4AC7

The crystal structure of Sporosarcina pasteurii urease in complex with citrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.117 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

  • DOI: 10.1007/s00775-013-0983-7
  • Also Cited By: 4CEU, 4CEX

  • PubMed Abstract: 
  • Urease, the enzyme that catalyses the hydrolysis of urea, is a virulence factor for a large number of ureolytic bacterial human pathogens. The increasing resistance of these pathogens to common antibiotics as well as the need to control urease activi ...

    Urease, the enzyme that catalyses the hydrolysis of urea, is a virulence factor for a large number of ureolytic bacterial human pathogens. The increasing resistance of these pathogens to common antibiotics as well as the need to control urease activity to improve the yield of soil nitrogen fertilization in agricultural applications has stimulated the development of novel classes of molecules that target urease as enzyme inhibitors. We report on the crystal structure at 1.50-Å resolution of a complex formed between citrate and urease from Sporosarcina pasteurii, a widespread and highly ureolytic soil bacterium. The fit of the ligand to the active site involves stabilizing interactions, such as a carboxylate group that binds the nickel ions at the active site and several hydrogen bonds with the surrounding residues. The citrate ligand has a significantly extended structure compared with previously reported ligands co-crystallized with urease and thus represents a unique and promising scaffold for the design of new, highly active, stable, selective inhibitors.


    Related Citations: 
    • 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 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
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

    Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UREASE SUBUNIT GAMMA
A
100Sporosarcina pasteuriiGene 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 pasteuriiGene 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 pasteuriiGene Names: ureC
EC: 3.5.1.5
Find proteins for P41020 (Sporosarcina pasteurii)
Go to UniProtKB:  P41020
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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

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Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
OH
Query on OH

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Download CCD File 
C
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
FLC
Query on FLC

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Download CCD File 
C
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
NI
Query on NI

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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: 1.5 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.117 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 131.555α = 90.00
b = 131.555β = 90.00
c = 189.521γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references
  • Version 1.2: 2014-12-03
    Type: Data collection