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

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.

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Publication Details

Journal
Nature Communications
Published
2024-11-15
DOI
https://doi.org/10.1038/s41467-024-54126-z
Citations
11
Primary Topic
Ubiquitin and proteasome pathways
Type
article
Field-Weighted Citation Impact
2.57

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article

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

Samuel Maiwald, Darcie J. Miller, Brenda Arlene Schulman, Daniel C. Scott et al.
11 citations
Nature Communications
Ubiquitin and proteasome pathways
2.57
article

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

Samuel Maiwald, Darcie J. Miller, Brenda Arlene Schulman, Daniel C. Scott, Stephen J. Elledge, João A. Paulo, Gary Kleiger, Kelly Churion, J. Wade Harper, Amanda Nourse, Nicholas Purser, Moeko T. King, Sagar Chittori, Chan Lee
article en
11 citations

Abstract

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.

Nature CommunicationsVol. 15(1)
Brigham and Women's Hospital (US), St. Jude Children's Research Hospital (US), University of Nevada, Las Vegas (US), Howard Hughes Medical Institute (US), Harvard University (US), Max Planck Institute of Biochemistry (DE)
Howard Hughes Medical Institute, U.S. Department of Energy, St. Jude Children's Research Hospital, Georgia Research Alliance, American Lebanese Syrian Associated Charities, National Institute for Health and Care Research, Max-Planck-Gesellschaft, National Institutes of Health, Office of Science, National Cancer Institute, National Institute of General Medical Sciences, Argonne National Laboratory
Openalex Percentile: Top 10%
Ubiquitin and proteasome pathways
2.57
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