› 8c56

X-ray diffraction
2.4Å resolution

CpG specific M.MpeI methyltransferase crystallized in the presence of 2'-deoxy-5-methylzebularine (5mZ) and 5-methylcytosine containing dsDNA

Released:
DOI: 10.2210/pdb8c56/pdb
PDB entry 8c56 coloured by chain, front view.
PDB entry 8c56 coloured by chain, side view.
PDB entry 8c56 coloured by chain, top view.
Source organisms:
Entry authors: Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D, Bochtler M

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-238856 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Cytosine-specific methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 395 amino acids
Theoretical weight: 46.24 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
DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(5PY)P*GP*CP*TP*GP*AP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.25 KDa
Source organism: synthetic construct
Expression system: synthetic construct
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: synthetic construct
Expression system: synthetic construct

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
2 bound ligands:
Ligand GOL 1 x GOL
Ligand NA 1 x NA
2 modified residues:
Ligand 5PY 1 x 5PY
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P41212
Unit cell:
a: 84.259Å b: 84.259Å c: 173.883Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.173 0.216
Expression systems:
  • Escherichia coli
  • synthetic construct

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