Ubiquitylated proteins are degraded by the 26 S protease, an enzyme complex that contains 30 or more unique subunits. One of these proteins, subunit 5a (S5a), has been shown to bind ubiquitin-lysozyme conjugates and free polyubiquitin chains. Using deletional analysis, we have identified in the carboxyl-terminal half of human S5a, two independent polyubiquitin binding sites whose sequences are highly conserved among higher eukaryotic S5a homologs. The sites are approximately 30-amino acids long and are separated by 50 intervening residues. When expressed as small fragments or when present in full-length S5a molecules, the sites differ at least 10-fold in their apparent affinity for polyubiquitin chains. Each binding site contains 5 hydrophobic residues that form an alternating pattern of large and small side chains, e.g. Leu-Ala-Leu-Ala-Leu, and this pattern is essential for binding ubiquitin chains. Based on the importance of the alternating hydrophobic residues in the binding sites and previous studies showing that a hydrophobic patch on the surface of ubiquitin is essential for proteolytic targeting, we propose a model for molecular recognition of polyubiquitin chains by S5a.Ubiquitin is a small, highly conserved eukaryotic protein that can be covalently attached to a variety of cellular proteins including itself (1). Ubiquitylation requires an activating enzyme E1, Ub 1 carrier proteins E2s, and substrate recognition components called E3s (2, 3). Post-translational modification of proteins by ubiquitin may serve several functions. Addition of monomers of ubiquitin to histones or insect actin appears to affect the higher order structure of chromatin or flight muscle, respectively (4, 5). More recently, ubiquitylation has been implicated in endocytosis of the Ste2p yeast mating type receptor (6), and ubiquitin has been proposed to serve a novel nonproteolytic role in the regulated activation of I␤␣ kinase (7). However, the best characterized function of ubiquitin is to promote the degradation of proteins to which it is attached especially when substrates are bound to a polyubiquitin chain rather than individual ubiquitin moieties (8). Polyubiquitin chains are formed by isopeptide linkages involving the C-terminal glycine (Gly 76 ) of one ubiquitin and a lysine ⑀ amino group on another. A ␤-galactosidase fusion protein covalently attached to a polyubiquitin chain consisting of 8 -12 ubiquitins linked by Gly 76 -Lys 48 isopeptide bonds is degraded approximately 10 times more rapidly than the monoubiquitylated substrate (8).The 26 S protease, which was discovered by its ability to degrade ubiquitin-lysozyme conjugates (9), is now known to be formed from two particles, the 19 S regulatory complex (10 -13) and the 20 S proteasome (14, 15). The regulatory complex confers substrate recognition and energy dependence upon the 26 S enzyme, and the proteasome provides proteolytic activities. Although the 26 S protease has been shown to degrade native unmodified ornithine decarboxylase (16), this enzyme of polyamine metab...

Ubiquitin conjugation is a signal for degradation of eukaryotic proteins by the 26S protease. Conjugation of a homopolymeric multiubiquitin chain to a substrate lysine residue results in 10-fold faster degradation than does conjugation of monoubiquitin, but the molecular basis of enhanced targeting by chains is unknown. We show that ubiquitin residues L8, I44, and V70 are critical for targeting. Mutation of pairs of these residues to alanine had little effect on attachment of ubiquitin to substrates but severely inhibited degradation of the resulting conjugates. The same mutations blocked the binding of chains to a specific subunit (S5a) of the regulatory complex of the 26S protease. The side chains implicated in this binding-L8, 144, and V70-form repeating patches on the chain surface. Thus, hydrophobic interactions between these patches and S5a apparently contribute to enhanced proteolytic targeting by multiubiquitin chains.

Ubiquitin is a covalent signal that targets cellular proteins to the 26 S proteasome. Multiple ubiquitins can be ligated together through the formation of isopeptide bonds between Lys 48 and Gly 76 of successive ubiquitins. Such a polyubiquitin chain constitutes a highly effective proteolytic targeting signal, but its mode of interaction with the proteasome is not well understood. Experiments to address this issue have been limited by difficulties in preparing useful quantities of polyubiquitin chains of uniform length. We report a simple method for large scale synthesis of Lys 48 -linked polyubiquitin chains of defined length. In the first round of synthesis, two ubiquitin derivatives (K48C-ubiquitin and Asp 77 -ubiquitin) were used as substrates for the well characterized ubiquitin-conjugating enzyme E2-25K. Diubiquitin blocked at the nascent proximal and distal chain termini was obtained in quantitative yield. Appropriately deblocked chains were then combined to synthesize higher order chains (tetramer and octamer in the present study). Deblocking was achieved either enzymatically (proximal terminus) or by chemical alkylation (distal terminus). Chains synthesized by this method were used to obtain the first quantitative information concerning the influence of polyubiquitin chain length on binding to the 26 S proteasome; this was done through comparison of different length (unanchored) polyubiquitin chains as inhibitors of ubiquitin-conjugate degradation. K 0.5 was found to decrease ϳ90-fold, from 430 to 4.8 M, as the chain was lengthened from two to eight ubiquitins. The implications of these results for the molecular basis of chain recognition are discussed.

The principal targeting signal used in the ubiquitin-proteasome degradation pathway is a homopolymeric, K48-linked polyubiquitin chain: the chain is recognized by a specific factor(s) in the 19S regulatory complex of the 26S proteasome, while the substrate is degraded by the 20S catalytic complex. We have previously presented evidence implicating the side chains of L8, I44, and V70 in the recognition of K48-linked chains. In the crystal structure of tetraubiquitin, these side chains form a repeating, surface-exposed hydrophobic patch. To test the hypothesis that a close-packing interaction involving this patch is important for the chain recognition, residue 8 was mutated to a series of smaller aliphatic amino acids (G, A, V). The effects of these mutations were first investigated in rabbit reticulocyte fraction II; even the severest truncating mutation (L8G) had only a modest inhibitory effect on the degradation of a model substrate (125I-lactalbumin). We show that these steady-state degradation data substantially underestimate the deleterious effects of these mutations on chain recognition by the proteasome, because the recognition step does not contribute to rate limitation in the fraction II system. Much stronger inhibition was observed when chain binding was measured in a competition assay using purified 26S proteasomes, and the change in binding free energy depended linearly on the surface area of the side chain. This behavior is consistent with a mode of binding in which the hydrophobic effect makes a favorable contribution; i.e., one or more L8 side chains is shielded from solvent when the chain binds to the 19S complex. A similar linear dependence of binding energy on side chain area was observed for chain binding to the 19S subunit known as S5a (as assayed using recombinant S5a bound to nickel beads). Octa-ubiquitin (K0.5 = 1.6 microM) bound to S5a 4.2-fold more tightly than tetra-ubiquitin; this is similar to the factor of 5. 8-fold relating the affinities of the same two chains for the 26S proteasome. Altogether, these findings indicate that the interaction of K48-linked chains with the 19S complex is substantially similar to the interaction of chains with isolated S5a. The results further suggest that the hydrophobic patch is part of a minimum element which allows for specific recognition of the polyubiquitin degradation signal by the 26S proteasome.