› 3pt6

X-ray diffraction
3Å resolution

Crystal structure of mouse DNMT1(650-1602) in complex with DNA

Released:
DOI: 10.2210/pdb3pt6/pdb
PDB entry 3pt6 coloured by chain, front view.
PDB entry 3pt6 coloured by chain, side view.
PDB entry 3pt6 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.
Song J, Rechkoblit O, Bestor TH, Patel DJ
Science 331 1036-40 (2011)
PMID: 21163962

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116711 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA (cytosine-5)-methyltransferase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 954 amino acids
Theoretical weight: 108.04 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P13864 (Residues: 650-1602; Coverage: 59%)
Gene names: Dnmt, Dnmt1, Met1, Uim
Sequence domains:
DNA (5'-D(*TP*CP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*CP*CP*GP*CP*AP*GP*G)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 19 nucleotides
Theoretical weight: 5.78 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*CP*CP*TP*GP*CP*GP*GP*AP*GP*GP*CP*TP*CP*AP*CP*GP*GP*GP*A)-3') Chains: I, J
Molecule details ›
Chains: I, J
Length: 19 nucleotides
Theoretical weight: 5.87 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
1 bound ligand:
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 83.192Å b: 213.507Å c: 86.274Å
α: 90° β: 99.64° γ: 90°
R-values:
R R work R free
0.213 0.211 0.266
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

87 review citations

DNA methylation: roles in mammalian development.
Smith et al. (2013)
86 more

21 mentions without citation

DNA methylation pathways and their crosstalk with histone methylation.
Du et al. (2015)
20 more