6ZO1 image
Entry Detail
PDB ID:
6ZO1
Title:
1.61 A resolution 3,5-dimethylcatechol (3,5-dimethylbenzene-1,2-diol) inhibited Sporosarcina pasteurii urease
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2020-07-07
Release Date:
2020-12-23
Method Details:
Experimental Method:
Resolution:
1.61 Å
R-Value Free:
0.15
R-Value Work:
0.13
Space Group:
P 63 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Urease subunit gamma
Chain IDs:A (auth: AAA)
Chain Length:100
Number of Molecules:1
Biological Source:Sporosarcina pasteurii
Polymer Type:polypeptide(L)
Description:Urease subunit beta
Chain IDs:B (auth: BBB)
Chain Length:122
Number of Molecules:1
Biological Source:Sporosarcina pasteurii
Polymer Type:polypeptide(L)
Description:Urease subunit alpha
Chain IDs:C (auth: CCC)
Chain Length:570
Number of Molecules:1
Biological Source:Sporosarcina pasteurii
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CXM A MET modified residue
KCX C LYS modified residue
QO5 C CYS modified residue
Primary Citation
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.
Angew.Chem.Int.Ed.Engl. 60 6029 6035 (2021)
PMID: 33245574 DOI: 10.1002/anie.202014706

Abstact

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.

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Primary Citation of related structures