› 4kyw

X-ray diffraction
2.35Å resolution

Restriction endonuclease DPNI in complex with two DNA molecules

Released:
DOI: 10.2210/pdb4kyw/pdb
PDB entry 4kyw coloured by chain, front view.
PDB entry 4kyw coloured by chain, side view.
PDB entry 4kyw coloured by chain, top view.
Source organism: Streptococcus pneumoniae TIGR4
Primary publication:
Structural basis of the methylation specificity of R.DpnI.
Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M
Nucleic Acids Res 42 8745-54 (2014)
PMID: 24966351

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117767 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Type II methyl-directed restriction enzyme DpnI Chain: A
Molecule details ›
Chain: A
Length: 257 amino acids
Theoretical weight: 30.08 KDa
Source organism: Streptococcus pneumoniae TIGR4
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A459 (Residues: 1-254; Coverage: 100%)
Gene names: SP_1850, dpnC
Sequence domains:
Structure domains:
5'-(*DC*DTP*DGP*DGP*6MAP*DTP*DCP*DCP*DAP*DG)-3' Chains: C, D, E, F
Molecule details ›
Chains: C, D, E, F
Length: 10 nucleotides
Theoretical weight: 3.06 KDa
Source organism: Streptococcus pneumoniae TIGR4
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand CA 1 x CA
Ligand NA 1 x NA
1 modified residue:
Ligand 6MA 4 x 6MA

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: C2221
Unit cell:
a: 95.7Å b: 101.05Å c: 114.85Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.201 0.219
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications.
Hong et al. (2016)
1 more

3 mentions without citation

Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing.
Wang et al. (2017)
2 more