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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1gxs
Original Entry
Title:
Lyase
Compound:
Hydroxynitrile lyase
Mutant:
No
UniProt/Swiss-Prot:
Q8W4X3-Q8W4X3
EC Class:
4.1.2.11
Other CSA Entries:
Overview of all sites for 1gxs
Homologues of 1gxs
Entries for UniProt/Swiss-Prot: Q8W4X3
Entries for EC: 4.1.2.11
Other Databases:
PDB entry: 1gxs
PDBsum entry: 1gxs
UniProt/Swiss-Prot: Q8W4X3
IntEnz entry: 4.1.2.11
Literature Report:
Introduction:
Hydroxynitrile 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.
Mechanism:
The 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.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
SERA 158 213Sidechain
ElectrostaticTransition state
ElectrostaticSubstrate
Hydrogen bonds to the substrate hydroxyl group (which becomes a carbonyl). This makes the substrate more acidic and stabilises the charge on the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12356304 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12356304 Current protein Computer modelling

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
TRPA 270 325Backbone carbonyl
Acid/baseWater
Acid/baseSubstrate
Deprotonates 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.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12356304 Current protein pH dependence of reaction
PubMed ID 12356304 Current protein Computer modelling
PubMed ID 12356304 Current protein Residue is positioned appropriately (ligand position known)
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.
References:
1
Crystal structure of hydroxynitrile lyase from Sorghum bicolor in complex with the inhibitor benzoic acid: a novel cyanogenic enzyme.
H. Lauble and B. Miehlich and S. Förster and H. Wajant and F. Effenberger
Biochemistry 41, (40) 12043-50, (2002).
12356304
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