› 4rtk

X-ray diffraction
1.96Å resolution

Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with SAH and with DNA Containing Distal Pap Regulon Sequence

Released:
DOI: 10.2210/pdb4rtk/pdb
PDB entry 4rtk coloured by chain, front view.
PDB entry 4rtk coloured by chain, side view.
PDB entry 4rtk coloured by chain, top view.
Source organisms:
Primary publication:
Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression.
Horton JR, Zhang X, Blumenthal RM, Cheng X
OpenAccess logo Nucleic Acids Res 43 4296-308 (2015)
PMID: 25845600

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 analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118141 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA adenine methylase Chain: A
Molecule details ›
Chain: A
Length: 298 amino acids
Theoretical weight: 34.33 KDa
Source organism: Escherichia coli str. K-12 substr. MDS42
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AEE8 (Residues: 1-278; Coverage: 100%)
Gene names: JW3350, b3387, dam
Sequence domains: D12 class N6 adenine-specific DNA methyltransferase
Structure domains:
DNA (5'-D(*TP*CP*TP*AP*AP*AP*GP*AP*TP*CP*G)-3') Chain: F
Molecule details ›
Chain: F
Length: 11 nucleotides
Theoretical weight: 3.36 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*CP*GP*AP*TP*CP*TP*TP*TP*AP*G)-3') Chain: G
Molecule details ›
Chain: G
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments


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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P212121
Unit cell:
a: 36.331Å b: 63.044Å c: 142.185Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.21 0.223
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria.
Gao et al. (2023)
7 other articles