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Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases
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In the largest E3 ligase subfamily, Cul3 binds a BTB domain, and an associated protein-interaction domain such as MATH recruits substrates for ubiquitination. Here, we present biochemical and structural analyses of the MATH-BTB protein, SPOP. We define a SPOP-binding consensus (SBC) and determine structures revealing recognition of SBCs from the phosphatase Puc, the transcriptional regulator Ci, and the chromatin component MacroH2A. We identify a dimeric SPOP-Cul3 assembly involving a conserved helical structure C-terminal of BTB domains, which we call "3-box" due to its facilitating Cul3 binding and its resemblance to F-/SOCS-boxes in other cullin-based E3s. Structural flexibility between the substrate-binding MATH and Cul3-binding BTB/3-box domains potentially allows a SPOP dimer to engage multiple SBCs found within a single substrate, such as Puc. These studies provide a molecular understanding of how MATH-BTB proteins recruit substrates to Cul3 and how their dimerization and conformational variability may facilitate avid interactions with diverse substrates.
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“BTB-containing E3 ligases are typically distinguished by the presence of a 3-box motif that enables high-affinity binding of Cullin 3 (refs 74,75 ).”
From Targeted protein degradation: expanding the toolbox (2019) · cites this paper as [75]
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Ye, Y., Yue, C., Zheng, Z., Ruan, H., Zhang, Y., Miao, Q., Zhang, X., Xiao, W., & Liu, L. (2025) · JCI Insight · doi:10.1172/jci.insight.180655 · Cited by 3
Bridged PROTAC, DNA-based PROTAC and hydrophobic tag technologies for targeted protein degradation
Gao, P., Zhong, Y., Luo, K., & Jin, J. J. (2026) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2026.115819 · Cited by 3
Prevalence of SPOP and IDH Gene Mutations in Prostate Cancer in a Jordanian Population
Alorjani, M. S., Bashir, S. M. A., Al-Zaareer, B., Al-Khatib, S., Al‐Zoubi, R. M., Al‐Trad, B., Alarjah, M. I. A., Alzu’bi, A., Al-Hamad, M., Al‐Batayneh, K., et al. (2024) · Biochemical Genetics · doi:10.1007/s10528-024-10974-4 · Cited by 3
Yao, Y., Hong, S., Yoshida, S., Swaroop, V., Curtin, B., & Inoki, K. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.115101 · Cited by 3
Cul3 substrate adaptor SPOP targets Nup153 for degradation
Ong, J. Y., Abdusamad, M., Ramírez, I., Gholkar, A. A., Zhang, X., Gimeno, T. V., & Torres, J. Z. (2025) · Molecular Biology of the Cell · doi:10.1091/mbc.e24-04-0198 · Cited by 3
Law, C. Y., & Lam, C. (2022) · Clinica Chimica Acta · doi:10.1016/j.cca.2022.08.019 · Cited by 3
Hidden tricks in MATH: Hypermorphic mutations in SPOP tumor suppressor explained by cryo-EM
Orme, J. J., Mer, G., & Huang, H. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.02.003 · Cited by 3
Vesicular mechanisms of drug resistance in apicomplexan parasites
Haldar, K., & Bhattacharjee, S. (2025) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00010-24 · Cited by 2
Wang, Z., Li, L., Ye, Q., Lei, Y., Lu, M., Ye, L., Kang, J., Huang, W., Xu, S., Wang, K., et al. (2025) · Journal of Clinical Investigation · doi:10.1172/jci189048 · Cited by 4
Self-citationCRL3-Mediated Ubiquitination in Arabidopsis: Roles of BTB Proteins in Diverse Biological Processes
Chung, S., Lee, S. J., & Lee, J. (2025) · Journal of Plant Biology · doi:10.1007/s12374-025-09492-6 · Cited by 2
Impact of SPOP Mutations on Clinical Outcomes in Metastatic Prostate Cancer
Kilari, D., Henderson, N., Yamamoto, K., Ye, Y., Hwang, C., Barata, P. C., Bilen, M. A., Graham, L. S., Garje, R., Rothstein, S. E., et al. (2025) · JCO Precision Oncology · doi:10.1200/po-25-00590 · Cited by 2
Molecular insights for the tumor suppressor role of SPOP in prostate cancer
Yan, P., Xue, X., Hou, T., Wang, J., Jiang, W., Wang, Z., Inuzuka, H., & Wei, W. (2026) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2026.189560 · Cited by 2
Su, S., Sun, M., Wang, H., Tang, Y.-D., Chen, J., Shi, X., Cai, S., Zhou, H., Yang, W., Zhang, N., et al. (2026) · Journal of Nanobiotechnology · doi:10.1186/s12951-026-04348-8 · Cited by 2
Metadata
- Authors
- Zhuang, M., Calabrese, M. F., Liu, J., Waddell, M. B., Nourse, A., Hammel, M., Miller, D. J., Walden, H., Duda, D. M., Seyedin, S. N., Hoggard, T., Harper, J. W., White, K. P., & Schulman, B. A.
- Affiliations
- St. Jude Children's Research Hospital (US)
- University of Chicago (US)
- Lawrence Berkeley National Laboratory (US)
- University of Wisconsin System (US)
- Harvard University (US)
- Corresponding author
- Schulman, Brenda A.
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2009-10
- Volume
- 36
- Issue
- 1
- Pages
- 39-50
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC2847577
- OpenAlex
- W1993550226
- Cited by
- 486
- References
- 60
- Citations by year
- 2026: 29 · 2025: 38 · 2024: 27 · 2023: 35 · 2022: 39 · 2021: 50 · 2020: 45 · 2019: 32 · 2018: 25 · 2017: 28 · 2016: 23 · 2015: 25 · 2014: 28 · 2013: 24 · 2012: 14
- FWCI
- 4.66
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute (DRG 2021-9)
- National Cancer Institute (CA92584, P01CA092584, P30CA021765)
- National Institute of General Medical Sciences (R01GM070565, R01GM069530, GM070565)
- National Center for Research Resources (RR 15301, P41RR015301)
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- SPOP, BTB domain, CUL3, E3 ubiquitin ligase, MATH domain, substrate recognition, macroH2A, protein dimerization, SOCS box
- MeSH terms
- Amino Acid Sequence, Animals, DNA-Binding Proteins, Drosophila melanogaster, Histones, Humans, Models, Molecular, Mutation, Nuclear Proteins, Peptide Fragments, Phosphoprotein Phosphatases, Protein Binding, Recombinant Fusion Proteins, Repressor Proteins, Transcription Factors, Consensus Sequence, Crystallography, X-Ray, Molecular Chaperones, Protein Structure, Quaternary, Drosophila Proteins, Ubiquitin-Protein Ligases, Cullin Proteins, Adaptor Proteins, Signal Transducing, Protein Interaction Domains and Motifs, Ubiquitination, Protein Multimerization, Co-Repressor Proteins
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