5D0M: Structure Of Ube2d2:rnf165:ub Complex

RING-domain E3 ligases enhance transfer of ubiquitin to substrate proteins by stabilizing the RING-bound thioester-linked E2 approximately ubiquitin conjugate in a defined conformation that primes the active site for nucleophilic attack. Here we report that the monomeric RING domains from the human E3 ligases Arkadia and Ark2C bind directly to free ubiquitin with an affinity comparable to that of other dedicated ubiquitin-binding domains. Further work showed that the Ark-like RING domain and the noncovalently bound ubiquitin molecule coordinately stabilize the E2-conjugated ubiquitin (donor ubiquitin) in the 'closed' conformation. Our studies identify the RING domain of Arkadia as a ubiquitin-binding domain and provide insight into a new ubiquitin-dependent mechanism used by monomeric RING domains to activate ubiquitin transfer. This study also suggests how substrates that have been monoubiquitinated could be favored for further ubiquitination.
PDB ID: 5D0MDownload
MMDB ID: 134712
PDB Deposition Date: 2015/8/3
Updated in MMDB: 2015/12
Experimental Method:
x-ray diffraction
Resolution: 1.91  Å
Source Organism:
Similar Structures:
Biological Unit for 5D0M: trimeric; determined by author
Molecular Components in 5D0M
Label Count Molecule
Proteins (3 molecules)
Ubiquitin-conjugating Enzyme E2 D2(Gene symbol: UBE2D2)
Molecule annotation
Ring Finger Protein 165(Gene symbol: RNF165)
Molecule annotation
Polyubiquitin-b(Gene symbol: UBB)
Molecule annotation
Chemicals (3 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB