3O2U

S. cerevisiae Ubc12

Summary for 3O2U

• Entry DOI: 10.2210/pdb3o2u/pdb
• Related: 3O2P 3O6B
• Descriptor: NEDD8-conjugating enzyme UBC12, GLYCEROL (3 entities in total)
• Functional Keywords: e2 conjugase, ligase
• Biological source: Saccharomyces cerevisiae (yeast)
• Total number of polymer chains: 2
• Total formula weight: 42929.03

Authors

Scott, D.C.,Monda, J.K.,Grace, C.R.R.,Duda, D.M.,Kriwacki, R.W.,Kurz, T.,Schulman, B.A. (deposition date: 2010-07-22, release date: 2010-09-15, Last modification date: 2023-09-06)

Primary citation

Scott, D.C.,Monda, J.K.,Grace, C.R.,Duda, D.M.,Kriwacki, R.W.,Kurz, T.,Schulman, B.A.
A dual E3 mechanism for Rub1 ligation to Cdc53.
Mol.Cell, 39:784-796, 2010

PubMed Abstract: In ubiquitin-like protein (UBL) cascades, a thioester-linked E2∼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∼Rub1. Dcn1's "potentiating neddylation" domain (Dcn1(P)) acts as an additional E3, reducing nonspecific Hrt1-mediated Ubc12∼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∼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.

PubMed: 20832729
DOI: 10.1016/j.molcel.2010.08.030

Experimental method

X-RAY DIFFRACTION (2.003 Å)