› 4dkj

X-ray diffraction
2.15Å resolution

CpG specific methyltransferase in complex with target DNA

Released:
DOI: 10.2210/pdb4dkj/pdb
PDB entry 4dkj coloured by chain, front view.
PDB entry 4dkj coloured by chain, side view.
PDB entry 4dkj coloured by chain, top view.
Source organism: Malacoplasma penetrans HF-2
Primary publication:
CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.
Wojciechowski M, Czapinska H, Bochtler M
Proc Natl Acad Sci U S A 110 105-10 (2013)
PMID: 23248272

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117321 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Cytosine-specific methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 403 amino acids
Theoretical weight: 47.31 KDa
Source organism: Malacoplasma penetrans HF-2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8EVR5 (Residues: 1-395; Coverage: 100%)
Gene name: MYPE4940
Sequence domains: C-5 cytosine-specific DNA methylase
Structure domains:
DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(C37)P*GP*CP*TP*GP*AP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.27 KDa
Source organism: Malacoplasma penetrans HF-2
Expression system: Not provided
DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.33 KDa
Source organism: Malacoplasma penetrans HF-2
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
1 bound ligand:
Ligand GOL 1 x GOL
2 modified residues:
Ligand C37 1 x C37
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P41212
Unit cell:
a: 83.95Å b: 83.95Å c: 173.84Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.216
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes.
Jeltsch et al. (2018)
4 more

5 mentions without citation

Reading between the Lines: "ADD"-ing Histone and DNA Methylation Marks toward a New Epigenetic "Sum".
Noh et al. (2016)
4 more