Protein-L-isoaspartate(D-aspartate) O-methyltransferase

 

Formation of isoaspartyl residues is one of several processes that damage proteins as they age. Protein L-isoaspartate (D-aspartate) O-methyltransferase (PIMT) is a conserved and nearly ubiquitous enzyme that catalyzes the repair of proteins damaged by isoaspartyl formation.

 

Reference Protein and Structure

Sequence
Q56308 UniProt (2.1.1.77) IPR000682 (Sequence Homologues) (PDB Homologues)
Biological species
Thermotoga maritima MSB8 (Bacteria) Uniprot
PDB
1dl5 - PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE (1.8 Å) PDBe PDBsum 1dl5
Catalytic CATH Domains
3.40.50.150 CATHdb (see all for 1dl5)
Click To Show Structure

Enzyme Reaction (EC:2.1.1.77)

L-beta-isoaspartate residue
CHEBI:90596ChEBI
+
S-adenosyl-L-methionine zwitterion
CHEBI:59789ChEBI
→
S-adenosyl-L-homocysteine zwitterion
CHEBI:57856ChEBI
+
L-aspartic acid alpha-methyl ester residue
CHEBI:90598ChEBI
Alternative enzyme names: D-aspartyl/L-isoaspartyl methyltransferase, L-aspartyl/L-isoaspartyl protein methyltransferase, L-isoaspartyl/D-aspartyl protein carboxyl methyltransferase, Protein (D-aspartate) methyltransferase, Protein O-methyltransferase (L-isoaspartate), Protein D-aspartate methyltransferase, Protein L-isoaspartate methyltransferase, Protein L-isoaspartyl methyltransferase, Protein beta-aspartate O-methyltransferase, Protein-L-isoaspartate O-methyltransferase, L-isoaspartyl protein carboxyl methyltransferase,

Enzyme Mechanism

Introduction

PIMT catalyses the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to the alpha-carboxylate side chain of the isoaspartyl residue. Through this transfer, the isoaspartyl group becomes activated for conversion back to the succinimide via a nonenzymatic attack of the nitrogen lone pair of the beta-peptide group on the alpha-carboxylate group. Once back in the succinimide form, hydrolysis can again occur at either carbonyl carbon, converting the protein to the aspartate form or regenerating the isoaspartate. This process cannot restore the amino group to the side chain of an original asparagine, but the pathway can restore the correct configuration to the protein backbone.

Catalytic Residues Roles

UniProt PDB* (1dl5)
Ser59 Ser59A Hydrogen bonds to the alpha-carboxylate group promoting the in line attack of O1 on SAM. 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 substitution, overall product formed, overall reactant used, cofactor used

References

  1. Skinner MM et al. (2000), Structure, 8, 1189-1201. Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair. PMID:11080641.
  2. Bennett EJ et al. (2003), Biochemistry, 42, 12844-12853. Catalytic implications from the Drosophila protein L-isoaspartyl methyltransferase structure and site-directed mutagenesis. DOI:10.1021/bi034891. PMID:14596598.
  3. Griffith SC et al. (2001), J Mol Biol, 313, 1103-1116. Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its l-isoaspartyl peptide substrate. DOI:10.1006/jmbi.2001.5095. PMID:11700066.

Step 1. In an SN2 reaction the carboxylate oxygen of the isoaspartyl group attacks the methyl of SAM. This forms the product and SAH.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser59A electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic substitution, overall product formed, overall reactant used, cofactor used
Download: Image, Marvin File

Step 1. In an SN2 reaction the carboxylate oxygen of the isoaspartyl group attacks the methyl of SAM. This forms the product and SAH.

Products.

Contributors

Gemma L. Holliday, Amelia Brasnett