The Molecular Basis of CRL4DDB2/CSA Ubiquitin Ligase Architecture, Targeting, and Activation

Fischer, Eric S.; Scrima, Andrea; Böhm, Kerstin; Matsumoto, Syota; Lingaraju, Gondichatnahalli M.; Faty, Mahamadou; Yasuda, Takeshi; Cavadini, Simone; Wakasugi, Mitsuo; Hanaoka, Fumio; Iwai, Shigenori; Gut, Heinz; Sugasawa, Kaoru; Thomä, Nicolas H.

doi:10.1016/j.cell.2011.10.035

Cited by 460Ubiquitin and proteasome pathwaysDNA Repair MechanismsGenomics and Chromatin Dynamics

The Molecular Basis of CRL4DDB2/CSA Ubiquitin Ligase Architecture, Targeting, and Activation

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Fischer, Eric S., Scrima, Andrea, Böhm, Kerstin, Matsumoto, Syota, Lingaraju, Gondichatnahalli M., Faty, Mahamadou, Yasuda, Takeshi, Cavadini, Simone +6 more·2011·Cell

DOI 10.1016/j.cell.2011.10.035

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Abstract

The DDB1-CUL4-RBX1 (CRL4) ubiquitin ligase family regulates a diverse set of cellular pathways through dedicated substrate receptors (DCAFs). The DCAF DDB2 detects UV-induced pyrimidine dimers in the genome and facilitates nucleotide excision repair. We provide the molecular basis for DDB2 receptor-mediated cyclobutane pyrimidine dimer recognition in chromatin. The structures of the fully assembled DDB1-DDB2-CUL4A/B-RBX1 (CRL4(DDB2)) ligases reveal that the mobility of the ligase arm creates a defined ubiquitination zone around the damage, which precludes direct ligase activation by DNA lesions. Instead, the COP9 signalosome (CSN) mediates the CRL4(DDB2) inhibition in a CSN5 independent, nonenzymatic, fashion. In turn, CSN inhibition is relieved upon DNA damage binding to the DDB2 module within CSN-CRL4(DDB2). The Cockayne syndrome A DCAF complex crystal structure shows that CRL4(DCAF(WD40)) ligases share common architectural features. Our data support a general mechanism of ligase activation, which is induced by CSN displacement from CRL4(DCAF) on substrate binding to the DCAF.

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The observed concomitant destabilization of CDK12 is likely due to MG-induced CycK degradation and not to CRL autodegradation after long compound exposure.
“Therefore, the observed concomitant destabilization of CDK12 is likely due to the MG-induced CycK degradation and not to CRL ''autodegradation'' after long compound exposure as observed for canonical substrate receptors like CRBN.44,158”
From Chasing molecular glue degraders: screening approaches (2022) · cites this paper as [158]
The architecture of these large complexes is expected to provide an extended ubiquitylation radius that can accommodate multiple ubiquitylation sites on substrates with diverse sizes and shapes.
“The architecture of these large complexes is expected to provide an extended ubiquitylation radius that can accommodate multiple ubiquitylation sites on substrates with diverse sizes and shapes 47,52 .”
From Targeted protein degradation: expanding the toolbox (2019) · cites this paper as [52]
Given the flexible nature of DDB1, the spectrum of substrates degraded by PROTACs recruiting the CRBN complex, and probably other DCAF E3 ligases, is expected to be dictated less by the accessibility of the ubiquitylation site and more by the protein synthesis rate as well as the affinity and kinetics of the ligase-PROTAC-target binding event.
“In particular, given the flexible nature of the adaptor protein DNA damage-binding protein 1 (DDB1), the spectrum of substrates degraded by PROTACs recruiting the CRBN complex (and probably other DDB1CUL4-associated factor (DCAF) E3 ligases) is expected to be dictated less by the accessibility of the ubiquitylation site and more by the protein synthesis rate as well as the affinity and kinetics of”
From Targeted protein degradation: expanding the toolbox (2019) · cites this paper as [52]

1 retracted

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Targeted Protein Degradation through Recruitment of the CUL4A Complex Adaptor Protein DDB1Preprint
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Authors: Fischer, E. S., Scrima, A., Böhm, K., Matsumoto, S., Lingaraju, G. M., Faty, M., Yasuda, T., Cavadini, S., Wakasugi, M., Hanaoka, F., Iwai, S., Gut, H., Sugasawa, K., & Thomä, N. H.
Affiliations: University of Basel (CH)
Friedrich Miescher Institute (CH)
Biosignal Research Center, Kobe University (JP)
National Institute of Radiological Sciences (JP)
Kanazawa University (JP)
Gakushuin University (JP)
The University of Osaka (JP)
Corresponding author: Thomä, Nicolas H.
ORCID: Fischer, Eric S.
Scrima, Andrea
Matsumoto, Syota
Yasuda, Takeshi
Cavadini, Simone
Wakasugi, Mitsuo
Hanaoka, Fumio
Iwai, Shigenori
Gut, Heinz
Sugasawa, Kaoru
Thomä, Nicolas H.
Venue: Cell
Publisher: Elsevier BV
Published: 2011-11
Volume: 147
Issue: 5
Pages: 1024-1039
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2011.10.035
OpenAlex: W2774864460
Cited by: 460
References: 87
Citations by year: 2026: 23 · 2025: 27 · 2024: 27 · 2023: 35 · 2022: 28 · 2021: 37 · 2020: 48 · 2019: 42 · 2018: 32 · 2017: 19 · 2016: 28 · 2015: 26 · 2014: 36 · 2013: 30 · 2012: 21
FWCI: 11.31
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 624 d)
Locations: Cell (publishedVersion)
PubMed (publishedVersion)
DORA PSI (Paul Scherrer Institute) (submittedVersion)
Institutional Repositories DataBase (IRDB) (submittedVersion, cc-by-nc-nd)
QST-Repository (National Institutes for Quantum and Radiological Science and Technology) (submittedVersion)
Funders: Paul Scherrer Institut
Japan Society for the Promotion of Science (20241013, 22249005, 21510055, 23651050)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords: DDB2, CUL4A, RBX1, COP9 signalosome, cyclobutane pyrimidine dimers, nucleotide excision repair, UV-induced DNA damage, ubiquitination
MeSH terms: Animals, DNA Damage, DNA-Binding Proteins, Enzyme Activation, Humans, Models, Molecular, Crystallography, X-Ray, Ubiquitin-Protein Ligases, Cullin Proteins, Xeroderma Pigmentosum Group A Protein

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The Molecular Basis of CRL4DDB2/CSA Ubiquitin Ligase Architecture, Targeting, and Activation

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