CUL5-ARIH2 E3-E3 ubiquitin ligase structure reveals cullin-specific NEDD8 activation

An emerging mechanism of ubiquitylation involves partnering of two distinct E3 ligases. In the best-characterized E3-E3 pathways, ARIH-family RING-between-RING (RBR) E3s ligate ubiquitin to substrates of neddylated cullin-RING E3s. The E3 ARIH2 has been implicated in ubiquitylation of substrates of neddylated CUL5-RBX2-based E3s, including APOBEC3-family substrates of the host E3 hijacked by HIV-1 virion infectivity factor (Vif). However, the structural mechanisms remained elusive. Here structural and biochemical analyses reveal distinctive ARIH2 autoinhibition, and activation on assembly with neddylated CUL5-RBX2. Comparison to structures of E3-E3 assemblies comprising ARIH1 and neddylated CUL1-RBX1-based E3s shows cullin-specific regulation by NEDD8. Whereas CUL1-linked NEDD8 directly recruits ARIH1, CUL5-linked NEDD8 does not bind ARIH2. Instead, the data reveal an allosteric mechanism. NEDD8 uniquely contacts covalently linked CUL5, and elicits structural rearrangements that unveil cryptic ARIH2-binding sites. The data reveal how a ubiquitin-like protein induces protein-protein interactions indirectly, through allostery. Allosteric specificity of ubiquitin-like protein modifications may offer opportunities for therapeutic targeting.We thank D. Bollschweiler and T. Schäfer of the cryo-EM facility and we thank the crystallography facility at Max Planck Institute of Biochemistry

Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly

E3 ligases are typically classified by hallmark domains such as RING and RBR, which are thought to specify unique catalytic mechanisms of ubiquitin transfer to recruited substrates(1,2). However, rather than functioning individually, many neddylated cullin-RING E3 ligases (CRLs) and RBR-type E3 ligases in the ARIH family-which together account for nearly half of all ubiquitin ligases in humans-form E3-E3 super-assemblies(3-7). Here, by studying CRLs in the SKP1-CUL1-F-box (SCF) family, we show how neddylated SCF ligases and ARIH1 (an RBR-type E3 ligase) co-evolved to ubiquitylate diverse substrates presented on various F-box proteins. We developed activity-based chemical probes that enabled cryo-electron microscopy visualization of steps in E3-E3 ubiquitylation, initiating with ubiquitin linked to the E2 enzyme UBE2L3, then transferred to the catalytic cysteine of ARIH1, and culminating in ubiquitin linkage to a substrate bound to the SCF E3 ligase. The E3-E3 mechanism places the ubiquitin-linked active site of ARIH1 adjacent to substrates bound to F-box proteins (for example, substrates with folded structures or limited length) that are incompatible with previously described conventional RING E3-only mechanisms. The versatile E3-E3 super-assembly may therefore underlie widespread ubiquitylation.Chemical Immunolog

New classes of E3 ligases illuminated by chemical probes

Specificity in the ubiquitin system depends on E3 ligases, largely belonging to a handful of families discovered more than a decade ago. However, the last two years brought a quantum leap in the identification and/or mechanistic characterization of eukaryotic ubiquitin ligases, in part through implementation of activity-based chemical probes and cryo-EM. Here, we survey recent discoveries of RING-Cys-Relay, RZ-finger, and neddylated cullin-RING-ARIH RBR E3- E3 ubiquitin ligase mechanisms. These ligases transfer ubiquitin through unprecedented mechanisms- via novel catalytic domains or domain combinations-and collectively modify unconventional amino acids, non-proteinaceous bacterial lipid targets, and structurally diverse substrates recruited to numerous cullin-RING ligases. We anticipate major expansion of the types, features, and mechanisms of E3 ligases will emerge from such chemical and structural approaches in the coming years

The behavior of truth and justification and their relationship to the assertive practice

Crispin Wright afirma que tanto la norma que insta a afirmar lo verdadero como la que exhorta a afirmar lo justificado son distintivas de la práctica asertórica. A pesar de que ellas no son diferentes en la práctica, son distintas. Pero Richard Rorty argumenta que las razones ofrecidas obligarían a Wright a aceptar demasiadas reglas como propias de dicha práctica. Wright admitiría que las normas pueden ser ilimitadas, pero no que son ilimitadas las normas correctas. Para defender esta posición, basta con distinguir, como hace, las normas descriptivas de las prescriptivas. A pesar de ello, la posición de Rorty es admisible, pues no parece haber ventajas visibles en distinguir ambas normas. Si no se exponen (y Wright no lo hace) estas ventajas, la teoría resultante será más débil que una que no lo pretenda (como la que Rorty defiende).Crispin Wright argues that both the standard that urges to assert the truth, and the one that told to assert what is justified, are distinctive of the assertoric practice. Despite that there’s no difference in practice between them, they are different. But Richard Rorty argues that the reasons given, would force Wright to accept too many rules as distinctive of the practice. Wright admits that those kinds of standards can be unlimited, but that the correct standards are not. To defend this position, it’s enough to distinguish descriptive rules from the prescriptive ones. However, Rorty’s position is admissible, because there seems to be no advantages in distinguishing between those two standards. If these advantages are not presented (and Wright does not), the resulting theory will be weaker than one that doesn’t pretend to do it (as Rorty claims).Fil: Pailos, Federico Matias. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin