› 1dct

X-ray diffraction
2.8Å resolution

DNA (CYTOSINE-5) METHYLASE FROM HAEIII COVALENTLY BOUND TO DNA

Released:
DOI: 10.2210/pdb1dct/pdb
PDB entry 1dct coloured by chain, front view.
PDB entry 1dct coloured by chain, side view.
PDB entry 1dct coloured by chain, top view.
Source organism: Haemophilus influenzae biotype aegyptius
Primary publication:
The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.
Reinisch KM, Chen L, Verdine GL, Lipscomb WN
Cell 82 143-53 (1995)
PMID: 7606780

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 domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113669 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type II methyltransferase M.HaeIII Chains: A, B
Molecule details ›
Chains: A, B
Length: 324 amino acids
Theoretical weight: 37.09 KDa
Source organism: Haemophilus influenzae biotype aegyptius
UniProt:
  • Canonical: P20589 (Residues: 1-324; Coverage: 98%)
Gene name: haeIIIM
Sequence domains: C-5 cytosine-specific DNA methylase
Structure domains:
DNA (5'-D(*AP*CP*CP*AP*GP*CP*AP*GP*GP*(C49)P*CP*AP*CP*CP*AP*GP*TP*G)-3') Chains: F, G
Molecule details ›
Chains: F, G
Length: 18 nucleotides
Theoretical weight: 5.56 KDa
Source organism: Haemophilus influenzae biotype aegyptius
Expression system: Not provided
DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*TP*GP*GP*(C5M)P*CP*TP*GP*CP*TP*GP*G)-3') Chains: M, N
Molecule details ›
Chains: M, N
Length: 18 nucleotides
Theoretical weight: 5.55 KDa
Source organism: Haemophilus influenzae biotype aegyptius
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 2 x CA
2 modified residues:
Ligand C49 2 x C49
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 57.57Å b: 108.04Å c: 155.79Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.226 0.326
Expression system: Not provided

Quick links

Citations

34 review citations

Eukaryotic cytosine methyltransferases.
Goll et al. (2005)
33 more

15 mentions without citation

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