5XKT

Klebsiella pneumoniae UreG in complex with GMPPNP and nickel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.2 of the entry. See complete history


Literature

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: 10.1073/pnas.1712658114
  • Primary Citation of Related Structures:  
    5XKT

  • 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 ...

    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 kbwong@cuhk.edu.hk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Urease accessory protein UreGA, B200Klebsiella pneumoniae subsp. rhinoscleromatis SB3432Mutation(s): 0 
Gene Names: ureGKPR_4504
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth B]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing

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