9HGH

MyD88 peptide_1 bound to SPOP MATH domain

Summary for 9HGH

• Entry DOI: 10.2210/pdb9hgh/pdb
• Descriptor: Speckle type BTB/POZ protein, Myeloid differentiation primary response protein MyD88 (3 entities in total)
• Functional Keywords: ubiquitination, ligase, immune signalling, degradation
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 17982.67

Authors

Makhlouf, L.,Zeqiraj, E. (deposition date: 2024-11-19, release date: 2025-04-23)

Primary citation

Makhlouf, L.,Mishra, M.,Makhlouf, H.,Manfield, I.,Busino, L.,Zeqiraj, E.
Sequence rules for a long SPOP-binding degron required for protein ubiquitylation.
Biochem.J., 2025

PubMed Abstract: The adaptor protein, Speckle-type BTB/POZ protein (SPOP), recruits substrates to the cullin-3-subclass of E3 ligase for selective protein ubiquitylation. The Myddosome protein, Myeloid differentiation primary response 88 (MyD88), is ubiquitylated by the SPOP-based E3 ligase to negatively regulate immune signaling, however, the sequence rules for SPOP-mediated substrate engagement and degradation are not fully understood. Here, we show that MyD88 interacts with SPOP through a long degron that contains the established SPOP-binding consensus and an N-terminal site that we name the Q-motif. Based on sequence similarity to MyD88, we show that additional substrates, including Steroid receptor coactivator-3 (SRC-3), SET domain-containing protein 2 (SETD2) and Caprin1, engage SPOP in this manner. We show that the Q-motif is a critical determinant of these interactions in mammalian cells and determine X-ray crystal structures that show the molecular basis of SPOP associations with these proteins. These studies reveal a new consensus sequence for substrate-binding to SPOP that is necessary for substrate ubiquitylation, thus expanding the sequence rules required for SPOP-mediated E3 ligase substrate recognition.

PubMed: 40178506
DOI: 10.1042/BCJ20253041

Experimental method

X-RAY DIFFRACTION (1.9 Å)