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Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases
Open accessAbstract
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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Tawaratsumida, K., Redecke, V., Wu, R., Kuriakose, J. A., Bouchard, J. J., Mittag, T., Lohman, B. K., Mishra, A., High, A. A., & Häcker, H. (2022) · Science Advances · doi:10.1126/sciadv.abq0084 · Cited by 17
Functional roles of E3 ubiquitin ligases in prostate cancer
Zhao, Y., Li, J., Chen, J., Ye, M., & Jin, X. (2022) · Journal of Molecular Medicine · doi:10.1007/s00109-022-02229-9 · Cited by 15
SPOP loss of function protects against tauopathy
Eck, R. J., Kow, R. L., Black, A. H., Liachko, N. F., & Kraemer, B. C. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2207250120 · Cited by 16
Stangl, A., Wilner, C., Li, P., Maahs, L., Hwang, C., & Pilling, A. B. (2023) · The Prostate · doi:10.1002/pros.24481 · Cited by 15
SPOP point mutations regulate substrate preference and affect its function
Deng, Y., Ding, W., Ma, K., Zhan, M., Sun, L., Zhou, Z., & Lu, L. (2024) · Cell Death and Disease · doi:10.1038/s41419-024-06565-1 · Cited by 15
Targeting kelch-like (KLHL) proteins: achievements, challenges and perspectives
Zhou, Y., Zhang, Q., Zhao, Z., Hu, X., You, Q., & Jiang, Z. (2024) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2024.116270 · Cited by 15
Yao, S., Chen, X., Chen, J., Guan, Y., Liu, Y., Chen, J., & Lv, X. (2018) · Cancer Cell International · doi:10.1186/s12935-018-0711-z · Cited by 15
Spop ameliorates diabetic nephropathy through restraining NLRP3 inflammasome
Wang, B., Dai, Z.-H., Gao, Q., Liu, Y., Gu, G., & Zheng, H. (2022) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2021.12.068 · Cited by 15
Phylogenetic Analysis of Brassica rapa MATH-Domain Proteins
Zhao, L., Huang, Y., Hu, Y., He, X., Shen, W., Liu, C., & Ruan, Y. (2013) · Current Genomics · doi:10.2174/1389202911314030007 · Cited by 15
Cook, E. C., Sahu, D., Bastidas, M., & Showalter, S. A. (2018) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b10051 · Cited by 15
In-Cell Approach to Evaluate E3 Ligases for Use in Targeted Protein Degradation
Zheng, Y., Singh, A., Niu, Z., Marin, V. L., Young, J., Richardson, P. L., Hemshorn, M. L., Cooley, R. B., Karplus, P. A., Puvar, K., et al. (2025) · Journal of the American Chemical Society · doi:10.1021/jacs.5c02741 · Cited by 16
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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