7P7N

X-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE INHIBITED BY THE GOLD(I)-PHOSPHINE COMPOUND Au(PEt3)I DETERMINED AT 1.80 ANGSTROMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.155 

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Literature

Medicinal Au(I) compounds targeting urease as prospective antimicrobial agents: unveiling the structural basis for enzyme inhibition.

Mazzei, L.Massai, L.Cianci, M.Messori, L.Ciurli, S.

(2021) Dalton Trans 50: 14444-14452

  • DOI: https://doi.org/10.1039/d1dt02488d
  • Primary Citation of Related Structures:  
    7P7N, 7P7O

  • PubMed Abstract: 

    A few gold compounds were recently found to show antimicrobial properties in vitro , holding great promise for the discovery of new drugs to overcome antibiotic resistance. Here, the inhibition of the bacterial virulence factor urease by four Au(I)-compounds, namely Au(PEt 3 )Cl, Au(PEt 3 )Br, Au(PEt 3 )I and [Au(PEt 3 ) 2 ]Cl, obtained from the antiarthritic Au(I)-drug Auranofin and earlier reported to act as antimicrobials, is investigated. The three monophosphino Au(I) complexes showed IC 50 values in the 30-100 nM range, while the diphosphino Au(I) complex, though being less active, still showed a IC 50 value of 7 μM. The structural basis for this inhibition was provided by solving the crystal structures of urease co-crystallized with Au(PEt 3 )I and [Au(PEt 3 ) 2 ]Cl: at least two Au(I) ions bind the enzyme in a flap domain involved in the catalysis, thus obliterating enzyme activity. Peculiar changes observed in the two structures reveal implications for the mechanism of soft metal binding and enzyme inactivation.


  • Organizational Affiliation

    Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna, Italy. luca.mazzei2@unibo.it.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urease subunit gammaA [auth AAA]100Sporosarcina pasteuriiMutation(s): 2 
EC: 3.5.1.5
UniProt
Find proteins for P41022 (Sporosarcina pasteurii)
Explore P41022 
Go to UniProtKB:  P41022
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41022
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Urease subunit betaB [auth BBB]122Sporosarcina pasteuriiMutation(s): 0 
EC: 3.5.1.5
UniProt
Find proteins for P41021 (Sporosarcina pasteurii)
Explore P41021 
Go to UniProtKB:  P41021
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41021
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Urease subunit alphaC [auth CCC]570Sporosarcina pasteuriiMutation(s): 0 
EC: 3.5.1.5
UniProt
Find proteins for P41020 (Sporosarcina pasteurii)
Explore P41020 
Go to UniProtKB:  P41020
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41020
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AUF
Query on AUF

Download Ideal Coordinates CCD File 
R [auth CCC]triethylphosphanuidylgold(1+)
C6 H15 Au P
NKNLIDCIHVTIMI-UHFFFAOYSA-N
AU
Query on AU

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S [auth CCC],
T [auth CCC],
U [auth CCC],
V [auth CCC],
W [auth CCC]
GOLD ION
Au
ZBKIUFWVEIBQRT-UHFFFAOYSA-N
SO4
Query on SO4

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AA [auth CCC]
BA [auth CCC]
CA [auth CCC]
DA [auth CCC]
EA [auth CCC]
AA [auth CCC],
BA [auth CCC],
CA [auth CCC],
DA [auth CCC],
EA [auth CCC],
FA [auth CCC],
GA [auth CCC],
HA [auth CCC],
I [auth BBB],
IA [auth CCC],
J [auth BBB],
JA [auth CCC],
X [auth CCC],
Y [auth CCC],
Z [auth CCC]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

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D [auth AAA]
E [auth AAA]
F [auth AAA]
G [auth AAA]
H [auth BBB]
D [auth AAA],
E [auth AAA],
F [auth AAA],
G [auth AAA],
H [auth BBB],
KA [auth CCC],
LA [auth CCC],
M [auth CCC],
MA [auth CCC],
N [auth CCC],
NA [auth CCC],
P [auth CCC],
Q [auth CCC]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI
Query on NI

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K [auth CCC],
L [auth CCC]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
O
Query on O

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O [auth CCC]OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CXM
Query on CXM
A [auth AAA]L-PEPTIDE LINKINGC6 H11 N O4 SMET
KCX
Query on KCX
C [auth CCC]L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.155 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.645α = 90
b = 131.645β = 90
c = 189.2γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description