Function and regulation of cullin–RING ubiquitin ligases

Abstract

Multisubunit UBIQUITIN LIGASES (E3s) that are assembled on a CULLIN scaffold were first reported seven years ago 1,2. The discovery of the archetypical cullin-RING ubiquitin ligase-SCF Cdc4-benefited from a strong foundation of genetic studies on cell division in Saccharomyces cerevisiae and Caenorhabditis elegans. The model established by SCF can now be extended to a superfamily of CULLIN-RING LIGASES (CRLS) that are found throughout eukaryotes. Together, these enzymes regulate a dazzling array of cellular and organismal processes-from glucose sensing and DNA replication to limb patterning and circadian rhythms. Although there is a great diversity of CRLs in terms of their composition and function, we propose that these enzymes can be characterized by a set of general principles that will apply to most members of the superfamily. In this review, we summarize what has been learned about SCF and other CRLs over the past seven years and, from this, we extract the key features that typify these enzymes. We also highlight the murky areas in which our understanding remains far from clear. Cullin-RING ligases are modular The cullin family. Human cells express seven different cullins (CUL1, 2, 3, 4A, 4B, 5 and 7) that each nucleate a multisubunit ubiquitin ligase (FIG. 1). In addition, at least two other proteins (the APC2 subunit of the ANAPHASE-PROMOTING COMPLEX/CYCLOSOME (APC/C) and the p53 cytoplasmic anchor protein PARC) contain a 'cullin-homology domain' 3-5. Although APC2 and PARC have ubiquitin-ligase activity, they are clearly distinct from the other cullins and are not considered here. The archetypal CRLs, which contain CUL1, are named SCF ubiquitin ligases, whereas the other CRLs have distinct subunit compositions and have been referred to by various names (TABLE 1). Cullin-RING ligases have an extended, rigid architecture. Much of what is known and inferred about the architecture of CRLs comes from protein-protein interaction studies and sequence comparisons that have been interpreted in light of three-dimensional (3D) X-ray crystal structures (for a summary of the solved structures for CRL complexes and related proteins, see online supplementary information S1 (table)). CUL1 and presumably all other cullins have a curved, yet rigid, N-terminal stalk that is comprised of three repeats of a five-helix bundle (cullin repeat (CR)1-3) and is linked to a C-terminal globular domain 6 (FIG. 2). The SKP1 adaptor binds to the N-terminal CR1 region, whereas the zinc-binding RING-H2-DOMAIN proteinwhich is known as either ROC1, RBX1 or HRT1 (REFS 7-10; and is referred to here as the 'RING' subunit)-binds 100 Å away from SKP1 and interdigitates itself with the C-terminal globular domain. SKP1 recruits substrate receptors and the RING subunit recruits the ubiquitin-conjugating enzyme (E2) to form the active ligase complex. The rigidity of the N-terminal stalk of CUL1 might juxtapose the E2 and the substrate to favour ubiquitin transfer, because a mutation that

The COP9 signalosome-mediated deneddylation is stimulated by caspases during apoptosis

“…The increase of CSN5 isopeptidase activity might be explained by a conformational change induced by cleaving off 23 amino acids of CSN6. Since CSN-mediated deneddylation prevents CRL complex assembly [2,4,43], it is conceivable to assume that the elevation of this activity is another strategy to knockout CRLs during apoptosis. In fact, it has been shown that the typical Cul1-CRL substrate, p27 Kip [44], is accumulated in tumor cells after treatment with etoposide [45].…”

“…The CSN interacts with components of the ubiquitin (Ub) proteasome system (UPS) known as cullin-RING Ub ligases (CRLs) [2]. These enzyme complexes select proteins for ubiquitination and are responsible for substrate specificity of the UPS.…”

“…These enzyme complexes select proteins for ubiquitination and are responsible for substrate specificity of the UPS. Besides a specific cullin, most of the CRLs contain a RING domain protein called ROC1/Rbx1 involved in the Ub ligation reaction as well as substrate recognition components [2,3]. The CSN removes the Ub-like protein Nedd8 from its covalent linkage to cullins, a process called deneddylation [4][5][6].…”

Building and remodelling Cullin–RING E3 ubiquitin ligases

“…DDB1 is unrelated to SKP1 and ELOC, but also associates with the N-terminus of the cullin. For each receptor family, between 20 and 100 specific receptor proteins have been identified [21,22]. In addition, PARC/CUL9 has been shown to bind to RBX1 and to be neddylated, but it does not associate with SKP1 or F-box proteins [101], and its molecular functions and adaptors remain to be identified.…”

“…As expanded on below, however, the available data indicate that the CRL is unlikely to be in this basal state for a substantial amount of time and, in principle, will probably populate a wide range of architectures during its lifetime. Relevant events that modify the CRL architecture include: activation through the process of neddylation; association of the active neddylated form with the COP9 signalosome (CSN) complex, a multisubunit deneddylase that can sterically block substrate access, catalyse cullin deneddylation, and remain bound to the CRL; loss of SR through proteolytic degradation; and SR exchange via a CAND1-driven mechanism [21,[34][35][36][37][38][40][41][42][43]. A confounding factor to understanding this regulation is that in cells these different events are generally not synchronized for CRLs en masse, or for individual CRL SR complexes.…”