› 4qdk

X-ray diffraction
1.7Å resolution

Crystal structure of magnesium protoporphyrin IX methyltransferase (ChlM) from Synechocystis PCC 6803 with bound SAH

Released:
DOI: 10.2210/pdb4qdk/pdb
PDB entry 4qdk coloured by chain, front view.
PDB entry 4qdk coloured by chain, side view.
PDB entry 4qdk coloured by chain, top view.
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
Primary publication:
Structural insights into the catalytic mechanism of Synechocystis magnesium protoporphyrin IX O-methyltransferase (ChlM).
Chen X, Wang X, Feng J, Chen Y, Fang Y, Zhao S, Zhao A, Zhang M, Liu L
J Biol Chem 289 25690-8 (2014)
PMID: 25077963

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + magnesium protoporphyrin IX = S-adenosyl-L-homocysteine + magnesium protoporphyrin IX 13-methyl ester
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176284 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Magnesium-protoporphyrin O-methyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 238 amino acids
Theoretical weight: 26.18 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q55467 (Residues: 1-230; Coverage: 100%)
Gene names: chlM, slr0525
Sequence domains: Magnesium-protoporphyrin IX methyltransferase C-terminus
Structure domains: Vaccinia Virus protein VP39

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
1 bound ligand:
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 49.059Å b: 98.876Å c: 52.935Å
α: 90° β: 95.84° γ: 90°
R-values:
R R work R free
0.19 0.188 0.224
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Biosynthesis of the modified tetrapyrroles-the pigments of life.
Bryant et al. (2020)
2 more

1 mention without citation

Structural insights into the catalytic mechanism of Synechocystis magnesium protoporphyrin IX O-methyltransferase (ChlM).
Chen et al. (2014)