6QDY image
Entry Detail
PDB ID:
6QDY
Keywords:
Title:
The crystal structure of Sporosarcina pasteurii urease in complex with its substrate urea
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2019-01-03
Release Date:
2019-11-13
Method Details:
Experimental Method:
Resolution:
1.42 Å
R-Value Free:
0.11
R-Value Work:
0.09
R-Value Observed:
0.09
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
The Structure of the Elusive Urease-Urea Complex Unveils the Mechanism of a Paradigmatic Nickel-Dependent Enzyme.
Angew.Chem.Int.Ed.Engl. 58 7415 7419 (2019)
PMID: 30969470 DOI: 10.1002/anie.201903565

Abstact

Urease, the most efficient enzyme known, contains an essential dinuclear NiII cluster in the active site. It catalyzes the hydrolysis of urea, inducing a rapid pH increase that has negative effects on human health and agriculture. Thus, the control of urease activity is of utmost importance in medical, pharmaceutical, and agro-environmental applications. All known urease inhibitors are either toxic or inefficient. The development of new and efficient chemicals able to inhibit urease relies on the knowledge of all steps of the catalytic mechanism. The short (microseconds) lifetime of the urease-urea complex has hampered the determination of its structure. The present study uses fluoride to substitute the hydroxide acting as the co-substrate in the reaction, preventing the occurrence of the catalytic steps that follow substrate binding. The 1.42 Å crystal structure of the urease-urea complex, reported here, resolves the enduring debate on the mechanism of this metalloenzyme.

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