BI82CH15-Hochstrasser ARI 2 May 2013 11:36 Molecular Architecture and Assembly of the Eukaryotic Proteasome Robert J. Tomko, Jr. and Mark Hochstrasser Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520; email: [email protected], [email protected] Annu. Rev. Biochem. 2013. 82:415–45 Keywords First published online as a Review in Advance on proteasome, ubiquitin, assembly, ATPase, deubiquitylation, March 13, 2013 proteolysis The Annual Review of Biochemistry is online at biochem.annualreviews.org Abstract This article’s doi: The eukaryotic ubiquitin-proteasome system is responsible for most 10.1146/annurev-biochem-060410-150257 aspects of regulatory and quality-control protein degradation in cells. Copyright c 2013 by Annual Reviews. Its substrates, which are usually modified by polymers of ubiquitin, All rights reserved are ultimately degraded by the 26S proteasome. This 2.6-MDa Annu. Rev. Biochem. 2013.82:415-445. Downloaded from www.annualreviews.org protein complex is separated into a barrel-shaped proteolytic 20S by Yale University - SOCIAL SCIENCE LIBRARY on 11/04/13. For personal use only. core particle (CP) of 28 subunits capped on one or both ends by a 19S regulatory particle (RP) comprising at least 19 subunits. The RP coordinates substrate recognition, removal of substrate polyubiquitin chains, and substrate unfolding and translocation into the CP for degradation. Although many atomic structures of the CP have been determined, the RP has resisted high-resolution analysis. Recently, however, a combination of cryo-electron microscopy, biochemical analysis, and crystal structure determination of several RP subunits has yielded a near-atomic-resolution view of much of the complex. Major new insights into chaperone-assisted proteasome assembly have also recently emerged. Here we review these novel findings. 415 BI82CH15-Hochstrasser ARI 2 May 2013 11:36 (Figure 1a). Additional Ubs can also be ligated Contents to the initial Ub via one of its seven lysines (or its N terminus), forming polyubiquitin (polyUb) INTRODUCTION.................. 416 chains. A chain of four or more Ubs is gener- THE 26S PROTEASOME: ally necessary and sufficient to create a target- ANATOMY OF A ing signal for delivery to the proteasome (3). PROTEIN-DESTROYING The proteasome is responsible for recogniz- MACHINE....................... 416 ing the substrate, removing its polyUb tag, un- The 20S Core Particle . 417 folding the substrate, and cleaving it into short The 19S Regulatory Particle. 419 peptides. ARCHITECTURE OF THE 19S In this review, we focus on the structure and REGULATORY PARTICLE . 421 assembly of the proteasome, particularly the The Regulatory Particle Base ....... 421 regulatory particle (RP), as numerous break- The Regulatory Particle Lid . 425 throughs have occurred in these areas over the STRUCTURAL INSIGHTS INTO past several years. For recent, more general SUBSTRATE SELECTION AND reviews of the UPS, we refer the reader to DEGRADATION................. 425 References 1 and 2 and references therein. Substrate Recognition and Positioning for Degradation . 425 Substrate Deubiquitylation . 426 THE 26S PROTEASOME: Substrate Unfolding by the AAA+ ANATOMY OF A ATPaseRing................... 426 PROTEIN-DESTROYING ASSEMBLY OF THE 26S MACHINE PROTEASOME.................. 427 The 26S proteasome is the largest and most 20S Core Particle Assembly . 427 complex member of an ancient superfamily of Assembly of the 19S Regulatory ATP-dependent chambered proteases found Particle......................... 432 in all domains of life (4, 5). These proteases Assembly of Alternative Proteasome are characterized by an ATPases associated Isoforms........................ 436 with various cellular activities (AAA)+-family Quality Control of Proteasome ATPase ring responsible for unfolding sub- Assembly....................... 436 strates and threading them through a narrow CONCLUDINGREMARKS......... 437 central pore into an interior proteolytic cham- ber, which is usually formed by an associated multimeric protein complex (Figure 1b). Sequestration of the proteolytic active sites Annu. Rev. Biochem. 2013.82:415-445. Downloaded from www.annualreviews.org INTRODUCTION within such a chamber prevents the unregu- by Yale University - SOCIAL SCIENCE LIBRARY on 11/04/13. For personal use only. Ubiquitin (Ub): a The ubiquitin-proteasome system (UPS) is re- lated destruction of folded cellular proteins. 