4CEX

1.59 A resolution Fluoride inhibited Sporosarcina pasteurii urease

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.589 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Fluoride Inhibition of Sporosarcina Pasteurii Urease: Structure and Thermodynamics.

Benini, S., Cianci, M., Mazzei, L., Ciurli, S.

(2014) J.Biol.Inorg.Chem. 19: 1243

  • DOI: 10.1007/s00775-014-1182-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Urease is a nickel-dependent enzyme and a virulence factor for ureolytic bacterial human pathogens, but it is also necessary to convert urea, the most worldwide used fertilizer, into forms of nitrogen that can be taken up by crop plants. A strategy t ...

    Urease is a nickel-dependent enzyme and a virulence factor for ureolytic bacterial human pathogens, but it is also necessary to convert urea, the most worldwide used fertilizer, into forms of nitrogen that can be taken up by crop plants. A strategy to control the activity of urease for medical and agricultural applications is to use enzyme inhibitors. Fluoride is a known urease inhibitor, but the structural basis of its mode of inhibition is still undetermined. Here, kinetic studies on the fluoride-induced inhibition of urease from Sporosarcina pasteurii, a widespread and highly ureolytic soil bacterium, were performed using isothermal titration calorimetry and revealed a mixed competitive and uncompetitive mechanism. The pH dependence of the inhibition constants, investigated in the 6.5-8.0 range, reveals a predominant uncompetitive mechanism that increases by increasing the pH, and a lesser competitive inhibition that increases by lowering the pH. Ten crystal structures of the enzyme were independently determined using five crystals of the native form and five crystals of the protein crystallized in the presence of fluoride. The analysis of these structures revealed the presence of two fluoride anions coordinated to the Ni(II) ions in the active site, in terminal and bridging positions. The present study consistently supports an interaction of fluoride with the nickel centers in the urease active site in which one fluoride competitively binds to the Ni(II) ion proposed to coordinate urea in the initial step of the catalytic mechanism, while another fluoride uncompetitively substitutes the Ni(II)-bridging hydroxide, blocking its nucleophilic attack on urea.

    Related Citations: 
    • Molecular Details of Urease Inhibition by Boric Acid: Insights Into the Catalytic Mechanism.
      Benini, S.,Rypniewski, W.R.,Wilson, K.S.,Mangani, S.,Ciurli, S.
      (2004) J.Am.Chem.Soc. 126: 3714
    • The Complex of Bacillus Pasteurii Urease with Acetohydroxamate Anion from X-Ray Data at 1.55 A Resolution.
      Benini, S.,Rypniewski, W.R.,Wilson, K.S.,Miletti, S.,Ciurli, S.,Mangani, S.
      (2000) J.Biol.Inorg.Chem. 5: 110
    • A New Proposal for Urease Mechanism Based on the Crystal Structures of the Native and Inhibited Enzyme from Bacillus Pasteurii: Why Urea Hydrolysis Costs Two Nickels.
      Benini, S.,Rypniewski, W.R.,Wilson, K.S.,Miletti, S.,Ciurli, S.,Mangani, S.
      (1999) Structure 7: 205
    • The Complex of Bacillus Pasteurii Urease with Beta-Mercaptoethanol from X-Ray Data at 1.65 A Resolution
      Benini, S.,Ciurli, S.,Rypniewski, W.R.,Wilson, K.S.,Mangani, S.
      (1998) J.Biol.Inorg.Chem. 3: 268
    • Structure-Based Rationalization of Urease Inhibition by Phosphate: Novel Insights Into the Enzyme Mechanism.
      Benini, S.,Rypniewski, W.R.,Wilson, K.S.,Ciurli, S.,Mangani, S.
      (2001) J.Biol.Inorg.Chem. 6: 778
    • The Crystal Structure of Sporosarcina Pasteurii Urease in a Complex with Citrate Provides New Hints for Inhibitor Design.
      Benini, S.,Kosikowska, P.,Cianci, M.,Mazzei, L.,Vara, A.G.,Berlicki, L.,Ciurli, S.
      (2013) J.Biol.Inorg.Chem. 18: 391
    • Crystallization and Preliminary High-Resolution X-Ray Diffraction Analysis of Native and Beta-Mercaptoethanol-Inhibited Urease from Bacillus Pasteurii.
      Benini, S.,Ciurli, S.,Rypniewski, W.R.,Wilson, K.S.,Mangani, S.
      (1998) Acta Crystallogr.,Sect.D 54: 409

    Organizational Affiliation: 

    Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy, stefano.benini@unibz.it.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UREASE SUBUNIT GAMMA
A
100Sporosarcina pasteuriiMutation(s): 0 
Gene Names: ureA
EC: 3.5.1.5
Find proteins for P41022 (Sporosarcina pasteurii)
Go to UniProtKB:  P41022
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UREASE SUBUNIT BETA
B
126Sporosarcina pasteuriiMutation(s): 0 
Gene Names: ureB
EC: 3.5.1.5
Find proteins for P41021 (Sporosarcina pasteurii)
Go to UniProtKB:  P41021
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UREASE SUBUNIT ALPHA
C
570Sporosarcina pasteuriiMutation(s): 0 
Gene Names: ureC
EC: 3.5.1.5
Find proteins for P41020 (Sporosarcina pasteurii)
Go to UniProtKB:  P41020
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F
Query on F
Download SDF File 
Download CCD File 
C
FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI
Download SDF File 
Download CCD File 
C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
A
L-PEPTIDE LINKINGC6 H11 N O4 SMET
KCX
Query on KCX
C
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.589 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.130 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 131.331α = 90.00
b = 131.331β = 90.00
c = 188.882γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Database references
  • Version 1.2: 2014-12-17
    Type: Data collection, Database references
  • Version 1.3: 2018-03-07
    Type: Data collection