9GML
Cryo-EM structure of Sporosarcina pasteurii urease
Summary for 9GML
| Entry DOI | 10.2210/pdb9gml/pdb |
| EMDB information | 51450 |
| Descriptor | Urease subunit gamma, Urease subunit beta, Urease subunit alpha, ... (6 entities in total) |
| Functional Keywords | urease, enzyme, nickel, urea, hydrolase |
| Biological source | Sporosarcina pasteurii More |
| Total number of polymer chains | 3 |
| Total formula weight | 86820.47 |
| Authors | |
| Primary citation | Mazzei, L.,Tria, G.,Ciurli, S.,Cianci, M. Exploring the conformational space of the mobile flap in Sporosarcina pasteurii urease by cryo-electron microscopy. Int.J.Biol.Macromol., 283:137904-137904, 2024 Cited by PubMed Abstract: 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. PubMed: 39571870DOI: 10.1016/j.ijbiomac.2024.137904 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.12 Å) |
Structure validation
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