Cited by 486Ubiquitin and proteasome pathwaysProtein Degradation and InhibitorsEnzyme Structure and Function

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Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases

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Zhuang, Min, Calabrese, Matthew F., Liu, Jiang, Waddell, M. Brett, Nourse, Amanda, Hammel, Michal, Miller, Darcie J., Walden, Helen, Duda, David M., Seyedin, Steven N., Hoggard, Timothy, Harper, J. Wade, White, Kevin P., Schulman, Brenda A.·2009·Molecular Cell

DOI 10.1016/j.molcel.2009.09.022PMC PMC2847577

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Abstract

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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Choi, C., Labriola, M., Henderson, N., Chu, A., Hwang, C., Barata, P. C., Cackowski, F., Broderick, A., Mckay, R., Bilen, M., et al. (2026) · Prostate Cancer and Prostatic Diseases · doi:10.1038/s41391-026-01150-3
SPOP-mediated nuclear ubiquitination degradation of p62/SQSTM1 contributes to HR repair
Yang, X., Zhou, Y., Huang, Q., Wang, L., Zhang, S., Yang, X., Qiu, L., Meng, Y., Wu, H. M., Zhang, B., et al. (2026) · Oncogene · doi:10.1038/s41388-026-03856-z
Divergent roles of SPOP and CHD1 in ACSL4 regulation reveal context-dependent vulnerabilities for targeting ferroptosis
Chen, F., Li, Q., Gu, Q., Leo, J., Liang, X., Mehta, N., Labanca, E., Shepherd, P. D. A., Mahmud, I., Wang, Y., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-75010-y
BET BD2 inhibition facilitates SPOP-mediated degradation of chromatin-associated BRD4/BRD4-NUT, a therapeutic vulnerability in NUT carcinomaPreprint
Bates, K. A., Nguyen, H. C. B., Eagen, K. P., Huang, J., Gokhale, P., Leeper, B., Eschle, B. K., Gray, S., Sampat, K., Durall, R. T., et al. (2026) · bioRxiv · doi:10.64898/2026.08.14.744905
Targeting Transcription Factor EB for Cardiac Hypertrophy: From Mechanisms to Potential Clinical Application
高, 文. (2026) · Advances in Clinical Medicine · doi:10.12677/acm.2026.1682990
ABTB1, as an E3 ubiquitin ligase, suppresses Th17 cell differentiation and mitigates autoimmune inflammation by promoting STAT3 ubiquitination and degradation
Xu, F., Zhao, S., Jiang, Y., Li, X., Wang, W., Zhou, Y., Wang, Y., Zhu, P., Shao, Y., Qiao, G., et al. (2026) · Cellular and Molecular Immunology · doi:10.1038/s41423-026-01464-1
Inter-domain distance analysis reveals conformational changes in the Keap1-Nrf2 stress sensor system
Saito, R., Kawabata, T., Yamashita, S., Oki, K., Fujii, T., Kawauchi, H., Doi, Y., Irie, M., Torizawa, T., Kinoshita, K., et al. (2026) · Redox Biology · doi:10.1016/j.redox.2026.104379
BindingDB Entry 50022106: Targeting kelch-like (KLHL) proteins: achievements, challenges and perspectives.
BindingDB (2025) · UC San Diego · doi:10.7270/q29028gr
BindingDB Entry 50023252: Harnessing the SPOP E3 Ubiquitin Ligase via a Bridged Proteolysis Targeting Chimera (PROTAC) Strategy for Targeted Protein Degradation.
BindingDB (2026) · UC San Diego · doi:10.7270/q26h4pbx
BindingDB Entry 50020099: Synthesis and Biological Evaluation of β-Lactam Derivatives Targeting Speckle-Type POZ Protein (SPOP).
BindingDB (2024) · UC San Diego · doi:10.7270/q2hd8136
BindingDB Entry 50009361: Structure-Activity Relationship of SPOP Inhibitors against Kidney Cancer.
BindingDB (2021) · UC San Diego · doi:10.7270/q2x351xf

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: Zhuang, Min
Calabrese, Matthew F.
Liu, Jiang
Nourse, Amanda
Hammel, Michal
Miller, Darcie J.
Walden, Helen
Seyedin, Steven N.
Hoggard, Timothy
Harper, J. Wade
White, Kevin P.
Schulman, Brenda A.
Venue: Molecular Cell
Publisher: Elsevier BV
Published: 2009-10
Volume: 36
Issue: 1
Pages: 39-50
ISSN: 1097-2765 (ISSN-L)
DOI: 10.1016/j.molcel.2009.09.022
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: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 1421 d)
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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Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases

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