› 5yy9

X-ray diffraction
2.65Å resolution

Crystal structure of Tandem Tudor Domain of human UHRF1 in complex with LIG1-K126me3

Released:
DOI: 10.2210/pdb5yy9/pdb
PDB entry 5yy9 coloured by chain, front view.
PDB entry 5yy9 coloured by chain, side view.
PDB entry 5yy9 coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation.
Kori S, Ferry L, Matano S, Jimenji T, Kodera N, Tsusaka T, Matsumura R, Oda T, Sato M, Dohmae N, Ando T, Shinkai Y, Defossez PA, Arita K
Structure 27 485-496.e7 (2019)
PMID: 30639225

Function and Biology Details

Reactions 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
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148457 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase UHRF1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 154 amino acids
Theoretical weight: 18.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96T88 (Residues: 123-285; Coverage: 19%)
Gene names: ICBP90, NP95, RNF106, UHRF1
Sequence domains: Tandem tudor domain within UHRF1
Structure domains: SH3 type barrels.
DNA ligase 1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 13 amino acids
Theoretical weight: 1.64 KDa
Source organism: synthetic construct
Expression system: Not provided
UniProt:
  • Canonical: P18858 (Residues: 118-130; Coverage: 1%)
Gene name: LIG1

Ligands and Environments

No bound ligands
1 modified residue:
Ligand M3L 2 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P212121
Unit cell:
a: 27.105Å b: 97.349Å c: 132.529Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.231 0.288
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

Lysine Methylation Regulators Moonlighting outside the Epigenome.
Cornett et al. (2019)
9 more

1 mention without citation

Refined read-out: The hUHRF1 Tandem-Tudor domain prefers binding to histone H3 tails containing K4me1 in the context of H3K9me2/3.
Choudalakis et al. (2023)