› 5gut

X-ray diffraction
2.1Å resolution

The crystal structure of mouse DNMT1 (731-1602) mutant - N1248A

Released:
DOI: 10.2210/pdb5gut/pdb
PDB entry 5gut coloured by chain, front view.
PDB entry 5gut coloured by chain, side view.
PDB entry 5gut coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in DNA Methyltransferase-1.
Ye F, Kong X, Zhang H, Liu Y, Shao Z, Jin J, Cai Y, Zhang R, Li L, Zhang YW, Liu YC, Zhang C, Xie W, Yu K, Ding H, Zhao K, Chen S, Jiang H, Baylin SB, Luo C
ACS Chem Biol 13 772-781 (2018)
PMID: 29381856

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146802 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA (cytosine-5)-methyltransferase 1 Chain: A
Molecule details ›
Chain: A
Length: 872 amino acids
Theoretical weight: 98.85 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P13864 (Residues: 731-1602; Coverage: 54%)
Gene names: Dnmt, Dnmt1, Met1, Uim
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
2 bound ligands:
Ligand ZN 2 x ZN
Ligand SO4 10 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 75.424Å b: 78.554Å c: 164.544Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.2 0.23
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Mammalian DNA methyltransferases: new discoveries and open questions.
Gowher et al. (2018)
5 more

2 mentions without citation

Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in DNA Methyltransferase-1.
Ye et al. (2018)
1 more