An Extended Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure

Abstract

Highlights d Chemical origin of Rpn13 preference for K48-linked ubiquitin chains revealed d NMR demonstrates highly dynamic interactions between hRpn2:hRpn13 and K48-diubiquitin d K48-diubiquitin adopts a dynamic, extended conformation that hRpn13 selects d Structure of hRpn2:Rpn13 bound to K48-diubiquitin described

Impact of Losing hRpn13 Pru or UCHL5 on Proteasome Clearance of Ubiquitinated Proteins and RA190 Cytotoxicity

“…2E), perhaps because the loss at the proteasome is compensated by correlative accumulation of ubiquitinated substrates that failed to be recruited or retained at proteasomes for degradation. Nonetheless, the data presented here do not We recently found that hRpn13 exchanges between the two ubiquitin moieties of K48-linked diubiquitin and maintains an extended conformational state for the ubiquitin chain(56), which would facilitate further interactions with other ubiquitin-binding sites of weaker affinity, such as in hRpn1. Moreover, hRpn13 is at an apical location of the RP (57-60), which is likely to be ideal for recruitment of proteins to the proteasome.…”

Structure, Dynamics and Function of the 26S Proteasome

“…The PRU domain of RPN13 selectively recognizes a dynamic, extended conformation of Lys48-linked diubiquitin via loops extending from the β-strands in the PRU domain and exhibits ∼90 nM K D for Lys48-linked diubiquitin. In the proteasome, the PRU domain binds a flexible C-terminal region of RPN2, which emanates from its LRR-like toroidal domain (Chen et al 2010;Sakata et al 2012;Lu et al 2017aLu et al , 2020. The recruitment of RPN13 near the toroid apex of RPN2 positions its PRU domain about four-ubiquitin away from the entrance of the ATPase ring, which is comparable to the distance from the ubiquitin-binding sites in RPN1 and RPN10 (Lu et al 2020).…”

“…In the proteasome, the PRU domain binds a flexible C-terminal region of RPN2, which emanates from its LRR-like toroidal domain (Chen et al 2010;Sakata et al 2012;Lu et al 2017aLu et al , 2020. The recruitment of RPN13 near the toroid apex of RPN2 positions its PRU domain about four-ubiquitin away from the entrance of the ATPase ring, which is comparable to the distance from the ubiquitin-binding sites in RPN1 and RPN10 (Lu et al 2020). The PRU domain of human RPN13 is connected by a flexible linker to a C-terminal helical DEUBAD (DEUBiquitinase ADaptor) domain that recruits and activates the DUB UCH37 (Lu et al 2017a;Sahtoe et al 2015;Hamazaki et al 2006;Qiu et al 2006;Yao et al 2006).…”

“…This prompts the possibility of promiscuous modes of polyubiquitin chain recognition by the intrinsic ubiquitin receptors in the context of the proteasome. It is conceivable that RPN1, RPN10 and RPN13 simultaneously bind polyubiquitin chains to orient substrates for optimal engagement and deubiquitylation (Zhang et al 2009d;Liu et al 2019;Lu et al 2020). This multi-site recognition is both kinetically and enthalpically favored and could be functionally adapted to tackle the vast conformational diversity of the polyubiquitin chains conjugated on protein substrates.…”

“…It might trim distal ubiquitin moieties, release them from the ubiquitin receptors and vacate the ubiquitin-binding sites in the proteasome (Zhang et al 2011). Despite its putative location that is about the length of tetraubiquitin away from the OB ring of the AAA-ATPase motor (Holzl et al 2000;Dong et al 2019;Lu et al 2020), UCH37 association with the proteasome can allosterically stimulate the proteasomal ATPase activity and CP gate opening (Peth et al 2013a). These allosteric effects are in line with those seen in the USP14-bound proteasome and further underscore the global allosteric coupling between all components of the proteasome.…”