Many UBDs of the UBA family bind to ubiquitin via a
hydrophobic patch centred on a particular
isoleucine residue (the "Ile44 patch"),[7] although binding to other surface patches has been observed, for example the "Ile36 patch".[8]Zinc finger UBDs have a broader range of binding modes including interactions with
polar residues.[5] Because many UBDs have a common or overlapping ubiquitin interaction surface, their interactions are often mutually exclusive; due to
steric clashes, more than one UBD cannot physically interact with the same Ile44-centered hydrophobic patch on a single ubiquitin molecule.[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.[citation needed]
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abRadley, Eh; Long, J; Gough, Kc; Layfield, R (20 December 2019). "The 'dark matter' of ubiquitin-mediated processes: opportunities and challenges in the identification of ubiquitin-binding domains". Biochemical Society Transactions. 47 (6): 1949–1962.
doi:
10.1042/BST20190869.
PMID31829417.
S2CID209328935.