Structural Basis for Recruitment of DAPK1 to the KLHL20 E3 Ligase
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Abstract
BTB-Kelch proteins form the largest subfamily of Cullin-RING E3 ligases, yet their substrate complexes are mapped and structurally characterized only for KEAP1 and KLHL3. KLHL20 is a related CUL3-dependent ubiquitin ligase linked to autophagy, cancer, and Alzheimer's disease that promotes the ubiquitination and degradation of substrates including DAPK1, PML, and ULK1. We identified an "LPDLV"-containing motif in the DAPK1 death domain that determines its recruitment and degradation by KLHL20. A 1.1-Å crystal structure of a KLHL20 Kelch domain-DAPK1 peptide complex reveals DAPK1 binding as a loose helical turn that inserts deeply into the central pocket of the Kelch domain to contact all six blades of the β propeller. Here, KLHL20 forms salt-bridge and hydrophobic interactions including tryptophan and cysteine residues ideally positioned for covalent inhibitor development. The structure highlights the diverse binding modes of β-propeller domains versus linear grooves and suggests a new target for structure-based drug design.
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Crystal structures of peptide substrate complexes have been reported for four BTB-Kelch family members, including KEAP1, KLHL2, KLHL3 and KLHL20.
“Crystal structures of peptide substrate complexes have been reported for four BTB-Kelch family members, including KEAP1, KLHL2, KLHL3 and KLHL20 (refs 80,81,82 ).”
From Targeted protein degradation: expanding the toolbox (2019) · cites this paper as [82]
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- Authors
- Chen, Z., Picaud, S., Filippakopoulos, P., D'Angiolella, V., & Bullock, A. N.
- Affiliations
- University of Oxford (GB)
- Corresponding author
- Bullock, Alex N.
- Venue
- Structure
- Publisher
- Elsevier BV
- Published
- 2019-09
- Volume
- 27
- Issue
- 9
- Pages
- 1395-1404.e4
- ISSN
- 0969-2126 (ISSN-L)
- PMC
- PMC6720452
- OpenAlex
- W2954075939
- Cited by
- 37
- References
- 43
- Citations by year
- 2026: 4 · 2025: 9 · 2024: 6 · 2023: 3 · 2022: 5 · 2021: 2 · 2020: 6 · 2019: 2
- FWCI
- 1.24
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Structure (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- Funders
- China Scholarship Council - Nuffield Department of Medicine Scholarship
- Medical Research Council (MR/N010051/1, MC_UU_00001/7)
- Cancer Research UK (C5255/A18085)
- AbbVie
- Bayer Pharma
- Boehringer Ingelheim
- Canada Foundation for Innovation
- Eshelman Institute for Innovation
- Genome Canada
- Innovative Medicines Initiative (115766)
- Janssen
- Merck Germany
- MSD
- Novartis Pharma
- Ontario Ministry of Economic Development and Innovation
- Pfizer
- São Paulo Research Foundation
- Takeda
- Wellcome (106169/ZZ14/Z)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- DAPK1, Kelch domain, death domain, substrate recognition motif, protein-protein interaction, crystal structure, beta-propeller, ubiquitination, structure-based drug design, autophagy, Alzheimer's disease
- MeSH terms
- Protein Domains, Binding Sites, Female, Humans, Models, Molecular, Protein Binding, Protein Structure, Secondary, Crystallography, X-Ray, Adaptor Proteins, Signal Transducing, Ubiquitination, HEK293 Cells, Hydrophobic and Hydrophilic Interactions, Proteolysis, Death-Associated Protein Kinases
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