Pectinesterase

 

Pectin methylesterases catalyse pectin deesterification by converting methyl-D-galactopyranosol residues of pectin to carboxylates and methanol. These enzymes have a role in plant cell wall metabolism.

 

Reference Protein and Structure

Sequence
P83218 UniProt (3.1.1.11) IPR000070 (Sequence Homologues) (PDB Homologues)
Biological species
Daucus carota (Carrot) Uniprot
PDB
1gq8 - Pectin methylesterase from Carrot (1.75 Å) PDBe PDBsum 1gq8
Catalytic CATH Domains
2.160.20.10 CATHdb (see all for 1gq8)
Click To Show Structure

Enzyme Reaction (EC:3.1.1.11)

water
CHEBI:15377ChEBI
+
pectin
CHEBI:17309ChEBI
→
pectate
CHEBI:68837ChEBI
+
methanol
CHEBI:17790ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: Pectase, Pectin demethoxylase, Pectin methoxylase, Pectin methyl esterase, Pectin methylesterase, Pectinoesterase,

Enzyme Mechanism

Introduction

Pectin methylesterases hydrolyse the ester bond of methylated galacturonid units - this produces a polymer and methanol. Asp 157 is the nucleophile for the attack on the carboxymethyl carbonyl carbon. A negatively-charged tetrahedral intermediate is then stabilised by the anion hole formed by Gln 113 and Gln 135. Asp 136 acts as a general acid catalyst in the first cleavage step where methanol is leaving. Then it acts as a general base catalyst in extracting a base from an incoming water molecule to active the water for nucleophilic attack in restoring the acyl-enzyme intermediate to the original state by cleavage of the covalent bond between Asp 157 and the substrate.

Catalytic Residues Roles

UniProt PDB* (1gq8)
Arg225 Arg225A Stabilizes Asp157 allowing it to perform the nucleophilic attack. electrostatic stabiliser
Gln113 Gln113A Forms part of the anion hole to stabilise the transition state. electrostatic stabiliser
Gln135 Gln135A Forms part of the anion hole involved in stabilising the tetrahedral transition state. electrostatic stabiliser
Asp136 Asp136A Acts as a general acid catalyst in the first cleavage step, then acts as a general base catalyst in activating water by proton abstraction for nucleophilic attack. increase nucleophilicity, proton acceptor, proton donor
Asp157 Asp157A Acts as a nucleophile for attack of the carboxymethyl carbonyl carbon of the substrate. covalently attached, nucleofuge, nucleophile
*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, intermediate formation, bimolecular nucleophilic addition, unimolecular elimination by the conjugate base, proton transfer, native state of enzyme regenerated, intermediate terminated, overall product formed

References

  1. Johansson K et al. (2002), FEBS Lett, 514, 243-249. Crystal structure of plant pectin methylesterase. DOI:10.1016/s0014-5793(02)02372-4. PMID:11943159.
  2. Fries M et al. (2007), EMBO J, 26, 3879-3887. Molecular basis of the activity of the phytopathogen pectin methylesterase. DOI:10.1038/sj.emboj.7601816. PMID:17717531.

Step 1. Asp157 performs a nucleophilic attack on the carbonyl carbon this forms an oxyanion intermediate which can be stabilized by Gln113 and Gln135.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gln113A electrostatic stabiliser
Gln135A electrostatic stabiliser
Asp157A covalently attached
Arg225A electrostatic stabiliser
Asp157A nucleophile

Chemical Components

overall reactant used, intermediate formation, ingold: bimolecular nucleophilic addition

Step 2. The tetrahedral intermediate collapses with Asp136 acting as an acid promoting the elimination of methanol.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gln135A electrostatic stabiliser
Arg225A electrostatic stabiliser
Gln113A electrostatic stabiliser
Asp157A covalently attached
Asp136A proton donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer

Step 3. Asp136 now acts as a base in order to activate a water molecule for nucleophilic attack on the carbonyl carbon forming a second oxyanion intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gln113A electrostatic stabiliser
Gln135A electrostatic stabiliser
Arg225A electrostatic stabiliser
Asp157A covalently attached
Asp136A increase nucleophilicity
Asp136A proton acceptor

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer

Step 4. Asp157 is then eliminated from the intermediate and the product is formed.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gln113A electrostatic stabiliser
Gln135A electrostatic stabiliser
Arg225A electrostatic stabiliser
Asp157A nucleofuge

Chemical Components

native state of enzyme regenerated, ingold: unimolecular elimination by the conjugate base, intermediate terminated, overall product formed
Download: Image, Marvin File

Step 1. Asp157 performs a nucleophilic attack on the carbonyl carbon this forms an oxyanion intermediate which can be stabilized by Gln113 and Gln135.

Step 2. The tetrahedral intermediate collapses with Asp136 acting as an acid promoting the elimination of methanol.

Step 3. Asp136 now acts as a base in order to activate a water molecule for nucleophilic attack on the carbonyl carbon forming a second oxyanion intermediate.

Step 4. Asp157 is then eliminated from the intermediate and the product is formed.

Products.

Contributors

Gary McDowell, Gemma L. Holliday, James Willey