9GKM

Structure of HECT E3 TRIP12 forming K29/K48-branched Ubiquitin chains

Summary for 9GKM

• Entry DOI: 10.2210/pdb9gkm/pdb
• EMDB information: 51429
• Descriptor: Ubiquitin, Polyubiquitin-C, Polyubiquitin-B, ... (5 entities in total)
• Functional Keywords: ligase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 201529.02

Authors

Maiwald, S.A.,Schulman, B.A. (deposition date: 2024-08-25, release date: 2025-05-21, Last modification date: 2025-10-01)

Primary citation

Maiwald, S.A.,Schneider, L.A.,Vollrath, R.,Liwocha, J.,Maletic, M.D.,Swatek, K.N.,Mulder, M.P.C.,Schulman, B.A.
TRIP12 structures reveal HECT E3 formation of K29 linkages and branched ubiquitin chains.
Nat.Struct.Mol.Biol., 32:1766-1775, 2025

PubMed Abstract: Regulation by ubiquitin depends on E3 ligases forging chains of specific topologies, yet the mechanisms underlying the generation of atypical linkages remain largely elusive. Here we utilize biochemistry, chemistry, and cryo-EM to define the catalytic architecture producing K29 linkages and K29/K48 branches for the human HECT E3 TRIP12. TRIP12 resembles a pincer. One pincer side comprises tandem ubiquitin-binding domains, engaging the proximal ubiquitin to direct its K29 towards the ubiquitylation active site, and selectively capturing a distal ubiquitin from a K48-linked chain. The opposite pincer side-the HECT domain-precisely juxtaposes the ubiquitins to be joined, further ensuring K29 linkage specificity. Comparison to the prior structure visualizing K48-linked chain formation by UBR5 reveals a similar mechanism shared by two human HECT enzymes: parallel features of the E3s, donor and acceptor ubiquitins configure the active site around the targeted lysine, with E3-specific domains buttressing the acceptor for linkage-specific polyubiquitylation.

PubMed: 40419785
DOI: 10.1038/s41594-025-01561-1

Experimental method

ELECTRON MICROSCOPY (3.69 Å)