› 3ubt

X-ray diffraction
2.5Å resolution

Crystal Structure of C71S Mutant of DNA Cytosine-5 Methyltransferase M.HaeIII Bound to DNA

Released:
DOI: 10.2210/pdb3ubt/pdb
PDB entry 3ubt coloured by chain, front view.
PDB entry 3ubt coloured by chain, side view.
PDB entry 3ubt coloured by chain, top view.
Source organism: Haemophilus aegyptius
Primary publication:
Structural origins of DNA target selection and nucleobase extrusion by a DNA cytosine methyltransferase.
Didovyk A, Verdine GL
J Biol Chem 287 40099-105 (2012)
PMID: 23012373

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-116978 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Type II methyltransferase M.HaeIII Chains: A, B, Y
Molecule details ›
Chains: A, B, Y
Length: 331 amino acids
Theoretical weight: 37.84 KDa
Source organism: Haemophilus aegyptius
Expression system: Escherichia coli
UniProt:
  • Canonical: P20589 (Residues: 1-330; Coverage: 100%)
Gene name: haeIIIM
Sequence domains: C-5 cytosine-specific DNA methylase
Structure domains:
5'-D(*TP*GP*GP*CP*CP*A)-3' Chains: C, D, E, F, G, H
Molecule details ›
Chains: C, D, E, F, G, H
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: Haemophilus aegyptius
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CL 3 x CL
Ligand ATP 3 x ATP
Ligand 2PE 3 x 2PE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 57.564Å b: 129.588Å c: 132.381Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.221
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria.
Gao et al. (2023)

1 mention without citation

Structural origins of DNA target selection and nucleobase extrusion by a DNA cytosine methyltransferase.
Didovyk et al. (2012)