› 1jg3

X-ray diffraction
2.1Å resolution

Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine & VYP(ISP)HA substrate

Released:
DOI: 10.2210/pdb1jg3/pdb
PDB entry 1jg3 coloured by chain, front view.
PDB entry 1jg3 coloured by chain, side view.
PDB entry 1jg3 coloured by chain, top view.
Source organism: Pyrococcus furiosus
Primary publication:
Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide substrate.
Griffith SC, Sawaya MR, Boutz DR, Thapar N, Katz JE, Clarke S, Yeates TO
J Mol Biol 313 1103-16 (2001)
PMID: 11700066

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + protein L-isoaspartate = S-adenosyl-L-homocysteine + protein L-isoaspartate alpha-methyl ester
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-162260 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein-L-isoaspartate O-methyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 235 amino acids
Theoretical weight: 26.61 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TZR3 (Residues: 1-219; Coverage: 100%)
Gene names: PF1922, pcm
Sequence domains: Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
Structure domains: Vaccinia Virus protein VP39
VYP(L-iso-ASP)HA Chains: C, D
Molecule details ›
Chains: C, D
Length: 6 amino acids
Theoretical weight: 702 Da
Source organism: Pyrococcus furiosus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CL 2 x CL
Ligand NA 2 x NA
Ligand ADN 2 x ADN
1 modified residue:
Ligand IAS 2 x IAS

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-D
Spacegroup: P61
Unit cell:
a: 91.573Å b: 91.573Å c: 124.547Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.211 0.204 0.233
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Aging as war between chemical and biochemical processes: protein methylation and the recognition of age-damaged proteins for repair.
Clarke S. (2003)
3 more

2 mentions without citation

Many paths to methyltransfer: a chronicle of convergence.
Schubert et al. (2003)
1 more