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TitleStructural Analysis and Molecular Dynamics Simulations of Urease From Ureaplasma parvum.
Journal, issue, pagesJ Mol Biol, Vol. 437, Issue 21, Page 169368, Year 2025
Publish dateAug 5, 2025
AuthorsHeng Ning Wu / Junso Fujita / Yukiko Nakura / Masao Inoue / Koichiro Suzuki / Toru Ekimoto / Bingjie Yin / Yohta Fukuda / Kazuo Harada / Tsuyoshi Inoue / Mitsunori Ikeguchi / Keiichi Namba / Itaru Yanagihara /
PubMed AbstractUreaplasma 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, ...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.
External linksJ Mol Biol / PubMed:40752870
MethodsEM (single particle)
Resolution2.03 Å
Structure data

60854

9it2

EMDB-60854, PDB-9it2:
Cryo-EM structure of urease from Ureaplasma parvum
Method: EM (single particle) / Resolution: 2.03 Å

Chemicals

ChemComp-BME:
BETA-MERCAPTOETHANOL

ChemComp-NI:
NICKEL (II) ION

ChemComp-HOH:
WATER

Source
  • ureaplasma parvum serovar 3 (strain atcc 700970) (bacteria)
KeywordsHYDROLASE / urease

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