Structural aspects of ubiquitin binding specificities.

Ubiquitin (Ub) is widely distributed in eukaryotic cells as its name means. There are many kinds of Ub-like proteins (for example, SUMO, NEDD8 and ISG15) and Ub-like domains (UbLs) included in multi-domain proteins. To date, a large number of Ub-binding domains (UBDs), such as UBA, CUE, UIM, ZnF, and Pru, are coming up to us with different affinities to Ub and its homologues. The binding specificities provide the basis for controlling various cellular events as well as for delivering ubiquitinated proteins to proteasome for degradation. Structural details of these UBDs and their complexes with Ub might as well show us the delicate mechanism of Ub recognition and regulation. This review summarizes recent progresses on deciphering the structure-based Ub-binding specificities, which are the importantly fundamental elements in orchestrating the ubiquitination and deubiquitination processes in eukaryotic cells.