Conformational flexibility of a ubiquitin conjugation enzyme (E2)

Ubiquitination plays important roles in a variety of biological processes, such as DNA repair, cell cycle regulation, and p53-dependent processes. Des pite intensive studies in ubiquitination, the mechanism of substrate recogn ition is still not well understood. Each E2 has its own substrate specifici ty, yet substrate proteins recognized by each E2 are highly diverse. To bet ter understand how E2 proteins confer both substrate specificity and divers ity, we have studied conformational flexibility of an E2, UBC9, using nucle ar magnetic resonance N-15 relaxation and hydrogen-deuterium exchange measu rements. Two regions in human UBC9 show higher mobility over a wide range o f time scales. Combined with previous biochemical studies, both regions are likely to be important for protein-protein recognition in the ubiquitin pa thway. The region near the N-terminus may be important for interactions wit h the E1-UBL1 conjugate. The region near the C-terminus, which undergoes co nformational exchange may be important for substrate binding and catalytic activity. Since E2 enzymes share high homology in primary sequences and thr ee-dimensional structures, the conformational flexibility of UBC9 may repre sent a general feature of E2 enzymes. This study provides a new perspective for further studies of protein-protein recognition in ubiquitination.