Structural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases

• Published in: Nature communications 2024-11, Vol.15 (1), p.9899-17, Article 9899
• Main Authors: Scott, Daniel C., Chittori, Sagar, Purser, Nicholas, King, Moeko T., Maiwald, Samuel A., Churion, Kelly, Nourse, Amanda, Lee, Chan, Paulo, Joao A., Miller, Darcie J., Elledge, Stephen J., Harper, J. Wade, Kleiger, Gary, Schulman, Brenda A.
• Format: Article
• Language: English
• Subjects: 101/28; 631/45/535/1258; 631/45/535/1266; 631/45/612/645; 82/103; Amino Acid Motifs; Binding; Biochemistry; C-Terminus; Combinatorial analysis; Cryoelectron Microscopy; Crystallography; Crystallography, X-Ray; Cullin; Degrons; Efficiency; Enzymes; Grooves; Humanities and Social Sciences; Humans; Models, Molecular; multidisciplinary; Propeller blades; Propellers; Proteasomes; Protein Binding; Proteins; Quality control; Science; Science (multidisciplinary); Sequences; Substrate Specificity; Substrates; Ubiquitin - metabolism; Ubiquitin-protein ligase; Ubiquitin-Protein Ligases - chemistry; Ubiquitin-Protein Ligases - genetics; Ubiquitin-Protein Ligases - metabolism; Ubiquitination
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-54126-z

Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the termini of substrates. However, our knowledge of structural features distinguishing closely related C-degron substrate-E3 pairings is limited. Here, by systematically comparing ubiquitylation activities towards a suite of common model substrates, and defining interactions by biochemistry, crystallography, and cryo-EM, we reveal principles of C-degron recognition across the KLHDCX family of Cullin-RING ligases (CRLs). First, a motif common across these E3 ligases anchors a substrate’s C-terminus. However, distinct locations of this C-terminus anchor motif in different blades of the KLHDC2, KLHDC3, and KLHDC10 β-propellers establishes distinct relative positioning and molecular environments for substrate C-termini. Second, our structural data show KLHDC3 has a pre-formed pocket establishing preference for an Arg or Gln preceding a C-terminal Gly, whereas conformational malleability contributes to KLHDC10’s recognition of varying features adjacent to substrate C-termini. Finally, additional non-consensus interactions, mediated by C-degron binding grooves and/or by distal propeller surfaces and substrate globular domains, can substantially impact substrate binding and ubiquitylatability. Overall, the data reveal combinatorial mechanisms determining specificity and plasticity of substrate recognition by KLDCX-family C-degron E3 ligases. 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.