7P7O | pdb_00007p7o

X-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE INHIBITED BY THE GOLD(I)-DIPHOSPHINE COMPOUND Au(PEt3)2Cl DETERMINED AT 1.87 ANGSTROMS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.210 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.167 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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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 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.

Macromolecule Content 

  • Total Structure Weight: 89.58 kDa 
  • Atom Count: 6,880 
  • Modeled Residue Count: 785 
  • Deposited Residue Count: 792 
  • Unique protein chains: 3

Macromolecules

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|  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
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|  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
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UniProt GroupP41021
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AUF

Query on AUF


Download:Ideal Coordinates CCD File
T [auth CCC],
U [auth CCC],
V [auth CCC]		triethylphosphanuidylgold(1+)
C6 H15 Au P
NKNLIDCIHVTIMI-UHFFFAOYSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
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],
F [auth AAA],
FA [auth CCC],
G [auth AAA],
GA [auth CCC],
H [auth AAA],
HA [auth CCC],
I [auth AAA],
IA [auth CCC],
K [auth BBB],
L [auth BBB],
W [auth CCC],
X [auth CCC],
Y [auth CCC],
Z [auth CCC]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO


Download:Ideal Coordinates CCD File
D [auth AAA]
E [auth AAA]
J [auth BBB]
O [auth CCC]
Q [auth CCC]
D [auth AAA],
E [auth AAA],
J [auth BBB],
O [auth CCC],
Q [auth CCC],
R [auth CCC],
S [auth CCC]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI

Query on NI


Download:Ideal Coordinates CCD File
M [auth CCC],
N [auth CCC]		NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
O

Query on O


Download:Ideal Coordinates CCD File
P [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: 1.87 Å
  • R-Value Free:  0.210 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.167 (DCC) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.797α = 90
b = 131.797β = 90
c = 189.381γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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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