› 2zkd

X-ray diffraction
1.6Å resolution

Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA

Released:
DOI: 10.2210/pdb2zkd/pdb
PDB entry 2zkd coloured by chain, front view.
PDB entry 2zkd coloured by chain, side view.
PDB entry 2zkd coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism.
Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M
Nature 455 818-21 (2008)
PMID: 18772891

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115967 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase UHRF1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 210 amino acids
Theoretical weight: 23.41 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8VDF2 (Residues: 404-613; Coverage: 27%)
Gene names: Np95, Uhrf1
Sequence domains: SAD/SRA domain
Structure domains: SRA-YDG
DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*DGP*DCP*DAP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DAP*DG)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ACT 1 x ACT
Ligand EDO 1 x EDO
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: C2
Unit cell:
a: 89.587Å b: 104.036Å c: 65.586Å
α: 90° β: 99.18° γ: 90°
R-values:
R R work R free
0.156 0.155 0.185
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

87 review citations

Establishing, maintaining and modifying DNA methylation patterns in plants and animals.
Law et al. (2010)
86 more

9 mentions without citation

The other face of restriction: modification-dependent enzymes.
Loenen et al. (2014)
8 more