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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 1gxs

E.C. namehydroxymandelonitrile lyase
SpeciesSorghum bicolor (Sorghum vulgare)
E.C. Number (IntEnz) 4.1.2.11
CSA Homologues of 1gxs
CSA Entries With UniProtID P52708
CSA Entries With EC Number 4.1.2.11
PDBe Entry 1gxs
PDBSum Entry 1gxs
MACiE Entry 1gxs

Literature Report

IntroductionHydroxynitrile lyases (HNLs)constitute a diverse family of enzymes that catalyse the stereospecific cleavage of a wide range of cyanohydrins into aldehydes or ketones and hydrogen cyanide. The release of HCN is a common defence of food plants against herbivores. The HNL of Sorghum bicolor (SbHNL) has no similarity to other HNLs except in function.
MechansimThe mechanism has been proposed to be E2 elimination of HCN from the hydroxynitrile group by:
1) Deprotonation of the substrate hydroxy group (activated by hydrogen bonding with Ser 158) by the carboxylate group of the C-terminal Trp 270, with concurrent formation of the C=O double bond and loss of cyanide. 2) Proton transfer from Trp 270 to cyanide via an active site water molecule.
Reaction

Catalytic Sites for 1gxs

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
SerA158213macie:sideChainHydrogen bonds to the substrate hydroxyl group (which becomes a carbonyl). This makes the substrate more acidic and stabilises the charge on the transition state.
TrpA270325macie:mainChainCarbonylDeprotonates the hydroxynitrile using the C-terminus carboxylate. This proton is later transferred to the active site water as the water transfers another proton to cyanide.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
SerC158213macie:sideChainHydrogen bonds to the substrate hydroxyl group (which becomes a carbonyl). This makes the substrate more acidic and stabilises the charge on the transition state.
TrpC270325macie:mainChainCarbonylDeprotonates the hydroxynitrile using the C-terminus carboxylate. This proton is later transferred to the active site water as the water transfers another proton to cyanide.

Literature References

Notes:Deprotonation is via the C-terminal carboxylate, not a main chain carbonyl. There is similarity to wheat serine carboxypeptidase, but significant structural difference in the active sites means the catalytic mechanism is not conserved.
Lauble H
Crystal structure of hydroxynitrile lyase from Sorghum bicolor in complex with the inhibitor benzoic acid: a novel cyanogenic enzyme.
Biochemistry 2002 41 12043-12050
PubMed: 12356304
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