› 6y3j

X-ray diffraction
2.6Å resolution

RING-DTC domains of Deltex 2, bound to ADP-ribose

Released:
DOI: 10.2210/pdb6y3j/pdb
PDB entry 6y3j coloured by chain, front view.
PDB entry 6y3j coloured by chain, side view.
PDB entry 6y3j coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
DELTEX2 C-terminal domain recognizes and recruits ADP-ribosylated proteins for ubiquitination.
Ahmed SF, Buetow L, Gabrielsen M, Lilla S, Chatrin C, Sibbet GJ, Zanivan S, Huang DT
Sci Adv 6 (2020)
PMID: 32937373

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:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183194 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable E3 ubiquitin-protein ligase DTX2 Chain: A
Molecule details ›
Chain: A
Length: 235 amino acids
Theoretical weight: 25.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q86UW9 (Residues: 390-622; Coverage: 38%)
Gene names: DTX2, KIAA1528, RNF58
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand APR 1 x APR
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P3221
Unit cell:
a: 104.933Å b: 104.933Å c: 74.544Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.24 0.238 0.282
Expression system: Escherichia coli

Quick links

Citations

8 review citations

An expanded lexicon for the ubiquitin code.
Dikic et al. (2023)
7 more

2 mentions without citation

ADP-ribose contributions to genome stability and PARP enzyme trapping on sites of DNA damage; paradigm shifts for a coming-of-age modification.
Rouleau-Turcotte et al. (2023)
1 more