2y7h

Electron Microscopy
18Å resolution

Atomic model of the DNA-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.

Released:

Function and Biology Details

Reactions catalysed:
Endonucleolytic cleavage of DNA to give random double-stranded fragments with terminal 5'-phosphates, ATP is simultaneously hydrolyzed.
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA 
Biochemical function:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-115949 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Type I restriction enzyme EcoKI specificity subunit Chain: A
Molecule details ›
Chain: A
Length: 464 amino acids
Theoretical weight: 51.47 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P05719 (Residues: 1-464; Coverage: 100%)
Gene names: JW4311, b4348, hsdS, hss
Sequence domains: Type I restriction modification DNA specificity domain
Type I restriction enzyme EcoKI methylase subunit Chains: B, C
Molecule details ›
Chains: B, C
Length: 529 amino acids
Theoretical weight: 59.38 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P08957 (Residues: 1-529; Coverage: 100%)
Gene names: JW4312, b4349, hsdM, hsm
Sequence domains:
5'-D(*GP*TP*TP*CP*AP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*GP*CP*AP*AP*C)-3' Chain: D
Molecule details ›
Chain: D
Length: 20 nucleotides
Theoretical weight: 6.12 KDa
5'-D(*GP*TP*TP*GP*CP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*TP*GP*AP*AP*C)-3' Chain: E
Molecule details ›
Chain: E
Length: 20 nucleotides
Theoretical weight: 6.15 KDa

Ligands and Environments


Cofactor: Ligand SAM 2 x SAM
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 18Å
Relevant EMDB volumes: EMD-1534