› 1dct

X-ray diffraction
2.8Å resolution

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

Released:
DOI: 10.2210/pdb1dct/pdb
PDB 1dct coloured by chain and viewed from the front.
PDB 1dct coloured by chain and viewed from the side.
PDB 1dct coloured by chain and viewed from the top.
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)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Modification methylase 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

32 review citations

DNA methyltransferases: mechanistic models derived from kinetic analysis.
Malygin et al. (2012)
31 more

11 mentions without citation

Recombination-independent recognition of DNA homology for repeat-induced point mutation.
Gladyshev et al. (2017)
10 more