76-residue protein that sponsible for the majority of regulatory and The ATPase ring converts the chemical energy is covalently conjugated to quality-control protein degradation in eukary- of ATP hydrolysis into mechanical force for substrates, often in the otic cells. Nearly every cellular process is af- substrate unfolding, allowing a polypeptide form of polymers fected by the UPS (1, 2). The UPS utilizes ATP end or interior loop to be translocated into the (polyUb) hydrolysis at several steps to mediate the selec- central chamber (Figure 1b). In the eukaryotic 26S proteasome: tive destruction of its substrates. Degradation of 26S proteasome (Figure 2a), the proteolytic an ATP-dependent a protein by the UPS is typically mediated by chamber is referred to as the 20S core particle intracellular protease the energy-dependent covalent attachment of (CP), whereas the AAA+ ATPase ring is composed of a 20S proteolytic CP and the small protein ubiquitin (Ub) to one or more contained within a separable complex called 19S RP lysines within the target protein via the con- the RP. In addition to the ATPase ring, the RP certed action of three enzymes: E1, E2, and E3 contains many additional specialized subunits 416 Tomko · Hochstrasser BI82CH15-Hochstrasser ARI 2 May 2013 11:36 ab Ub Substrate entry port Ub Ub Ub Ub AAA+ Ub ATPase +ATP E2 Substrate E1 E1 26S E3 + Ub Cleaved substrate Chambered protease Figure 1 Schematics of the ubiquitin (Ub)-proteasome system and an AAA+ chambered protease. (a) Through the sequential actions of E1, E2, and E3 enzymes, a protein to be degraded is modified with a polyUb chain, which serves as a targeting signal for the proteasome. (b)A cutaway view of an AAA+ chambered protease that displays the path of substrates through the ATPase ring and into the proteolytic chamber. The width of the passage into the protease chamber is delineated by yellow lines, and the proteolytic active sites are shown as purple dots. In this protease, the catalytic chamber is bracketed by two antechambers. Panel b adapted with permission from Nature Publishing Group (142), copyright c 2012. including ones that function as receptors for inner rings contain seven distinct β-subunits the polyUb tag and others that cleave the tag (β1–β7), whereas the outer rings consist of from substrates prior to their degradation. seven different α-subunits (α1-α7). The β1-, The 26S proteasome is highly conserved β2-, and β5-subunits contain the proteolytic throughout the Eukarya, where it is found in active sites, and each site cleaves preferentially both the nucleus and cytoplasm. Simpler forms after particular amino acid residues (13). In of the proteasome have been identified in ar- mammals, four additional β-subunits have chaea as well as in actinobacteria, although Ub been discovered: β1i, β2i, β5i, and β5t, where has been found only in eukaryotes (6, 7). Sev- “i” and “t” stand for immuno- and thymo-, eral other protein complexes can bind the ends respectively (14, 15). These subunits are highly of the CP cylinder, but their precise contribu- expressed in certain immune system tissues tions to the regulation of the CP remain less or are induced by particular stimuli, such as clear (Table 1). Because of space constraints, interferon-γ exposure, and they replace the only RP-CP complexes, i.e., the 26S protea- canonical active site–bearing β-subunits within Annu. Rev. Biochem. 2013.82:415-445. Downloaded from www.annualreviews.org some, are discussed in this review. the CP, altering CP proteolytic specificity. The by Yale University - SOCIAL SCIENCE LIBRARY on 11/04/13. For personal use only. β1i-, β2i-, β5i-substituted CP, called the im- munoproteasome, generates substrate cleavage The 20S Core Particle patterns that enhance loading of peptides onto The twofold-symmetric CP comprises 28 the class I major histocompatibility complex related polypeptides encoded by 14 separate for immune presentation to killer T cells (16). genes. Atomic structures of the CP from yeast Thymoproteasomes, which contain β1i, β2i, ATPases associated and mammals have been solved (8–12), and and β5t, appear to increase the repertoire of with various cellular + their overall structures and subunit arrange- self peptides for positive selection during T activities (AAA) : a family of ATPases ments are virtually identical, despite millions of cell development in the thymus (15). forming oligomeric years of evolutionary divergence between these In the crystal structures of the isolated rings that unfold or species. The CP consists of four axially stacked CP, the entrances into the internal prote- remodel substrates heteroheptameric rings (Figure 2b). The olytic chamber are usually occluded by the www.annualreviews.org • Proteasome Structure and Assembly 417 BI82CH15-Hochstrasser ARI 2 May 2013 11:36 a Assembly chaperones: RP base 19S RP Lid: Hsp90? Others? RP lid Base: Rpn14, Nas6, Nas2, Hsm3 20S CP CP: Ump1 CP Pba1/2 Pba3/4 b c α-ring β-ring β-ring α-ring d Annu. Rev. Biochem. 2013.82:415-445. Downloaded from www.annualreviews.org by Yale University - SOCIAL