› 1yfj

X-ray diffraction
2.69Å resolution

T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact

Released:
DOI: 10.2210/pdb1yfj/pdb
PDB entry 1yfj coloured by chain, front view.
PDB entry 1yfj coloured by chain, side view.
PDB entry 1yfj coloured by chain, top view.
Source organism: Tequatrovirus T4
Primary publication:
Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase.
Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X
Cell 121 349-61 (2005)
PMID: 15882618

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-114862 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA adenine methylase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 259 amino acids
Theoretical weight: 30.46 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli
UniProt:
  • Canonical: P04392 (Residues: 1-259; Coverage: 100%)
Gene name: DAM
Sequence domains: D12 class N6 adenine-specific DNA methyltransferase
Structure domains:
5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3' Chains: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9
Molecule details ›
Chains: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9
Length: 15 nucleotides
Theoretical weight: 4.58 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 6 x SAH
2 bound ligands:
Ligand CL 4 x CL
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 111.2Å b: 133Å c: 189.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.202 0.25
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

Type I restriction enzymes and their relatives.
Loenen et al. (2014)
12 more

2 mentions without citation

Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase.
Horton et al. (2005)
1 more