Epoxide hydrolase

 

Epoxide hydrolases convert epoxides into more soluble and less toxic products, an essential process within cells. As a result, these enzymes have been found in a wide variety of organisms. Their ability to react enantioselectively with industrially important epoxides makes epoxide hydrolases promising bio-catalysts for the preparation of enantiomerically pure epoxides, and/or their corresponding vicinal diols.

 

Reference Protein and Structure

Sequence
O31243 UniProt (3.3.2.3) IPR000639 (Sequence Homologues) (PDB Homologues)
Biological species
Agrobacterium tumefaciens (Bacteria) Uniprot
PDB
1ehy - X-ray structure of the epoxide hydrolase from agrobacterium radiobacter ad1 (2.1 Å) PDBe PDBsum 1ehy
Catalytic CATH Domains
3.40.50.1820 CATHdb (see all for 1ehy)
Click To Show Structure

Enzyme Reaction (EC:3.3.2.10)

oxirane
CHEBI:27561ChEBI
+
water
CHEBI:15377ChEBI
→
ethylene glycol
CHEBI:30742ChEBI
Alternative enzyme names: Epoxide hydrase, Epoxide hydratase, Arene-oxide hydratase, Aryl epoxide hydrase, Trans-stilbene oxide hydrolase, SEH, Cytosolic epoxide hydrolase,

Enzyme Mechanism

Introduction

The mechanism involves two steps. In the first reaction an ester bond is formed between the enzyme and substrate by attack of the nucleophilic Asp 107 on the primary carbon of the substrate; in the second step this ester bond is hydrolysed by a water molecule, activated by the His275/Asp246 pair. The anionic tetrahedral intermediate is stabilised by hydrogen bond interactions with the backbone amide nitrogens of Phe 108 and Trp 38.

Catalytic Residues Roles

UniProt PDB* (1ehy)
Tyr152 Tyr152A This residue is less well conserved that Tyr215, but also forms a hydrogen bond with the epoxide oxygen so could also act as the general acid/base. However, it is more likely to help stabilise the negatively charged Tyr215 that results from the removal of its proton. increase basicity, electrostatic stabiliser
Asp107 Asp107A Acts as a nucleophile, forming a covalent bond with the epoxide substrate. covalently attached, nucleophile, increase acidity, electrofuge, electrophile
His275 His275A Acts as a general acid/base. Part of a catalytic dyad with Asp246. proton acceptor, proton donor
Phe108 (main-N), Trp38 (main-N) Phe108A (main-N), Trp38A (main-N) Helps activate the nucleophilic Asp side chain. Helps stabilise the reactive intermediates and transition states. electrostatic stabiliser
Asp246 Asp246A Activates the general acid/base His275. increase basicity, electrostatic stabiliser
Tyr215 Tyr215A Possible general acid/base that protonates the epoxide oxygen during the step in which the nucleophilic aspartate forms a covalent bond with the substrate. proton acceptor, proton donor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, bimolecular nucleophilic addition, overall reactant used, enzyme-substrate complex formation, enzyme-substrate complex cleavage, overall product formed, unimolecular elimination by the conjugate base, inferred reaction step, native state of enzyme regenerated

References

  1. Nardini M et al. (1999), J Biol Chem, 274, 14579-14586. The X-ray Structure of Epoxide Hydrolase from Agrobacterium radiobacter AD1: AN ENZYME TO DETOXIFY HARMFUL EPOXIDES. DOI:10.1074/jbc.274.21.14579. PMID:10329649.
  2. Lonsdale R et al. (2012), Biochemistry, 51, 1774-1786. Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling. DOI:10.1021/bi201722j. PMID:22280021.
  3. Blée E et al. (2005), J Biol Chem, 280, 6479-6487. Soybean epoxide hydrolase: identification of the catalytic residues and probing of the reaction mechanism with secondary kinetic isotope effects. DOI:10.1074/jbc.M411366200. PMID:15596432.

Step 1. Asp107 initiates a nucleophilic attack on the epoxide, forming an covalently bound intermediate with concommittant abstraction of a proton from Tyr215.

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Catalytic Residues Roles

Residue Roles
Trp38A (main-N) electrostatic stabiliser
Phe108A (main-N) electrostatic stabiliser
Tyr152A electrostatic stabiliser
Asp107A nucleophile
Tyr215A proton donor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, overall reactant used, enzyme-substrate complex formation

Step 2. His275 abstracts a proton from the substrate water, which attacks the bound aspartate residue.

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Catalytic Residues Roles

Residue Roles
Trp38A (main-N) electrostatic stabiliser
Phe108A (main-N) electrostatic stabiliser
Tyr152A electrostatic stabiliser
Asp246A increase basicity
Asp107A covalently attached
His275A proton acceptor
Asp107A electrophile

Chemical Components

proton transfer, overall reactant used, ingold: bimolecular nucleophilic addition

Step 3. The oxyanion collapses, eliminating the product and re-forming the asparate residue.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Trp38A (main-N) electrostatic stabiliser
Phe108A (main-N) electrostatic stabiliser
Tyr152A electrostatic stabiliser
Asp246A electrostatic stabiliser
Asp107A electrofuge

Chemical Components

enzyme-substrate complex cleavage, overall product formed, proton transfer, ingold: unimolecular elimination by the conjugate base
Download: Image, Marvin File
Download: Image, Marvin File

Step 1. Asp107 initiates a nucleophilic attack on the epoxide, forming an covalently bound intermediate with concommittant abstraction of a proton from Tyr215.

Step 2. His275 abstracts a proton from the substrate water, which attacks the bound aspartate residue.

Step 3. The oxyanion collapses, eliminating the product and re-forming the asparate residue.

Products.

Products.

Contributors

James W. Murray, Craig Porter, Gemma L. Holliday