5D0K

Structure of UbE2D2:RNF165:Ub complex

Summary for 5D0K

• Entry DOI: 10.2210/pdb5d0k/pdb
• Related: 5D0I 5D0M
• Descriptor: Ubiquitin-conjugating enzyme E2 D2, RING finger protein 165, Polyubiquitin-B, ... (5 entities in total)
• Functional Keywords: complex, ubiquitin, ligase
• Biological source: Homo sapiens (Human); More
• Cellular location: Ubiquitin: Cytoplasm : P0CG47
• Total number of polymer chains: 12
• Total formula weight: 144852.12

Authors

Wright, J.D.,Day, C.L.,Mace, P.D. (deposition date: 2015-08-03, release date: 2015-12-09, Last modification date: 2024-03-06)

Primary citation

Wright, J.D.,Mace, P.D.,Day, C.L.
Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity.
Nat.Struct.Mol.Biol., 23:45-52, 2016

PubMed Abstract: RING-domain E3 ligases enhance transfer of ubiquitin to substrate proteins by stabilizing the RING-bound thioester-linked E2∼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.

PubMed: 26656854
DOI: 10.1038/nsmb.3142

Experimental method

X-RAY DIFFRACTION (2.65 Å)