6JC4

Crystal structure of the urease accessory protein UreF from Klebsiella pneumoniae

• PDB DOI:  https://doi.org/10.2210/pdb6JC4/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-28 Released: 2020-01-29 
• Deposition Author(s): Wu, W., Zhang, Q., Bartlam, M.
• Funding Organization(s): National Natural Science Foundation of China, Ministry of Science and Technology (China)

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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 

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

• PubMed: 35102896 
• 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.

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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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114.85 kDa 
• Atom Count: 6,715 
• Modelled Residue Count: 800 
• Deposited Residue Count: 1,028 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease accessory protein UreF	A, B, C, D	257	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: ureF, ureF_1, ureF_2, NCTC204_02890, NCTC5052_03968, NCTC8849_05426, NCTC9637_01222, NCTC9661_01459, SAMEA104305404_01442, SAMEA24002668_02244
UniProt
Find proteins for A6TE44 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TE44  Go to UniProtKB:  A6TE44

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 = 121.886	α = 90
b = 121.886	β = 90
c = 63.578	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Wu, W., Zhang, Q., Bartlam, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570128
Ministry of Science and Technology (China)	China	2014CB560709

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2022-02-09
  Changes: Database references