5OL4

1.28 A resolution of Sporosarcina pasteurii urease inhibited in the presence of NBPT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.120 

wwPDB Validation 3D Report Full Report



Literature

Urease Inhibition in the Presence of N-(n-Butyl)thiophosphoric Triamide, a Suicide Substrate: Structure and Kinetics.

Mazzei, L.Cianci, M.Contaldo, U.Musiani, F.Ciurli, S.

(2017) Biochemistry 56: 5391-5404

  • DOI: 10.1021/acs.biochem.7b00750
  • Primary Citation of Related Structures:  
    5OL4

  • PubMed Abstract: 
  • The nickel-dependent enzyme urease is a virulence factor for a large number of pathogenic and antibiotic-resistant bacteria, as well as a negative factor for the efficiency of soil nitrogen fertilization for crop production. The use of urease inhibit ...

    The nickel-dependent enzyme urease is a virulence factor for a large number of pathogenic and antibiotic-resistant bacteria, as well as a negative factor for the efficiency of soil nitrogen fertilization for crop production. The use of urease inhibitors to offset these effects requires knowledge, at a molecular level, of their mode of action. The 1.28 Å resolution structure of the enzyme-inhibitor complex obtained upon incubation of Sporosarcina pasteurii urease with N-(n-butyl)thiophosphoric triamide (NBPT), a molecule largely utilized in agriculture, reveals the presence of the monoamidothiophosphoric acid (MATP) moiety, obtained upon enzymatic hydrolysis of the diamide derivative of NBPT (NBPD) to yield n-butyl amine. MATP is bound to the two Ni(II) ions in the active site of urease using a μ 2 -bridging O atom and terminally bound O and NH 2 groups, with the S atom of the thiophosphoric amide pointing away from the metal center. The mobile flap modulating the size of the active site cavity is found in the closed conformation. Docking calculations suggest that the interaction between urease in the open flap conformation and NBPD involves a role for the conserved αArg339 in capturing and orienting the inhibitor prior to flap closure. Calorimetric and spectrophotometric determinations of the kinetic parameters of this inhibition indicate the occurrence of a reversible slow inhibition mode of action, characterized, for both bacterial and plant ureases, by a very small value of the dissociation constant of the urease-MATP complex. No need to convert NBPT to its oxo derivative NBPTO, as previously proposed, is necessary for urease inhibition.


    Organizational Affiliation

    Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna , Bologna, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Urease subunit gammaA100Sporosarcina pasteuriiMutation(s): 0 
Gene Names: ureA
EC: 3.5.1.5
Find proteins for P41022 (Sporosarcina pasteurii)
Explore P41022 
Go to UniProtKB:  P41022
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Urease subunit betaB122Sporosarcina pasteuriiMutation(s): 0 
Gene Names: ureB
EC: 3.5.1.5
Find proteins for P41021 (Sporosarcina pasteurii)
Explore P41021 
Go to UniProtKB:  P41021
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Urease subunit alphaC570Sporosarcina pasteuriiMutation(s): 0 
Gene Names: ureC
EC: 3.5.1.5
Find proteins for P41020 (Sporosarcina pasteurii)
Explore P41020 
Go to UniProtKB:  P41020
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9XN
Query on 9XN

Download CCD File 
C
Phosphoramidothioic O,O-acid
H4 N O2 P S
RJBIAAZJODIFHR-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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A, B, C
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
AL-PEPTIDE LINKINGC6 H11 N O4 SMET
KCX
Query on KCX
CL-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.120 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.742α = 90
b = 131.742β = 90
c = 188.93γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release