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Branching via K11 and K48 Bestows Ubiquitin Chains with a Unique Interdomain Interface and Enhanced Affinity for Proteasomal Subunit Rpn1



Andrew J. Boughton, Susan T. Krueger, David Fushman


Post-translational substrate modification with ubiquitin (Ub) plays an essential role in eukaryotic cellular signaling. Polymeric Ub (polyUb) chains can be assembled with specific architectures, which convey distinct signaling outcomes depending on the linkages involved. Recent studies have show that branched K11/K48-linked polyUb enhances proteasomal degradation during cell division. To better understand this signaling pathway, we determined the crystal structure of branched K11/K48-linked tri-Ub (Ub3), which possessess a previously unobserved interdomain interface between the two distal Ubs. Solution NMR, SANS, and site-directed mutagenesis experiments corroborated the presence of this interface, which we hypothesized to be influential in the physiological role of branched K11/K48-linked chains. Yet, experiments probing known polyUb interactions - deubiquitinating enzyme assays and binding of proteasomal shuttling factor hHR23A - showed negligible differences between branched K11/K48-linked Ub3 and related di-Ub species. However, a significantly stronger binding affinity for brancehed K11/K48-linked Ub3 was observed with proteasomal subunit Rpn1, thereby suggesting a functional impact of this interdomain interface and pinpointing the mechanistic site of enhanced degradation. Therefore, our work indicates that branched K11/K48-linked polyUb contains a unique interface and facilitates more efficient processing directly at the level of proteasomal recognition, thus functioning as en enhanced proteolytic signal.


ubiquitin, proteasome, Rpn1, branched polyubiquitin, mixed-linkage polyubiquitin, K11-linkedubiquitin, K48-linked ubiquitin, Rad23 UBA domain, deubiquitinase


Boughton, A. , Krueger, S. and Fushman, D. (2020), Branching via K11 and K48 Bestows Ubiquitin Chains with a Unique Interdomain Interface and Enhanced Affinity for Proteasomal Subunit Rpn1, Structure, [online], (Accessed May 23, 2024)


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Created January 26, 2020, Updated October 12, 2021