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Jakob Farnung and Brenda Schulman detail chemical diversification that endows the protein ubiquitin with many important cellular functions.

In targeted protein degradation, a degrader molecule brings a neosubstrate protein proximal to a hijacked E3 ligase for its ubiquitination. Here, pseudo-natural products derived from (−)-myrtanol—iDegs—are identified to inhibit and induce degradation of the immunomodulatory enzyme indoleamine-2,3-dioxygenase 1 (IDO1) by a distinct mechanism. iDegs prime apo-IDO1 ubiquitination and subsequent degradation using its native proteolytic pathway.

As Nature Chemical Biology approaches its third decade we asked a collection of chemical biologists, “What do you think are the most exciting frontiers or the most needed developments in your main field of research?” — here is what they said.

The structure of the enzyme E1 bound to its four substrates is described, showing how a thioester switch toggles E1-E2 affinities. Transferring the Ubl's thioester linkage between successive conjugation enzymes induces striking conformational changes and alters interaction networks to drive consecutive steps in Ubl cascades.

Using biochemistry, chemical biology, and cryo-EM, Maiwald et al. elucidate how TRIP12 forms K29 linkages and K29/K48-linked branched ubiquitin chains, revealing a mechanism for polyubiquitylation shared by some HECT E3s.

The authors define a NEDD8-activated cullin-RING E3 poly-ubiquitylation mechanism using chemistry, cryo-EM and rapid kinetics. Near-perfect catalytic efficiency is achieved by an E2 ‘synergy loop’ connecting to the E3, donor and acceptor ubiquitins.

Transmembrane E3 ligases are crucial in cellular homeostasis and metabolic regulation. Here, the authors provide the structural details of the ER-resident E3 ligase MARCH6/Doa10, uncovering its unique circular membrane structure and its role in ubiquitylation processes, essential for protein quality control.

The mechanistic details of the attachment of a small protein, ubiquitin, to other proteins are unclear. Crystal structures of the complexes formed by the E2–ubiquitin and RING E3 enzymes offer new insights. See Article p.115

Kelch-domain KLHDCX E3 ligases bind substrate C-terminal glycines. This study reveals substrate selectivity by E3s with similar structures; C-degrons are perceived by a “C-terminus anchor motif”, whose display on different Kelch propeller blades along with distal interactions establish specificity.

KLHDC2 is a promising E3 ligase for targeted protein degradation (TPD). In this study, the authors demonstrate that heterobifunctional degraders induce cooperative ternary complexes with KLHDC2 and BRD3. They highlight exit vector, neo-substrate, E3 ligase selectivity, and prodrug choice can effectively leverage C-degron E3s for TPD.

RING E3 ligases mediate transfer of ubiquitin-like proteins from an E2 ligase to a substrate, but how this occurs is a long-standing mystery. Docking E2-RING structures onto a new crystal structure of the C-terminal domain of the E3-RING CUL1 in complex with the RBX1 RING protein now shows how a conformational change in RBX1 allows for the transfer by closing a gap between CUL1 and the E2.

The anaphase promoting complex (APC) is a key cell-cycle regulator that has ubiquitin-ligase activity. The first structure of a complex formed between APC subunits, that of CDC26 and APC6, provides detailed structural information of APC components and suggests how CDC26 may stabilize APC6 and other complex subunits.

Interferon stimulated gene 15 (ISG15) is a ubiquitin-like protein with critical roles in the innate immune response. Here, the authors present a Cryo-EM structure of ISG15 in complex with its E1 and E2 enzymes, providing insights into the specificity determinants of this pathway.

Homologous to E6AP C-terminus (HECT) E3s forge polyubiquitin chains through multiple reaction steps. A HECT polyubiquitylation cascade was visualized step-by-step, through use of chemical tools and cryo‐EM, and revealed how K48 linkage-specificity is attained by oligomeric UBR5.

Researchers have met the challenge of capturing transient states of the SUMO E1 activating enzyme. Their pictures show radically different crystal structures for two of the steps in this enzyme's activity.

The GID E3 ligase regulates glucose-induced degradation in yeast, and key physiology. This study unveils E3 ligase regulation by reshaping the substrate binding site, blocking substrate access to ubiquitination active sites, and a Cage-like assembly.

Targeted protein degradation uses small molecules to recruit proteins to E3 ligases to induce their ubiquitylation and degradation, but only a few human E3 ligases are amenable to this strategy. Here, the authors identify and characterize SP3N, a specific degrader of the prolyl isomerase FKBP12, containing an FKBP12 ligand appended with a flexible alkylamine tail that is metabolized to an active aldehyde species which recruits the SCF^FBXO22 ligase for FKBP12 degradation.

Host cells battle invading bacteria using a degradation process facilitated by the protein ubiquitin. The discovery of the host enzyme responsible and its bacterial target reveals that this process defies convention.

Structures and biochemistry reveal how covalent linkage of a ubiquitin-like protein elicits protein–protein interactions indirectly. NEDD8 allosterically activates CUL5-RBX2 cullin-RING E3 binding to the ARIH2 RBR-type E3 for joint ubiquitylation.

The attachment of ubiquitin-like proteins (UBLs) to proteins is a central mechanism of modulation of protein function. Enzymatic, structural and genetic studies have elucidated how mechanistically and structurally related E1 enzymes activate UBLs and selectively direct them to downstream pathways.

