8Q2E image
Entry Detail
PDB ID:
8Q2E
Keywords:
Title:
The 1.68-A X-ray crystal structure of Sporosarcina pasteurii urease inhibited by thiram and bound to dimethylditiocarbamate
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2023-08-02
Release Date:
2023-11-01
Method Details:
Experimental Method:
Resolution:
1.68 Å
R-Value Free:
0.16
R-Value Work:
0.13
R-Value Observed:
0.13
Space Group:
P 63 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Urease subunit gamma
Chain IDs:A
Chain Length:100
Number of Molecules:1
Biological Source:Sporosarcina pasteurii
Polymer Type:polypeptide(L)
Description:Urease subunit beta
Chain IDs:B
Chain Length:122
Number of Molecules:1
Biological Source:Sporosarcina pasteurii
Polymer Type:polypeptide(L)
Description:Urease subunit alpha
Chain IDs:C
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
Primary Citation
Kinetic and structural details of urease inactivation by thiuram disulphides.
J.Inorg.Biochem. 250 112398 112398 (2023)
PMID: 37879152 DOI: 10.1016/j.jinorgbio.2023.112398

Abstact

This paper reports on the molecular details of the reactivity of urease, a nickel-dependent enzyme that catalyses the last step of organic nitrogen mineralization, with thiuram disulphides, a class of molecules known to inactivate the enzyme with high efficacy but for which the mechanism of action had not been yet established. IC50 values of tetramethylthiuram disulphide (TMTD or Thiram) and tetraethylthiuram disulphide (TETD or Disulfiram) in the low micromolar range were determined for plant and bacterial ureases. The X-ray crystal structure of Sporosarcina pasteurii urease inactivated by Thiram, determined at 1.68 Å resolution, revealed the presence of a covalent modification of the catalytically essential cysteine residue. This is located on the flexible flap that modulates the size of the active site channel and cavity. Formation of a Cys-S-S-C(S)-N(CH3)2 functionality responsible for enzyme inactivation was observed. Quantum-mechanical calculations carried out to rationalise the large reactivity of the active site cysteine support the view that a conserved histidine residue, adjacent to the cysteine in the active site flap, modulates the charge and electron density along the thiol SH bond by shifting electrons towards the sulphur atom and rendering the thiol proton more reactive. We speculate that this proton could be transferred to the nickel-coordinated urea amide group to yield a molecule of ammonia from the generated Curea-NH3+ functionality during catalysis.

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