Deubiquitinating enzymes (DUBs) employ different strategies to recognize polyubiquitin. In addition to removing ubiquitin from proteins, DUBs also cleave polyubiquitin chains to edit the ubiquitin signal. Some DUBs display remarkable preference for certain polyubiquitin linkage types. To study how DUBs specifically recognize and hydrolyze different polyubiquitin chains, a novel set of DUB probes was reported by Ovaa and co-workers (Cell Chemical Biology 2016, 23, 472). These can be used to study DUBs that use S2 pocket binding to modulate DUB activity and specificity (Figure 3).
1st generation (Figure 1)
These probes target the S1 pocket and have contributed greatly to our understanding of DUBs. However these probes provide limited information on how DUBs process polyubiquitin chains.
Figure 1
2nd generation (Figure 2)
These di-ubiquitin-based probes with an electrophilic group between the two ubiquitins have been developed to capture DUBs with ubiquitins positioned in the S1 and S1’ pockets.
Figure 2
3rd generation (Figure 3)
These di-ubiquitin probes that target the S1 and S2 pocket. These will be useful tools to identify DUBs that rely on S2 site interactions to fine tune their activity.
