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Catalytic Site Atlas

CSA LITERATURE entry for 1nu3

E.C. namelimonene-1,2-epoxide hydrolase
SpeciesRhodococcus erythropolis (Bacteria)
E.C. Number (IntEnz) 3.3.2.8
CSA Homologues of 1nu31nww,2bng,
CSA Entries With UniProtID Q9ZAG3
CSA Entries With EC Number 3.3.2.8
PDBe Entry 1nu3
PDBSum Entry 1nu3
MACiE Entry 1nu3

Literature Report

IntroductionLimonene-1,2-epoxide hydrolase(LEH) catalyses the hydrolysis of limonene-1,2-epoxide to limonene-1,2-diol. This enzyme allows the bacterium Rhodococcus erythropolis to grow on limonene as a sole source of carbon and energy. The hydrolysis catalysed by LEH is enantioconvergent, therefore attracting wide interest in industrial applications.
MechansimThe catalysis follows a single-step push-pull mechanism. The active site consists of a Asp-Arg-Asp triad. Asp132 acts as a base to deprotonate a water molecule, which performs a nucleophilic attack at one of the ring carbons, forcing epoxide ring opening. At the same time, Asp101 donates a proton to the oxygen atom of the epoxide ring to encourage the ring opening. Each carboxylate group of Asp132 and Asp101 maintains a pair of hydrogen bonds with guanidino group of Arg99 during the reaction and Arg99 acts as a proton shuttle to reverse the charge of Asp132 and Asp101 after the reaction.
Reaction

Catalytic Sites for 1nu3

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgA9999macie:sideChainIt acts as a proton shuttle to reverse the charge of Asp 132 and Asp 101 after the reaction.
AspA101101macie:sideChainIt acts as a base to protonate the oxygen atom of the epoxide to encourage ring opening.
AspA132132macie:sideChainIt acts as a base to deprotonate a water molecule to promote its nucleophilic attack on one of the ring carbons, forcing epoxide ring opening.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgB9999macie:sideChainIt acts as a proton shuttle to reverse the charge of Asp 132 and Asp 101 after the reaction.
AspB101101macie:sideChainIt acts as a base to protonate the oxygen atom of the epoxide to encourage ring opening.
AspB132132macie:sideChainIt acts as a base to deprotonate a water molecule to promote its nucleophilic attack on one of the ring carbons, forcing epoxide ring opening.

Literature References

Notes:
Arand M
Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site.
EMBO J 2003 22 2583-2592
PubMed: 12773375
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