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Structure-function relationship between soluble epoxide hydrolases structure and their tunnel network.

Karolina Mitusińska1, Piotr Wojsa1, Maria Bzówka1

  • 1Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland.

Computational and Structural Biotechnology Journal
|January 13, 2022
PubMed
Summary

Soluble epoxide hydrolases (sEHs) use tunnel networks for catalysis. Enzyme structure and tunnel architecture correlate with evolutionary history, guiding protein engineering for improved enzyme function.

Keywords:
CH65-EH, soluble epoxide hydrolase from an unknown source, sampled in hot springs in ChinaProtein engineeringSibe-EH, soluble epoxide hydrolase from an unknown source, sampled in hot springs in RussiaSoluble epoxide hydrolasesStEH1, Solanum tuberosum soluble epoxide hydrolaseStructure–function relationshipTrEH, Trichoderma reesei soluble epoxide hydrolaseTunnel networkVrEH2, Vigna radiata soluble epoxide hydrolasebmEH, Bacillus megaterium soluble epoxide hydrolasehsEH, Homo sapiens soluble epoxide hydrolasemsEH, Mus musculus soluble epoxide hydrolasesEHs, soluble epoxide hydrolases

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Enzymology

Background:

  • Enzymes with buried active sites rely on tunnels for substrate access and product release.
  • Soluble epoxide hydrolases (sEHs) are a key class of enzymes with such architecture.

Purpose of the Study:

  • To analyze the functionality of the sEH tunnel network.
  • To correlate tunnel architecture with enzyme structure, evolutionary lineage, and substrate preferences.

Main Methods:

  • Comparative analysis of sEH structures and tunnel networks.
  • Classification of sEHs into groups based on structural and functional tunnel characteristics.
  • Integration of structural data with evolutionary and substrate specificity information.

Main Results:

  • sEHs were categorized into three distinct groups based on their tunnel network architecture.
  • Tunnel network structure strongly correlated with the evolutionary lineage of the enzyme's source organism.
  • Significant structural variations, attributed to fragment insertions, were observed between different sEH groups.

Conclusions:

  • The tunnel network architecture of sEHs is a significant evolutionary marker.
  • Understanding tunnel network functionality aids in predicting enzyme behavior and substrate specificity.
  • This knowledge can inform protein engineering strategies for both large modifications and fine-tuning of enzyme activity.