E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin

• DOI: 10.1038/nchembio.1412
• Publication Date: 2013-12-08T19:20:28Z
• Authors: Hao Huang; Derek F Ceccarelli; Stephen Orlicky; Daniel J St-Cyr; Amy Ziemba; Pankaj Garg; Serge Plamondon; Manfred Auer; Sachdev Sidhu; Anne Marinier; Gary Kleiger; Mike Tyers; Frank Sicheri
• Keywords: Models, Molecular; 0303 health sciences; Binding Sites; Protein Stability; Ubiquitin; Biphenyl Compounds; Crystallography, X-Ray; Article; Enzyme Activation; Small Molecule Libraries; Inhibitory Concentration 50; 03 medical and health sciences; Coordination Complexes; Ubiquitin-Conjugating Enzymes; Amino Acids; Enzyme Inhibitors; Protein Binding

Weak protein interactions between ubiquitin and the ubiquitin-proteasome system (UPS) enzymes that mediate its covalent attachment to substrates serve to position ubiquitin for optimal catalytic transfer. We show that a small-molecule inhibitor of the E2 ubiquitin-conjugating enzyme Cdc34A, called CC0651, acts by trapping a weak interaction between ubiquitin and the E2 donor ubiquitin-binding site. A structure of the ternary CC0651-Cdc34A-ubiquitin complex reveals that the inhibitor engages a composite binding pocket formed from Cdc34A and ubiquitin. CC0651 also suppresses the spontaneous hydrolysis rate of the Cdc34A-ubiquitin thioester without decreasing the interaction between Cdc34A and the RING domain subunit of the E3 enzyme. Stabilization of the numerous other weak interactions between ubiquitin and UPS enzymes by small molecules may be a feasible strategy to selectively inhibit different UPS activities.