Esterase (estA)

 

This esterase enzyme is secreted by the bacterium Streptomyces scabies, a causal agent of the potato scab decease. Invasion into the plant host is brought about by the liplytic action of the secreted esterase, which is presumed to hydrolyse specific ester bonds within the suberin lipid which covers the plant tubers. Although the esterase possesses a catalytic triad similar to that of other serine hydrolases, the structure remains unique among known proteins. It is the first example of a naturally occurring enzyme in which a neutral hydrogen bond acceptor, a main chain carbonyl, replaces a carboxylic acid within the triad.

 

Reference Protein and Structure

Sequence
P22266 UniProt (3.1.1.-) IPR013830 (Sequence Homologues) (PDB Homologues)
Biological species
Streptomyces scabiei (Streptomyces scabiei) Uniprot
PDB
1esc - THE MOLECULAR MECHANISM OF ENANTIORECOGNITION BY ESTERASES (2.1 Å) PDBe PDBsum 1esc
Catalytic CATH Domains
3.40.50.1110 CATHdb (see all for 1esc)
Click To Show Structure

Enzyme Reaction (EC:3.1.1.-)

water
CHEBI:15377ChEBI
+
carboxylic ester
CHEBI:33308ChEBI
→
alcohol
CHEBI:30879ChEBI
+
carboxylic acid
CHEBI:33575ChEBI

Enzyme Mechanism

Introduction

A nucleophilic residue attacks at the substrate carbonyl, forming a tetrahedral intermediate (the anionic transition state being stabilised by an oxyanion hole). This collapses to give an acyl-enzyme intermediate, which is hydrolysed to yield the free residue and substrate.

Catalytic Residues Roles

UniProt PDB* (1esc)
His322 His283A The residue forms a neutral hydrogen bond with the backbone carbonyl of Typ 280, which enhances its basic character towards the nucleophilic Ser 14 and controls the residue's orientation within the active site. This is a unique example of a neutral hydrogen bond in the absence of a carboxylic acid group among the serine hydrolase enzymes. The residue is also hydrogen bonded to Ser 14, and donates a proton to the anionic transition state, regaining neutrality within the active site. proton acceptor, electrostatic stabiliser, proton donor
Ser53 Ser14A The residue acts as a nucleophile towards the ester substrate, forming a tetrahedral intermediate. The hydroxyl group hydrogen bonds to the His 283, which then acts as a base to deprotonate the residue, enhancing its nucleophilic character. The residue's backbone amide is implicated in forming an oxyanion hole, lowering the energy of the anionic transition state. nucleofuge, nucleophile, proton acceptor, proton donor, electrostatic stabiliser
Gly105 (main-N), Asn145 Gly66A (main-N), Asn106A The residue is implicated in forming an oxyanion hole which stabilises the anionic tetrahedral transition state formed in hydrolysis. electrostatic stabiliser
*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

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

References

  1. Hale VA et al. (1996), Appl Microbiol Biotechnol, 45, 189-198. Mutational analysis of the Streptomyces scabies esterase signal peptide. DOI:10.1007/s002530050669. PMID:8920191.
  2. Wei Y et al. (1995), Nat Struct Biol, 2, 218-223. A novel variant of the catalytic triad in the Streptomyces scabies esterase. PMID:7773790.

Step 1. His283 abstracts a proton from Ser14, which initates a nucleophilic attack on the carbonyl group of the substrate.

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Catalytic Residues Roles

Residue Roles
Ser14A electrostatic stabiliser
His283A electrostatic stabiliser
Asn106A electrostatic stabiliser
Gly66A (main-N) electrostatic stabiliser
Asn106A modifies pKa
Ser14A proton donor, nucleophile
His283A proton acceptor

Chemical Components

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

Step 2. The tetrahedral intermediate collapses liberating the alcohol product.

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Catalytic Residues Roles

Residue Roles
Gly66A (main-N) electrostatic stabiliser
Asn106A electrostatic stabiliser
His283A electrostatic stabiliser
Asn106A modifies pKa
His283A proton donor

Chemical Components

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

Step 3. His283 abstracts a proton from a water molecule, which initiates a nucleophilic attack on the carbonyl carbon of the covalent enzyme-substrate intermediate.

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Catalytic Residues Roles

Residue Roles
Gly66A (main-N) electrostatic stabiliser
Asn106A electrostatic stabiliser
His283A electrostatic stabiliser
Asn106A modifies pKa
His283A proton acceptor

Chemical Components

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

Step 4. The tetrahedral intermediate collapses eliminating the serine with concomitant deprotonation of His283 to regenerate the active site and final product.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gly66A (main-N) electrostatic stabiliser
Asn106A electrostatic stabiliser
His283A electrostatic stabiliser
Asn106A modifies pKa
Ser14A proton acceptor
His283A proton donor
Ser14A nucleofuge

Chemical Components

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

Step 1. His283 abstracts a proton from Ser14, which initates a nucleophilic attack on the carbonyl group of the substrate.

Step 2. The tetrahedral intermediate collapses liberating the alcohol product.

Step 3. His283 abstracts a proton from a water molecule, which initiates a nucleophilic attack on the carbonyl carbon of the covalent enzyme-substrate intermediate.

Step 4. The tetrahedral intermediate collapses eliminating the serine with concomitant deprotonation of His283 to regenerate the active site and final product.

Products.

Contributors

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