8JAU

Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (dimer)

This is a non-PDB format compatible entry.

Summary for 8JAU

• Entry DOI: 10.2210/pdb8jau/pdb
• EMDB information: 36134
• Descriptor: Amyloid protein-binding protein 2, Cullin-2, Elongin-B, ... (6 entities in total)
• Functional Keywords: e3 ubiquitination ligase, protein binding
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 10
• Total formula weight: 359417.73

Authors

Zhao, S.,Zhang, K.,Xu, C. (deposition date: 2023-05-07, release date: 2023-10-18, Last modification date: 2023-10-25)

Primary citation

Zhao, S.,Olmayev-Yaakobov, D.,Ru, W.,Li, S.,Chen, X.,Zhang, J.,Yao, X.,Koren, I.,Zhang, K.,Xu, C.
Molecular basis for C-degron recognition by CRL2 APPBP2 ubiquitin ligase.
Proc.Natl.Acad.Sci.USA, 120:e2308870120-e2308870120, 2023

PubMed Abstract: E3 ubiquitin ligases determine the specificity of eukaryotic protein degradation by selective binding to destabilizing protein motifs, termed degrons, in substrates for ubiquitin-mediated proteolysis. The exposed C-terminal residues of proteins can act as C-degrons that are recognized by distinct substrate receptors (SRs) as part of dedicated cullin-RING E3 ubiquitin ligase (CRL) complexes. APPBP2, an SR of Cullin 2-RING ligase (CRL2), has been shown to recognize R-x-x-G/C-degron; however, the molecular mechanism of recognition remains elusive. By solving several cryogenic electron microscopy structures of active CRL2 bound with different R-x-x-G/C-degrons, we unveiled the molecular mechanisms underlying the assembly of the CRL2 dimer and tetramer, as well as C-degron recognition. The structural study, complemented by binding experiments and cell-based assays, demonstrates that APPBP2 specifically recognizes the R-x-x-G/C-degron via a bipartite mechanism; arginine and glycine, which play critical roles in C-degron recognition, accommodate distinct pockets that are spaced by two residues. In addition, the binding pocket is deep enough to enable the interaction of APPBP2 with the motif placed at or up to three residues upstream of the C-end. Overall, our study not only provides structural insight into CRL2-mediated protein turnover but also serves as the basis for future structure-based chemical probe design.

PubMed: 37844242
DOI: 10.1073/pnas.2308870120

Experimental method

ELECTRON MICROSCOPY (3.22 Å)