6JC4

Crystal structure of the urease accessory protein UreF from Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural characterization of the urease accessory protein UreF from Klebsiella pneumoniae.

Liu, S.Wu, W.Zhao, Q.Liang, H.Che, S.Zhang, H.Liu, R.Zhang, Q.Bartlam, M.

(2022) Acta Crystallogr F Struct Biol Commun 78: 75-80

  • DOI: https://doi.org/10.1107/S2053230X22000474
  • Primary Citation of Related Structures:  
    6JC4

  • PubMed Abstract: 

    Klebsiella pneumoniae is an opportunistic pathogen that mostly affects those with weakened immune systems. Urease is a vital enzyme that can hydrolyze urea to ammonia and carbon dioxide as a source of nitrogen for growth. Urease is also a K. pneumoniae virulence factor that enables survival of the bacterium under nutrient-limiting conditions. UreF, an important nickel-binding urease accessory protein, is involved in the insertion of Ni 2+ into the active site of urease. Here, the crystal structure of UreF from K. pneumoniae (KpUreF) is reported. Functional data show that KpUreF forms a stable dimer in solution. These results may provide a starting point for the design of urease inhibitors.


  • Organizational Affiliation

    College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Protein Science, Nankai University, 38 Tongyan Road, Tianjin 300350, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urease accessory protein UreF
A, B, C, D
257Klebsiella pneumoniaeMutation(s): 0 
Gene Names: ureFureF_1ureF_2NCTC204_02890NCTC5052_03968NCTC8849_05426NCTC9637_01222NCTC9661_01459SAMEA104305404_01442SAMEA24002668_02244
UniProt
Find proteins for A6TE44 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6TE44 
Go to UniProtKB:  A6TE44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6TE44
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.886α = 90
b = 121.886β = 90
c = 63.578γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31570128
Ministry of Science and Technology (China)China2014CB560709

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection, Refinement description