3O2U: S. cerevisiae Ubc12

In ubiquitin-like protein (UBL) cascades, a thioester-linked E2 approximately UBL complex typically interacts with an E3 enzyme for UBL transfer to the target. Here we demonstrate a variant mechanism, whereby the E2 Ubc12 functions with two E3s, Hrt1 and Dcn1, for ligation of the UBL Rub1 to Cdc53's WHB subdomain. Hrt1 functions like a conventional RING E3, with its N terminus recruiting Cdc53 and C-terminal RING activating Ubc12 approximately Rub1. Dcn1's "potentiating neddylation" domain (Dcn1(P)) acts as an additional E3, reducing nonspecific Hrt1-mediated Ubc12 approximately Rub1 discharge and directing Ubc12's active site to Cdc53. Crystal structures of Dcn1(P)-Cdc53(WHB) and Ubc12 allow modeling of a catalytic complex, supported by mutational data. We propose that Dcn1's interactions with both Cdc53 and Ubc12 would restrict the otherwise flexible Hrt1 RING-bound Ubc12 approximately Rub1 to a catalytically competent orientation. Our data reveal mechanisms by which two E3s function synergistically to promote UBL transfer from one E2 to a target.
PDB ID: 3O2UDownload
MMDB ID: 84885
PDB Deposition Date: 2010/7/22
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.003  Å
Source Organism:
Similar Structures:
Biological Unit for 3O2U: monomeric; determined by author and by software (PISA)
Molecular Components in 3O2U
Label Count Molecule
Protein (1 molecule)
Nedd8-conjugating Enzyme Ubc12(Gene symbol: UBC12)
Molecule annotation
Chemical (1 molecule)
* Click molecule labels to explore molecular sequence information.

Citing MMDB