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The urea cycle describes how liver cells convert ammonia to urea. Ammonia is a toxic waste product of protein catabolism. Land animals must convert ammonia into the less toxic urea which can be safely eliminated by the kidneys through urine. Marine animals excrete ammonia directly, and the surrounding water dilutes the ammonia to safe levels.
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Hot Biological Catalysis: Isothermal Titration Calorimetry to Characterize Enzymatic Reactions
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Structural Analysis and Molecular Dynamics Simulations of Urease From Ureaplasma parvum.

Heng Ning Wu1, Junso Fujita2, Yukiko Nakura1

  • 1Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi City 594-1101 Osaka, Japan.

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Summary

Ureaplasma parvum urease (UPU) is highly efficient due to its open flap structure, which facilitates nickel delivery and high activity. Key amino acid changes in the flap region significantly reduce UPU

Keywords:
Ureaplasmacryo-EMmobile flapmolecular dynamicsurease

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Area of Science:

  • Biochemistry
  • Microbiology
  • Structural Biology

Background:

  • Ureaplasma is a small pathogenic bacterium relying on urease for energy.
  • Urease inhibitors are known to impede Ureaplasma growth.
  • The kinetic parameters (Km and Vmax) of Ureaplasma parvum urease (UPU) have been characterized.

Purpose of the Study:

  • To elucidate the structural and functional basis for the high catalytic efficiency of Ureaplasma parvum urease (UPU).
  • To investigate the role of the flap region and nickel content in UPU's enzymatic activity.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) for structural determination of UPU.
  • All-atom molecular dynamics simulations to compare UPU with other ureases.
  • Site-directed mutagenesis of UPU flap region variants.
  • Inductively coupled plasma mass spectrometry (ICP-MS) for nickel quantification.

Main Results:

  • The cryo-EM structure of UPU revealed a unique trimer of heterotrimers with an open flap conformation.
  • UPU exhibited a significantly higher Vmax compared to ureases from Sporosarcina pasteurii (SPU) and Klebsiella aerogenes (KAU).
  • A specific mutation (K331N) in the flap region drastically reduced Vmax and nickel content, while the wild-type UPU had higher nickel content than recombinant variants.

Conclusions:

  • The open flap structure of UPU is crucial for its high catalytic efficiency, likely by facilitating nickel cofactor incorporation.
  • Specific amino acid substitutions in the flap region are responsible for Ureaplasma's evolution of a highly active urease.
  • Understanding UPU's mechanism provides insights into urease function and potential therapeutic targets.