim, Y.S.Lau, P.H.Wong, K.B.

(2017) Proc Natl Acad Sci U S A 114: E10890-E10898

  • DOI: https://doi.org/10.1073/pnas.1712658114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The ability of metallochaperones to allosterically regulate the binding/release of metal ions and to switch protein-binding partners along the metal delivery pathway is essential to the metallation of the metalloenzymes. Urease, catalyzing the hydrolysis of urea into ammonia and carbon dioxide, contains two nickel ions bound by a carbamylated lysine in its active site. Delivery of nickel ions for urease maturation is dependent on GTP hydrolysis and is assisted by four urease accessory proteins UreE, UreF, UreG, and UreH(UreD). Here, we determined the crystal structure of the UreG dimer from Klebsiella pneumoniae in complex with nickel and GMPPNP, a nonhydrolyzable analog of GTP. Comparison with the structure of the GDP-bound Helicobacter pylori UreG ( Hp UreG) in the UreG 2 F 2 H 2 complex reveals large conformational changes in the G2 region and residues near the 66 CPH 68 metal-binding motif. Upon GTP binding, the side chains of Cys66 and His68 from each of the UreG protomers rotate toward each other to coordinate a nickel ion in a square-planar geometry. Mutagenesis studies on Hp UreG support the conformational changes induced by GTP binding as essential to dimerization of UreG, GTPase activity, in vitro urease activation, and the switching of UreG from the UreG 2 F 2 H 2 complex to form the UreE 2 G 2 complex with the UreE dimer. The nickel-charged UreE dimer, providing the sole source of nickel, and the UreG 2 F 2 H 2 complex could activate urease in vitro in the presence of GTP. Based on our results, we propose a mechanism of how conformational changes of UreG during the GTP hydrolysis/binding cycle facilitate urease maturation.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urease accessory protein UreG
A, B
200Klebsiella pneumoniae subsp. rhinoscleromatis SB3432Mutation(s): 0 
Gene Names: ureGKPR_4504
Find proteins for R4YE37 (Klebsiella pneumoniae subsp. rhinoscleromatis SB3432)
Explore R4YE37 
Go to UniProtKB:  R4YE37
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4YE37
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.553α = 90
b = 49.318β = 103.16
c = 129.708γ = 90
Software Package:
Software NamePurpose
xia2data reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Research Grants CouncilHong Kong14117314
Research Grants CouncilHong KongAoE/M-05/12
The Chinese University of Hong KongHong Kong3132814

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references
  • Version 1.2: 2018-01-03
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description