Here, using cryo-EM, biochemistry and cell biology, the authors reveal the unique assembly, catalytic mechanism, multimodal substrate recruitment and regulation of the atypical ubiquitin ligase complex CUL9–RBX1.

Precise protease positioning and gating of the proteasome core require the ordered assembly of 28 subunits. Cryo-EM structures of seven intermediates visualize five dedicated chaperones and three propeptides mediating step-by-step assembly of the human 20S proteasome.

A cryo-electron microscopy structure provides insights into the activation of cullin–RING E3 ligases by NEDD8 and the consequent catalysis of ubiquitylation reactions.

Autophagy mediated by the conjugation pathway for ubiquitin-like proteins plays a key role in controlling homeostasis in eukaryotic cells. Here the authors provide a molecular basis for allosteric activation of the E2 ligase Atg3, uncovering the mechanism underlying Atg8 lipidation and a novel mechanism regulating E1-E2-E3-mediated ubiquitin-like protein conjugation.

SCF–FBXO31 scans proteins for C-terminal amidation and marks them for subsequent proteasomal degradation.

Henneberg et al. developed conformation-specific antibodies enabling probing NEDD8-activated cullin–RING ubiquitin E3 ligase networks in response to extracellular stimuli, metabolic signals and degrader drugs.

High-throughput screening and structure-guided design identified small-molecule inhibitors that prevent the interaction between N-terminally acetylated E2 conjugating enzyme UBE2M and DCN1, an E3 ligase for the ubiquitin-like protein Nedd8.

The cryo-EM structure of CRL7^FBXW8 shows that CUL7–RBX1 binds FBXW8–SKP1 in an F-box-independent manner. Bridged by FBXW8–SKP1, CRL7^FBXW8 forms a multi-cullin E3 ligase complex with neddylated CUL1–RBX1, which ubiquitinates a substrate recruited to CUL7.

APC/C is an E3 ligase complex of ~1.5 MDa that regulates cell division. APC/C^CDH1 is inhibited during interphase by EMI1. Now, NMR spectroscopy, electron microscopy and enzymology analyses are integrated, revealing that EMI1's 143-residue C-terminal domain binds distinct regions of APC/C^CDH1 to block the substrate-binding site and inhibit ubiquitin-chain elongation.

An early step in the autophagy process is the conjugation of the ubiquitin-like proteins (UBLs) Atg8 and Atg12 to their targets. Structural and functional experiments reveal how the autophagy E1 Atg7 uses a trans mechanism to catalyze the charging of the autophagy UBLs onto their respective carrier E2 proteins, Atg3 and Atg10.

Activation of the anaphase-promoting complex/cyclosome (APC/C) depends on disassembly of the mitotic checkpoint complex (MCC), which has been proposed to require CDC20 autoubiquitylation. A new study involving reconstituted recombinant human APC/C supports the view that the APC15 subunit of APC/C localizes near the MCC binding site and mediates CDC20 autoubiquitylation, thereby promoting MCC disassembly.

Cryo-electron microscopy of neddylated SCF-family ligases interacting with the RBR-type E3 ligase ARIH1 reveals the steps through which E3–E3 super-assemblies ubiquitylate a diverse set of substrates presented on F-box proteins.

Using synthetic ubiquitins with non-natural acceptor site, the authors revealed that the length of lysine side chain in acceptor ubiquitins affects ubiquitin chain linkage specificity with native lysine as the preferred geometry.

Hoyer et al. establish that selective autophagy mechanisms are needed to remodel the ER and its proteome during in vitro neurogenesis across neuronal subcompartments and decode the substrate selectivity of ER-phagy receptors.

Mass photometry is a label-free optical approach capable of detecting, imaging and accurately measuring the mass of single biomolecules in solution. Here, the authors demonstrate the potential of mass photometry for quantitatively characterizing sample heterogeneity of purified protein complexes with implications for structural studies specifically and in vitro studies more generally.

Ubiquitination of the receptor FAM134B regulates ER-phagy and remodelling of the endoplasmic reticulum in response to cellular demands.

Ubiquitin-like protein (Ubl)-specific proteases catalyze Ubl precursor processing and deconjugation. Two recent structural studies of SUMO-specific protease (SENP)–substrate complexes provide new insight into hydrolysis of the peptide bond at the C terminus of SUMO. A kinked, cis configuration for the scissile bond is crucial for proteolysis.

Protein ubiquitylation is often studied by proteomics but how data independent acquisition (DIA) may advance these studies remains to be explored. Here, the authors show that DIA improves ubiquitylation site identification and quantification, enabling them to characterize the circadian ubiquitinome in human cells.

A small-molecule ligand of the APC/C activator Cdc20, which prolongs mitosis in unperturbed cells, instead shortens mitosis when the spindle checkpoint is activated, producing an opposite effect in a different regulatory context.

Molecular-glue-mediated proximity-induced degradation now allows unprecedented therapeutic targeting of previously undruggable proteins. Structures showing how aryl-sulfonamides mediate recruitment of the splicing factor RBM39 to the E3 CRL4^DCAF15 broaden the mechanistic principles by which molecular glues target ubiquitylation.