9GML

Cryo-EM structure of Sporosarcina pasteurii urease

9GML の概要

• エントリーDOI: 10.2210/pdb9gml/pdb
• EMDBエントリー: 51450
• 分子名称: Urease subunit gamma, Urease subunit beta, Urease subunit alpha, ... (6 entities in total)
• 機能のキーワード: urease, enzyme, nickel, urea, hydrolase
• 由来する生物種: Sporosarcina pasteurii; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 86820.47

構造登録者

Mazzei, L.,Tria, G.,Ciurli, S.,Cianci, M. (登録日: 2024-08-29, 公開日: 2025-07-23)

主引用文献

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

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: 39571870
DOI: 10.1016/j.ijbiomac.2024.137904

実験手法

ELECTRON MICROSCOPY (3.12 Å)