› 7btq

Electron Microscopy
4.54Å resolution

EcoR124I-DNA in the Restriction-Alleviation State

Released:
DOI: 10.2210/pdb7btq/pdb
PDB entry 7btq coloured by chain, front view.
PDB entry 7btq coloured by chain, side view.
PDB entry 7btq coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural insights into assembly, operation and inhibition of a type I restriction-modification system.
Gao Y, Cao D, Zhu J, Feng H, Luo X, Liu S, Yan XX, Zhang X, Gao P
Nat Microbiol 5 1107-1118 (2020)
PMID: 32483229
Related structures: EMD-30182

Function and Biology Details

Reactions catalysed: 
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA 
Endonucleolytic cleavage of DNA to give random double-stranded fragments with terminal 5'-phosphates, ATP is simultaneously hydrolyzed.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121130 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (5 distinct):
Type I restriction enzyme EcoR124I/EcoR124II methylase subunit Chains: A, D
Molecule details ›
Chains: A, D
Length: 520 amino acids
Theoretical weight: 58.08 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P10484 (Residues: 1-520; Coverage: 100%)
Gene names: hsdM, hsm
Sequence domains:
Type I restriction enzyme EcoR124I/EcoR124II specificity subunit Chain: E
Molecule details ›
Chain: E
Length: 404 amino acids
Theoretical weight: 46.24 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P10485 (Residues: 1-404; Coverage: 100%)
Gene names: hsdS, hss
Sequence domains: Type I restriction modification DNA specificity domain
Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit Chain: F
Molecule details ›
Chain: F
Length: 1038 amino acids
Theoretical weight: 120.28 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P10486 (Residues: 1-1038; Coverage: 100%)
Gene names: hsdR, hsr
Sequence domains:
DNA (64-MER) Chain: B
Molecule details ›
Chain: B
Length: 64 nucleotides
Theoretical weight: 19.66 KDa
DNA (64-MER) Chain: C
Molecule details ›
Chain: C
Length: 64 nucleotides
Theoretical weight: 19.79 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.54Å
Relevant EMDB volumes: EMD-30182
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Towards a better understanding of antimicrobial resistance dissemination: what can be learnt from studying model conjugative plasmids?
Shen et al. (2022)
1 more

1 mention without citation

The extremophile Picrophilus torridus carries a DNA adenine methylase M.PtoI that is part of a Type I restriction-modification system.
Gulati et al. (2023)