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TitleExploring the conformational space of the mobile flap in Sporosarcina pasteurii urease by cryo-electron microscopy.
Journal, issue, pagesInt J Biol Macromol, Vol. 283, Issue Pt 3, Page 137904, Year 2024
Publish dateNov 20, 2024
AuthorsLuca Mazzei / Giancarlo Tria / Stefano Ciurli / Michele Cianci /
PubMed AbstractTo fully understand enzymatic dynamics, it is essential to explore the complete conformational space of a biological catalyst. The catalytic mechanism of the nickel-dependent urease, the most ...To fully understand enzymatic dynamics, it is essential to explore the complete conformational space of a biological catalyst. The catalytic mechanism of the nickel-dependent urease, the most efficient enzyme known, holds significant relevance for medical, pharmaceutical, and agro-environmental applications. A critical aspect of urease function is the conformational change of a helix-turn-helix motif that covers the active site cavity, known as the mobile flap. This motif has been observed in either an open or a closed conformation through X-ray crystallography studies and has been proposed to stabilize the coordination of a urea molecule to the essential dinuclear Ni(II) cluster in the active site, a requisite for subsequent substrate hydrolysis. This study employs cryo-electron microscopy (cryo-EM) to investigate the transient states within the conformational space of the mobile flap, devoid of the possible constraints of crystallization conditions and solid-state effects. By comparing two cryo-EM structures of Sporosarcina pasteurii urease, one in its native form and the other inhibited by N-(n-butyl) phosphoric triamide (NBPTO), we have unprecedently identified an intermediate state between the open and the catalytically efficient closed conformation of the helix-turn-helix motif, suggesting a role of its tip region in this transition between the two states.
External linksInt J Biol Macromol / PubMed:39571870
MethodsEM (single particle)
Resolution2.92 - 3.12 Å
Structure data

51450

9gml

EMDB-51450, PDB-9gml:
Cryo-EM structure of Sporosarcina pasteurii urease
Method: EM (single particle) / Resolution: 3.12 Å

51478

9gnr

EMDB-51478, PDB-9gnr:
Cryo-EM structure of Sporosarcina pasteurii urease inhibited by NBPTO
Method: EM (single particle) / Resolution: 2.92 Å

Chemicals

ChemComp-NI:
NICKEL (II) ION

ChemComp-OH:
HYDROXIDE ION

ChemComp-HOH:
WATER

ChemComp-2PA:
DIAMIDOPHOSPHATE

Source
  • sporosarcina pasteurii (bacteria)
KeywordsHYDROLASE / Urease / enzyme / Nickel / urea / NBPTO

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