Caffeate O-methyltransferase

 

COMT is involved in lignin biosynthesis - it methylates caffeoyl- and 5-hydroxyferuloyl-containing acids, aldehydes and alcohols. Lignin polymerisation has implications in industrial, environmental and agricultural areas.

 

Reference Protein and Structure

Sequence
P28002 UniProt (2.1.1.68) IPR016461 (Sequence Homologues) (PDB Homologues)
Biological species
Medicago sativa (Alfalfa) Uniprot
PDB
1kyw - Crystal Structure Analysis of Caffeic Acid/5-hydroxyferulic acid 3/5-O-methyltransferase in complex with 5-hydroxyconiferaldehyde (2.4 Å) PDBe PDBsum 1kyw
Catalytic CATH Domains
3.40.50.150 CATHdb (see all for 1kyw)
Click To Show Structure

Enzyme Reaction (EC:2.1.1.68)

trans-caffeate
CHEBI:57770ChEBI
+
S-adenosyl-L-methionine zwitterion
CHEBI:59789ChEBI
→
S-adenosyl-L-homocysteine zwitterion
CHEBI:57856ChEBI
+
ferulate
CHEBI:29749ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: S-adenosyl-L-methionine:caffeic acid-O-methyltransferase, Caffeate 3-O-methyltransferase, Caffeate methyltransferase,

Enzyme Mechanism

Introduction

COMT is an S-adenosyl-L-Met-dependent methyltransferase that methylates 3'-hydroxyl- and 5'-hydroxyl-containing phenylpropanoid-derived lignin precursors. Using His 269 as a general base, the 3'- or 5'-hydroxyl group is deprotonated, facilitating the transfer of the reactive methyl group of S-adenosyl-L-Met to the phenolate anion by nucleophilic attack.

Catalytic Residues Roles

UniProt PDB* (1kyw)
Glu329 Glu329A Glu 329 is hydrogen bonded to His 269 and holds it in a catalytically productive position. hydrogen bond donor, steric role, electrostatic stabiliser
Glu297, Asp270 Glu297A, Asp270A Position His 269 for catalysis. steric role, electrostatic stabiliser
His269 His269A Functions as a general base to deprotonate the hydroxyl group and increase the nucleophilicity of the oxygen. 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

proton transfer, overall reactant used, bimolecular nucleophilic substitution, overall product formed, cofactor used, inferred reaction step, native state of enzyme regenerated

References

  1. Zubieta C et al. (2002), Plant Cell, 14, 1265-1277. Structural Basis for the Modulation of Lignin Monomer Methylation by Caffeic Acid/5-Hydroxyferulic Acid 3/5-O-Methyltransferase. DOI:10.1105/tpc.001412. PMID:12084826.
  2. Zubieta C et al. (2001), Nat Struct Biol, 8, 271-279. Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases. DOI:10.1038/85029. PMID:11224575.

Step 1. His269 deprotonates the hydroxyl group of the substrate.

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Catalytic Residues Roles

Residue Roles
Asp270A steric role
Glu297A steric role
Glu329A steric role, hydrogen bond donor
Asp270A electrostatic stabiliser
Glu297A electrostatic stabiliser
Glu329A electrostatic stabiliser
His269A proton acceptor

Chemical Components

proton transfer, overall reactant used

Step 2. In an SN2 reaction the hydroxy group of the substrate attacks the methyl group of SAM, forming the product and SAH.

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Catalytic Residues Roles

Residue Roles
Asp270A electrostatic stabiliser
Glu297A electrostatic stabiliser
Glu329A electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic substitution, overall product formed, cofactor used

Step 3. In an inferred mechanism step His269 is deprotonated to regenerate the native state of the enzyme.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His269A proton donor

Chemical Components

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

Step 1. His269 deprotonates the hydroxyl group of the substrate.

Step 2. In an SN2 reaction the hydroxy group of the substrate attacks the methyl group of SAM, forming the product and SAH.

Step 3. In an inferred mechanism step His269 is deprotonated to regenerate the native state of the enzyme.

Products.

Contributors

Hannah Gilbert, Gary McDowell, Gemma L. Holliday, Amelia Brasnett