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› 1yfl

X-ray diffraction
3.09Å resolution

T4Dam in Complex with Sinefungin and 16-mer Oligonucleotide Showing Semi-specific and Specific Contact and Flipped Base

Released:
DOI: 10.2210/pdb1yfl/pdb
Model geometry
Fit model/data
Data not deposited
PDB entry 1yfl coloured by chain, front view.
PDB entry 1yfl coloured by chain, side view.
PDB entry 1yfl 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: 
a 2'-deoxyadenosine in DNA + S-adenosyl-L-methionine = an N(6)-methyl-2'-deoxyadenosine in DNA + S-adenosyl-L-homocysteine + H(+).
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-114863 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA adenine methylase Chains: A, B, D, E
Molecule details ›
Chains: A, B, D, E
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(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3' Chains: F, G, H, I
Molecule details ›
Chains: F, G, H, I
Length: 16 nucleotides
Theoretical weight: 4.9 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SFG 4 x SFG
No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 87.871Å b: 117.648Å c: 87.865Å
α: 90° β: 90.02° γ: 90°
R-values:
R R work R free
0.217 0.214 0.265
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

Dancing on DNA: kinetic aspects of search processes on DNA.
Tafvizi et al. (2011)
11 more

4 mentions without citation

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