Ubiquitin binding domains

Ubiquitin-Binding Domains (UBDs) are modular protein domains that recognise and bind non-covalently to ubiquitin. To date, more than 20 families of UBDs have been identified and most bind to ubiquitin only weakly (in the range of hundreds of µM). Most UBDs are of small size (< 50 amino acids) and adopt many different folds. Many UBDs are all alpha domains (e.g. UBA, CUE, UIM, MIU, VHS, GAT, UBAN), while some are all beta domains (e.g. NZF, UBC, WD40) and others are alpha/beta domains (e.g. UBZ, UEV, PFU). Many of the UBDs bind to ubiquitin via a hydrophobic patch centred on Ile44 (i.e. "Ile44 patch"), although binding to other surfaces patches have been observed (e.g. "Ile36 patch'). Most UBDs described to date bind to monoubiquitin and thus do not show a linkage-preference for the differently linked ubiquitin chains. There are, however, a handful of known, linkage-specific UBDs, that can specifically differentiate between the eight different ubiquitin linkages. This is important as the different linkage types are thought to signal for different molecular processes and linkage-specific recognition of these chains ensures the appropriate cellular response.