The cullin protein family

Abstract

Cullin proteins are molecular scaffolds that have crucial roles in the post-translational modification of cellular proteins involving ubiquitin. The mammalian cullin protein family comprises eight members (CUL1 to CUL7 and PARC), which are characterized by a cullin homology domain. CUL1 to CUL7 assemble multi-subunit Cullin-RING E3 ubiquitin ligase (CRL) complexes, the largest family of E3 ligases with more than 200 members. Although CUL7 and PARC are present only in chordates, other members of the cullin protein family are found in Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and yeast. A cullin protein tethers both a substrate-targeting unit, often through an adaptor protein, and the RING finger component in a CRL. The cullin-organized CRL thus positions a substrate close to the RING-bound E2 ubiquitin-conjugating enzyme, which catalyzes the transfer of ubiquitin to the substrate. In addition, conjugation of cullins with the ubiquitin-like molecule Nedd8 modulates activation of the corresponding CRL complex, probably through conformational regulation of the interactions between cullin's carboxy-terminal tail and CRL's RING subunit. Genetic studies in several model organisms have helped to unravel a multitude of physiological functions associated with cullin proteins and their respective CRLs. CRLs target numerous substrates and thus have an impact on a range of biological processes, including cell growth, development, signal transduction, transcriptional control, genomic integrity and tumor suppression. Moreover, mutations in CUL7 and CUL4B genes have been linked to hereditary human diseases.

Figure 1

Phylogenetic tree of the cullin gene family. Phylogenetic tree based on the alignment of cullins of Homo sapiens (Hs), Mus musculus (Mm), Rattus norvegicus (Rn), Drosophila melanogaster (Dm) and Caenorhabditis elegans (Ce). Gene IDs are as listed in Table 1. ClustalX was used to align sequences using the standard settings. The tree was drawn using Figtree v1.3.1. The bar indicates the proportion of amino acid sites at which two compared sequences are different. Iso, isoform.

Figure 2

Cullin protein domain organization in humans. Cullin repeat 1 (CR1) anchors the cognate adaptor proteins, and the cullin homology domain (CH) at the carboxyl terminus is critical for binding of the RING-finger protein. The red line indicates the position of the neddylation site. For CUL7 and PARC the neddylation site is based on consensus sequence alignment without experimental verification. Size and location of the individual domains are schematic representations and do not depict the exact proportions. Abbreviations: aa, amino acids; CH, cullin homology domain; CPH, conserved domain in CUL7, PARC and HERC2; CR, cullin repeat; DOC, a domain similar to the DOC1 domain of the anaphase-promoting complex/cyclosome but of unknown function; IBR, in between RING; RING, really interesting new gene.

Figure 3

The ubiquitin-proteasome system. The conserved 76-amino-acid polypeptide ubiquitin (Ub) is activated in an ATP-dependent reaction by an E1 ubiquitin-activating enzyme and transferred to an E2 ubiquitin-conjugating enzyme. An E3 ubiquitin ligase binds both the substrate protein and a ubiquitin-charged E2 enzyme for ubiquitin transfer, resulting in the mono-, multi- (not shown) or polyubiquitination of the substrate. The mode of ubiquitination determines whether the substrate protein is degraded by the 26S proteasome or altered in a non-proteolytic manner. See Boxes 1 and 2 for additional information.

Figure 4

Modularity of cullin-RING E3 ligases. Cullin proteins are molecular scaffolds that assemble multi-subunit cullin-RING E3 ubiquitin ligase (CRL) complexes. The mammalian cullin protein family comprises eight members (CUL1 to CUL7 and PARC). In CRL, a cullin protein tethers both a substrate-recognition subunit, often through an adaptor protein, and the RING finger component. The cullin-organized CRL thus positions a substrate in close proximity to the RING-bound E2 ubiquitin-conjugating enzyme (not shown), which catalyzes the transfer of ubiquitin to the substrate. (a) General CRL composition. (b) Specific composition of the CRLs 1 to 7 and PARC. BTB, Bric-a-brac, Tramtrack, Broad-complex domain; DCAF, DDB1-CUL4 associated factor; DDB1, DNA damage-binding protein 1; Fbw8, F-box and WD repeat domain containing protein 8; PARC, p53-associated parkin-like cytoplasmic protein; SOCS, Suppressors of cytokine signaling; Skp1, S-phase kinase-associated protein 1; VHL-Box, von Hippel-Lindau box.

Figure 5

Cullins assemble the largest subfamily of E3 ubiquitin ligases. Pie chart of the numbers of human E3 ubiquitin ligases, estimated from the numerical distribution of genes predicted to encode E3 RING or HECT polypeptides or, in the case of CRLs, the substrate-recognition molecules that include F-box, SOCS, BTB with 3-box and DCAF proteins. Numbers refer to human gene numbers for F-box, SOCS, HECT, U-box and non-CRL RING proteins, derived from Li et al. [53]. The estimation for the human DCAF family is described by Lee and Zhou [34]. Kay Hofmann has kindly provided the tally of human genes encoding BTB and 3-box proteins (personal communication). The Hofmann estimation is based on the structural work from Schulman and colleagues [13], which identified a critical role for the 3-box in the assembly of CRL3 with the SPOP BTB protein. 72 BTB-only (without 3-box) genes have not been counted for the estimation of CRL3s.