Download MendeleyStructural Analysis and Molecular Dynamics Simulations of Urease From Ureaplasma parvum.
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.(2025) J Mol Biology 437: 169368-169368
- PubMed: 40752870
- DOI: https://doi.org/10.1016/j.jmb.2025.169368
- Primary Citation of Related Structures:
9IT2 - 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 m and V max of the urease-mediated reaction were estimated to be 4.3 ± 0.2 mM and 3,333.3 ± 38.0 μmol NH 3 /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 max 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 m and V max values of 4.1 ± 0.3 mM and 769.2 ± 7.4 µmol NH 3 /min/mg protein, respectively. Amino acid substitutions of recombinant UPUs within the flap region to SPU. Amongst the flap region variants, the V max 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 2+ atoms, respectively, suggesting that a wide-open flap of urease may contribute to delivering nickel into the enzyme, resulting in a high V max . Ureaplasma evolved highly efficient UPU through a few amino acid substitutions in the disorganized loop of the mobile flap region.
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi City 594-1101 Osaka, Japan.
Organizational Affiliation:
