NORMAL GENOMIC

• Kurz T et al.
• Dcn1 functions as a scaffold-type E3 ligase for cullin neddylation.
• Mol Cell. 2008; 29: 23-35
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• Cullin-based E3 ubiquitin ligases are activated through modification ofthe cullin subunit with the ubiquitin-like protein Nedd8. Dcn1 regulatescullin neddylation and thus ubiquitin ligase activity. Here we describethe 1.9 A X-ray crystal structure of yeast Dcn1 encompassing an N-terminalubiquitin-binding (UBA) domain and a C-terminal domain of uniquearchitecture, which we termed PONY domain. A conserved surface on Dcn1 isrequired for direct binding to cullins and for neddylation. The reciprocalbinding site for Dcn1 on Cdc53 is located approximately 18 A from the siteof neddylation. Dcn1 does not require cysteine residues for catalyticfunction, and directly interacts with the Nedd8 E2 Ubc12 on a surface thatoverlaps with the E1-binding site. We show that Dcn1 is necessary andsufficient for cullin neddylation in a purified recombinant system. Takentogether, these data demonstrate that Dcn1 is a scaffold-like E3 ligasefor cullin neddylation.

• Li W, Ye Y
• Polyubiquitin chains: functions, structures, and mechanisms.
• Cell Mol Life Sci. 2008; 65: 2397-406
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• Ubiquitin is a highly conserved 76-amino acid polypeptide that is foundthroughout the eukaryotic kingdom. The covalent conjugation of ubiquitin(often in the form of a polymer) to substrates governs a variety ofbiological processes ranging from proteolysis to DNA damage tolerance. Thefunctional flexibility of this post-translational modification has itsroots in the existence of a large number of ubiquitinating enzymes thatcatalyze the formation of distinct ubiquitin polymers, which in turnencode different signals. This review summarizes recent advances in thefield with an emphasis on the non-canonical functions ofpolyubiquitination. We also discuss the potential mechanism of chainlinkage specification as well as how structural disparity in ubiquitinpolymers may be distinguished by ubiquitin receptors to translate theversatile ubiquitin signals into various cellular functions.

• Canning M, Boutell C, Parkinson J, Everett RD
• A RING finger ubiquitin ligase is protected from autocatalyzedubiquitination and degradation by binding to ubiquitin-specific proteaseUSP7.
• J Biol Chem. 2004; 279: 38160-8
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• Herpes simplex virus type 1 immediate-early regulatory protein ICP0stimulates lytic infection and reactivation from latency, processes thatrequire the ubiquitin E3 ligase activity mediated by the RING fingerdomain in the N-terminal portion of the protein. ICP0 stimulates theproduction of polyubiquitin chains by the ubiquitin-conjugating enzymesUbcH5a and UbcH6 in vitro, and in infected and transfected cells itinduces the proteasome-dependent degradation of a number of cellularproteins including PML, the major constituent protein of PML nuclearbodies. However, ICP0 binds strongly to the cellular ubiquitin-specificprotease USP7, a member of a family of proteins that cleave polyubiquitinchains and/or ubiquitin precursors. The region of ICP0 that is requiredfor its interaction with USP7 has been mapped, and mutations in thisdomain reduce the functionality of ICP0. These findings pose the question:why does ICP0 include domains that are associated with the potentiallyantagonistic functions of ubiquitin conjugation and deconjugation? Here wereport that although neither protein affected the intrinsic activities ofthe other in vitro, USP7 protected ICP0 from autoubiquitination in vitro,and their interaction can greatly increase the stability of ICP0 in vivo.These results demonstrate that RING finger-mediated autoubiquitination ofICP0 is biologically relevant and can be regulated by interaction withUSP7. This principle may extend to a number of cellular RING finger E3ubiquitin ligase proteins that have analogous interactions withubiquitin-specific cleavage enzymes.

• Matsumoto M et al.
• Molecular clearance of ataxin-3 is regulated by a mammalian E4.
• EMBO J. 2004; 23: 659-69
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• Insoluble aggregates of polyglutamine-containing proteins are usuallyconjugated with ubiquitin in neurons of individuals with polyglutaminediseases. We now show that ataxin-3, in which the abnormal expansion of apolyglutamine tract is responsible for spinocerebellar ataxia type 3(SCA3), undergoes ubiquitylation and degradation by the proteasome.Mammalian E4B (UFD2a), a ubiquitin chain assembly factor (E4), copurifiedwith the polyubiquitylation activity for ataxin-3. E4B interacted with,and thereby mediated polyubiquitylation of, ataxin-3. Expression of E4Bpromoted degradation of a pathological form of ataxin-3. In contrast, adominant-negative mutant of E4B inhibited degradation of this form ofataxin-3, resulting in the formation of intracellular aggregates. In aDrosophila model of SCA3, expression of E4B suppressed theneurodegeneration induced by an ataxin-3 mutant. These observationssuggest that E4 is a rate-limiting factor in the degradation ofpathological forms of ataxin-3, and that targeted expression of E4B is apotential gene therapy for SCA3.

• Pickart CM
• Ubiquitin biology: an old dog learns an old trick.
• Nat Cell Biol. 2000; 2: 13941-13941
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• Regulated protein degradation in eukaryotes occurs principally throughcovalent tagging of substrates with ubiquitin, thereby targeting them fordestruction by 26S proteasomes. Classical allostery has now been added tothe repertoire of mechanisms that can modulate ubiquitin tagging, allowingfeed-forward regulation to be achieved through targeted proteindestruction.

• Chen P, Johnson P, Sommer T, Jentsch S, Hochstrasser M
• Multiple ubiquitin-conjugating enzymes participate in the in vivodegradation of the yeast MAT alpha 2 repressor.
• Cell. 1993; 74: 357-69
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• Attachment of ubiquitin to proteins is catalyzed by a family ofubiquitin-conjugating (UBC) enzymes. Although these enzymes are essentialfor many cellular processes; their molecular functions remain unclearbecause no physiological target has been identified for any of them. Herewe show that four UBC proteins (UBC4, UBC5, UBC6, and UBC7) target theyeast MAT alpha 2 transcriptional regulator for intracellular degradationby two distinct ubiquitination pathways. UBC6 and UBC7 define one of thepathways and can physically associate. The UBC6/UBC7-containing complextargets the Deg1 degradation signal of alpha 2, a conclusion underscoredby the finding that UBC6 is encoded by DOA2, a gene previously implicatedin Deg1-mediated degradation. These data reveal an unexpected overlap insubstrate specificity among diverse UBC enzymes and suggest acombinatorial mechanism of substrate selection in which UBC enzymespartition into multiple ubiquitination complexes.