› 1yf3

X-ray diffraction
2.29Å resolution

T4Dam in Complex with AdoHcy and 13-mer Oligonucleotide Making Non- and Semi-specific (~1/4) Contact

Released:
DOI: 10.2210/pdb1yf3/pdb
PDB entry 1yf3 coloured by chain, front view.
PDB entry 1yf3 coloured by chain, side view.
PDB entry 1yf3 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

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114859 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA adenine methylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 259 amino acids
Theoretical weight: 30.51 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(*AP*CP*CP*AP*TP*GP*AP*TP*CP*TP*GP*AP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.94 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided
5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*CP*AP*TP*GP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 13 nucleotides
Theoretical weight: 4.01 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided

Ligands and Environments


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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P21
Unit cell:
a: 38.9Å b: 125.8Å c: 73.2Å
α: 90° β: 104.7° γ: 90°
R-values:
R R work R free
0.221 0.214 0.27
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

3 mentions without citation

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