Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11

Abstract

The ATP-dependent degradation of polyubiquitylated proteins by the 26S proteasome is essential for the maintenance of proteome stability and the regulation of a plethora of cellular processes. Degradation of substrates is preceded by the removal of polyubiquitin moieties through the isopeptidase activity of the subunit Rpn11. Here we describe three crystal structures of the heterodimer of the Mpr1-Pad1-N-terminal domains of Rpn8 and Rpn11, crystallized as a fusion protein in complex with a nanobody. This fusion protein exhibits modest deubiquitylation activity toward a model substrate. Full activation requires incorporation of Rpn11 into the 26S proteasome and is dependent on ATP hydrolysis, suggesting that substrate processing and polyubiquitin removal are coupled. Based on our structures, we propose that premature activation is prevented by the combined effects of low intrinsic ubiquitin affinity, an insertion segment acting as a physical barrier across the substrate access channel, and a conformationally unstable catalytic loop in Rpn11. The docking of the structure into the proteasome EM density revealed contacts of Rpn11 with ATPase subunits, which likely stabilize the active conformation and boost the affinity for the proximal ubiquitin moiety. The narrow space around the Rpn11 active site at the entrance to the ATPase ring pore is likely to prevent erroneous deubiquitylation of folded proteins.n eukaryotes, the ubiquitin (Ub) proteasome system (UPS) is responsible for the regulated degradation of proteins (1-5). The UPS plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer needed. Consequently, the UPS is critically involved in numerous cellular processes, including cell cycle progression, apoptosis, and DNA damage repair, and malfunctions of the system often result in disease.The 26S proteasome executes the degradation of substrates that are marked for destruction by the covalent attachment of polyubiquitin chains. It is a molecular machine of 2.5 MDa comprising two subcomplexes, the 20S core particle (CP) and one or two 19S regulatory particles (RPs), which associate with the ends of the cylinder-shaped CP (6-8). The recognition and recruitment of polyubiquitylated substrates, their deubiquitylation, ATP-dependent unfolding, and translocation into the core particle take place in the RP. The structurally and mechanistically well-characterized CP houses the proteolytic activities and sequesters them from the environment, thereby avoiding collateral damage (9).The RPs attach to the outer α-rings of the CP, which control access to the proteolytic chamber formed by the inner β-subunit rings (10). Recently, the molecular architecture of the 26S holocomplex was established using cryo-EM-based approaches (11,12), and a pseudoatomic model of the holocomplex was put forward (13). The RP is formed by two subcomplexes, known as the base and the lid, which assemble independent...

Structure of the human 26S proteasome at a resolution of 3.9 Å

“…4D). We have previously proposed that this cavity forms a composite active site where substrate deubiquitylation and unfolding occurs (40). The Rpn3 C terminus may be a sensor for substrates engaged in the OB mouth that initiates conformational changes of the lid for activation of Rpn11 and hence the composite active site (15,16).…”

Structural basis for dynamic regulation of the human 26S proteasome

“…This may topologically destabilize the lid conformation in the S A state, allowing it to rotate around ATPase with a large angle (∼40°). The key consequence of this lid rotation is the repositioning of Rpn11 above the OB ring, which was thought to free the Rpn11 catalytic loop and mobilize its Ins-1 region (15,18,25). This suggests that Rpn11 may be enhanced in its deubiquitinating activity in the S B , S C , and S D states (25).…”

“…The intact proteasome has not been resolved to a level at which a reliable Cα-backbone can be traced with spatial assignment of amino acids, although major advances have been made in recent years (2,3,(7)(8)(9)(10)(11)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25). Several RP subunits have been resolved at high resolution by X-ray crystallography (14-16, 18, 21-24).…”

Sequential ubiquitination and deubiquitination enzymes synchronize the dual sensor and effector functions of TRIM21

“…Poh1 is a degradationcoupled DUB (25,29), with Ub-63 Ub specificity in vitro (18,19) and in cells (30). Electron microscopy experiments position Poh1's active site directly above the pore formed by the heterohexameric ATPase ring of the 19S base, through which a substrate must pass before entering the core particle (31)(32)(33). Although the removal en bloc of a Ub chain by Poh1 is a noted feature of its mechanism (26,34), and one that distinguishes it from other 19S DUBs (15), the reason for this singular activity is not well understood.…”