Structure of epoxide hydrolase 2 from Mangifera indica throws light on the substrate specificity determinants of plant epoxide hydrolases

Epoxide hydrolases (EHs) are a group of ubiquitous enzymes that catalyze hydrolysis of chemically reactive epoxides to yield corresponding dihydrodiols. Despite extensive studies on EHs from different clades, generic rules governing their substrate specificity determinants have remained elusive. Her...

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Bibliographic Details
Published in:Biochemical and biophysical research communications 2024-11, Vol.733, p.150444, Article 150444
Main Authors: Bhoite, Ashwini, Gaur, Neeraj K., Palange, Megha, Kontham, Ravindar, Gupta, Vidya, Kulkarni, Kiran
Format: Article
Language:English
Subjects:
Enantioselectivity
Epoxide hydrolase
Molecular dynamics simulation
Regioselectivity
X-ray crystallography
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Summary:Epoxide hydrolases (EHs) are a group of ubiquitous enzymes that catalyze hydrolysis of chemically reactive epoxides to yield corresponding dihydrodiols. Despite extensive studies on EHs from different clades, generic rules governing their substrate specificity determinants have remained elusive. Here, we present structural, biochemical and molecular dynamics simulation studies on MiEH2, a plant epoxide hydrolase from Mangifera indica. Comparative structure-function analysis of nine homologs of MiEH2, which include a few AlphaFold structural models, show that the two conserved tyrosines (MiEH2Y152 and MiEH2Y232) from the lid domain dissect substrate binding tunnel into two halves, forming substrate-binding-pocket one (BP1) and two (BP2). This compartmentalization offers diverse binding modes to their substrates, as exemplified by the binding of smaller aromatic substrates, such as styrene oxide (SO). Docking and molecular dynamics simulations reveal that the linear epoxy fatty acid substrates predominantly occupy BP1, while the aromatic substrates can bind to either BP1 or BP2. Furthermore, SO preferentially binds to BP2, by stacking against catalytically important histidine (MiEH2H297) with the conserved lid tyrosines engaging its epoxide oxygen. Residue (MiEH2L263) next to the catalytic aspartate (MiEH2D262) modulates substrate binding modes. Thus, the divergent binding modes correlate with the differential affinities of the EHs for their substrates. Furthermore, long-range dynamical coupling between the lid and core domains critically influences substrate enantioselectivity in plant EHs. •Structure of epoxide hydrolase from Mangifera indica, MiEH2, has been determined.•Sequence-structure comparison of plant EHs unravel substrate specificity determinants.•Docking and MD simulations highlight enantiospecificity defining residues for SO.•Dynamical sectoral analysis shows long-range coupling between core and lid residues.
ISSN:0006-291X
1090-2104
1090-2104
DOI:10.1016/j.bbrc.2024.150444