Ubiquitin-binding domain

Many UBDs can be roughly classified into four broad categories: alpha-helical structures (in some cases as small as a single helix, as in the ubiquitin-interacting motif); zinc fingers; pleckstrin homology (PH) domains; and domains similar to those in ubiquitin-conjugating (also known as E2) enzymes.

[8] Zinc finger UBDs have a broader range of binding modes including interactions with polar residues.

[5] 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.

The NMR structure of a UBA domain , among the most common types of ubiquitin-binding domain, from the protein ubiquilin-1 (top, cyan) bound to ubiquitin (bottom, orange). Isoleucine 44, the center of a hydrophobic patch on the ubiquitin surface that interacts with a number of ubiquitin-binding domains, is highlighted in blue. Rendered from PDB : 2JY6 ​. [ 1 ]