Arylesterase

 

This variant of serum paraoxonase (PON1) was obtained by directed evolution. Members of the PON family have been identified, and PON1 is present in Homo sapiens, Oryctolagns cuniculus, Mus musculus and Rattus rattus. It catalyses the hydrolysis and thereby inactivation of various organophosphates, including the nerve agents sarin and soman. Recently, PON1 has been found to play an important role in drug metabolism and in the prevention of atherosclerosis.

 

Reference Protein and Structure

Sequence
P27170 UniProt (3.1.1.2, 3.1.1.81, 3.1.8.1) IPR008363 (Sequence Homologues) (PDB Homologues)
Biological species
Oryctolagus cuniculus (rabbit) Uniprot
PDB
1v04 - serum paraoxonase by directed evolution (2.2 Å) PDBe PDBsum 1v04
Catalytic CATH Domains
2.120.10.30 CATHdb (see all for 1v04)
Cofactors
Calcium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:3.1.1.2)

water
CHEBI:15377ChEBI
+
phenyl acetate
CHEBI:8082ChEBI
→
hydron
CHEBI:15378ChEBI
+
acetate
CHEBI:30089ChEBI
+
phenol
CHEBI:15882ChEBI
Alternative enzyme names: A-esterase, Aromatic esterase, Paraoxonase,

Enzyme Mechanism

Introduction

His 115 acts as a general base by deprotonating a water molecule, activating it for nucleophilic attack on the substrate ester carbonyl. His 134 acts as a 'proton shuttle' to take a proton away from His 115, thereby increasing its basicity. A negatively charged, tetrahedral intermediate is formed, which is stabilised by a positively charged Ca2+. As the carbonyl is reformed, the ester bond is broken, forming the products.

Catalytic Residues Roles

UniProt PDB* (1v04)
Glu53, Asn270, Asp269, Asn224, Asn168 Glu53A, Asn270A, Asp269A, Asn224A, Asn168A Coordinate the calcium ion metal ligand
His115 His115A Acts as a general acid by deprotonating a water molecule, activating it for nucleophilic attack. proton relay, increase nucleophilicity, proton acceptor, proton donor
His134 His134A Acts as a 'proton shuttle', moving protons away from His 115, thereby increasing the basicity of His 115. increase basicity, 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

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

References

  1. Harel M et al. (2004), Nat Struct Mol Biol, 11, 412-419. Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes. DOI:10.1038/nsmb767. PMID:15098021.
  2. Ben-David M et al. (2013), J Mol Biol, 425, 1028-1038. Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme. DOI:10.1016/j.jmb.2013.01.009. PMID:23318950.

Step 1. His 115 acts as a general base by deprotonating a water molecule, activating it for nucleophilic attack on the substrate ester carbonyl. His 134 acts as a 'proton shuttle' to take a proton away from His 115, thereby increasing its basicity. A negatively charged, tetrahedral intermediate is formed, which is stabilised by a positively charged Ca2+.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu53A metal ligand
Asn168A metal ligand
Asn224A metal ligand
Asp269A metal ligand
Asn270A metal ligand
His134A increase basicity
His115A increase nucleophilicity
His115A proton acceptor, proton donor
His134A proton acceptor
His115A proton relay

Chemical Components

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

Step 2. The carbonyl reforms and the ester bond is broken creating the products.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu53A metal ligand
Asn168A metal ligand
Asn224A metal ligand
Asp269A metal ligand
Asn270A metal ligand

Chemical Components

overall product formed, ingold: unimolecular elimination by the conjugate base

Step 3. Inferred reaction step, restoring the enzyme to its native state.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu53A metal ligand
Asn168A metal ligand
Asn224A metal ligand
Asp269A metal ligand
Asn270A metal ligand
His115A proton relay
His134A proton donor
His115A proton donor, proton acceptor

Chemical Components

proton transfer, inferred reaction step, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. His 115 acts as a general base by deprotonating a water molecule, activating it for nucleophilic attack on the substrate ester carbonyl. His 134 acts as a 'proton shuttle' to take a proton away from His 115, thereby increasing its basicity. A negatively charged, tetrahedral intermediate is formed, which is stabilised by a positively charged Ca2+.

Step 2. The carbonyl reforms and the ester bond is broken creating the products.

Step 3. Inferred reaction step, restoring the enzyme to its native state.

Products.

Contributors

Ellie Wright, Gemma L. Holliday, James Willey