6ZO2

1.65 A resolution 4,5-dimethylcatechol (4,5-dimethylbenzene-1,2-diol) inhibited Sporosarcina pasteurii urease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.134 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Inhibition of Urease, a Ni-Enzyme: The Reactivity of a Key Thiol With Mono- and Di-Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies.

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

(2021) Angew Chem Int Ed Engl 60: 6029-6035

  • DOI: https://doi.org/10.1002/anie.202014706

  • PubMed Abstract: 

    The inhibition of urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) by a class of six aromatic poly-hydroxylated molecules, namely mono- and dimethyl-substituted catechols, was investigated on the basis of the inhibitory efficiency of the catechol scaffold. The aim was to probe the key step of a mechanism proposed for the inhibition of SPU by catechol, namely the sulfanyl radical attack on the aromatic ring, as well as to obtain critical information on the effect of substituents of the catechol aromatic ring on the inhibition efficacy of its derivatives. The crystal structures of all six SPU-inhibitors complexes, determined at high resolution, as well as kinetic data obtained on JBU and theoretical studies of the reaction mechanism using quantum mechanical calculations, revealed the occurrence of an irreversible inactivation of urease by means of a radical-based autocatalytic multistep mechanism, and indicate that, among all tested catechols, the mono-substituted 3-methyl-catechol is the most efficient inhibitor for urease.


  • Organizational Affiliation

    Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urease subunit gammaA [auth AAA]100Sporosarcina pasteuriiMutation(s): 0 
EC: 3.5.1.5
UniProt
Find proteins for A0A0H3YGY5 (Sporosarcina pasteurii)
Explore A0A0H3YGY5 
Go to UniProtKB:  A0A0H3YGY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3YGY5
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
JA [auth CCC]
K [auth AAA]
KA [auth CCC]
L [auth AAA]
LA [auth CCC]
JA [auth CCC],
K [auth AAA],
KA [auth CCC],
L [auth AAA],
LA [auth CCC],
MA [auth CCC],
N [auth BBB],
NA [auth CCC],
O [auth BBB],
OA [auth CCC],
P [auth BBB]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth CCC]
BA [auth CCC]
CA [auth CCC]
D [auth AAA]
DA [auth CCC]
AA [auth CCC],
BA [auth CCC],
CA [auth CCC],
D [auth AAA],
DA [auth CCC],
E [auth AAA],
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],
J [auth AAA],
M [auth BBB],
T [auth CCC],
U [auth CCC],
V [auth CCC],
W [auth CCC],
X [auth CCC],
Y [auth CCC],
Z [auth CCC]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
Q [auth CCC],
R [auth CCC]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
OH
Query on OH

Download Ideal Coordinates CCD File 
S [auth CCC]HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Modified Residues  3 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
QO2
Query on QO2
C [auth CCC]L-PEPTIDE LINKINGC11 H15 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.134 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.64α = 90
b = 131.64β = 90
c = 189.254γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description