Linkage-Specific Avidity Defines the Lysine 63-Linked Polyubiquitin-Binding Preference of Rap80

Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.
Molecular cell (Impact Factor: 14.02). 04/2009; 33(6):775-83. DOI: 10.1016/j.molcel.2009.02.011
Source: PubMed


Linkage-specific polyubiquitin recognition is thought to make possible the diverse set of functional outcomes associated with ubiquitination. Thus far, mechanistic insight into this selectivity has been largely limited to single domains that preferentially bind to lysine 48-linked polyubiquitin (K48-polyUb) in isolation. Here, we propose a mechanism, linkage-specific avidity, in which multiple ubiquitin-binding domains are arranged in space so that simultaneous, high-affinity interactions are optimum with one polyUb linkage but unfavorable or impossible with other polyUb topologies and monoUb. Our model is human Rap80, which contains tandem ubiquitin interacting motifs (UIMs) that bind to K63-polyUb at DNA double-strand breaks. We show how the sequence between the Rap80 UIMs positions the domains for efficient avid binding across a single K63 linkage, thus defining selectivity. We also demonstrate K48-specific avidity in a different protein, ataxin-3. Using tandem UIMs, we establish the general principles governing polyUb linkage selectivity and affinity in multivalent ubiquitin receptors.

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    • "See also Figure S1. (Sims and Cohen, 2009). We first analyzed the linkage preference of the proteasome shuttling protein RAD23B that has been well characterized as a K48 binding protein (Rao and Sastry, 2002; Varadan et al., 2005). "
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    • "The selectivity of Eps15 tUIM for binding different ubiquitin chains has not been reported. The distance between the two UIMs would fit the configuration of a K63-linked diubiquitin (Sims and Cohen, 2009), which is consistent with our finding. Of note, molecular modeling predicts that the K33-linked diubiquitin adopts an extended conformation (Fushman and Walker, 2010), similar to the K63-linked diubiquitin. "
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    • "In addition, many UBDs have been shown to exhibit selectivity for certain types of polyubiquitin chains [7] [11] [13]. The linkage selectivity may also arise from multivalent binding between tandem UBD arrays in a given protein and ubiquitin monomers or linkages in a polyubiquitin chain [34] [35]. The function of tandem UBD arrays has been recently hypothesized to increase the affinity for a given ubiquitinated substrate rather than simultaneously engaging multiple substrates. "
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