9IT2

Cryo-EM structure of urease from Ureaplasma parvum

Summary for 9IT2

• Entry DOI: 10.2210/pdb9it2/pdb
• EMDB information: 60854
• Descriptor: Urease subunit gamma, Urease subunit beta, Urease subunit alpha, ... (6 entities in total)
• Functional Keywords: urease, hydrolase
• Biological source: Ureaplasma parvum serovar 3 (strain ATCC 700970); More
• Total number of polymer chains: 9
• Total formula weight: 268860.82

Authors

Fujita, J.,Namba, K.,Wu, H.N.,Yanagihara, I. (deposition date: 2024-07-19, release date: 2025-08-20)

Primary citation

Wu, H.N.,Fujita, J.,Nakura, Y.,Inoue, M.,Suzuki, K.,Ekimoto, T.,Yin, B.,Fukuda, Y.,Harada, K.,Inoue, T.,Ikeguchi, M.,Namba, K.,Yanagihara, I.
Structural Analysis and Molecular Dynamics Simulations of Urease From Ureaplasma parvum.
J.Mol.Biol., 437:169368-169368, 2025

PubMed Abstract: Ureaplasma is one of the smallest pathogenic bacteria, generating approximately 95% of its adenosine triphosphate (ATP) solely through urease. Studies on Ureaplasma parvum, a species of Ureaplasma, have confirmed that adding urease inhibitors inhibits bacterial growth. The K and V of the urease-mediated reaction were estimated to be 4.3 ± 0.2 mM and 3,333.3 ± 38.0 μmol NH/min/mg protein, respectively. The cryo-electron microscopy (cryo-EM) structure of Ureaplasma parvum urease (UPU) at a resolution of 2.03 Å reveals a trimer of heterotrimers comprising three proteins: UreA, UreB, and UreC. The active site is well conserved among the known ureases. However, the V of UPU was higher than that of most known ureases, including those ureases derived from Sporosarcina pasteurii (SPU) and Klebsiella aerogenes (KAU) with identical oligomeric state. All-atom molecular dynamics simulations showed that the flap and UreB are more open in UPU than SPU and KAU. His-tagged wild-type recombinant UPU (WT-rUPU) revealed estimated K and V values of 4.1 ± 0.3 mM and 769.2 ± 7.4 µmol NH/min/mg protein, respectively. Amino acid substitutions of recombinant UPUs within the flap region to SPU. Amongst the flap region variants, the V of K331N variant was 48-fold lower than that of WT-rUPU. ICP-MS analysis reveals that one molecule of UPU, WT-rUPU, and K331N-rUPU contains 3.7, 0.8, and 0.1 Ni atoms, respectively, suggesting that a wide-open flap of urease may contribute to delivering nickel into the enzyme, resulting in a high V. Ureaplasma evolved highly efficient UPU through a few amino acid substitutions in the disorganized loop of the mobile flap region.

PubMed: 40752870
DOI: 10.1016/j.jmb.2025.169368

Experimental method

ELECTRON MICROSCOPY (2.03 Å)