9F6G

Human USP30 chimera bound to Ubiquitin-PA

Summary for 9F6G

• Entry DOI: 10.2210/pdb9f6g/pdb
• Related: 9F19
• Descriptor: Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 14,Ubiquitin carboxyl-terminal hydrolase 35, Polyubiquitin-B, prop-2-en-1-amine, ... (4 entities in total)
• Functional Keywords: usp30, ubiquitin, dub, deubiquitinating enzyme, usp14, usp35, mitophagy, usp, ubiquitin-specific protease, ubiquitin carboxyl-terminal hydrolase 30, ubiquitin-pa, ub-pa, hydrolase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 44703.54

Authors

Kazi, N.H.,Gersch, M. (deposition date: 2024-05-01, release date: 2025-03-19, Last modification date: 2025-05-14)

Primary citation

Kazi, N.H.,Klink, N.,Gallant, K.,Kipka, G.M.,Gersch, M.
Chimeric deubiquitinase engineering reveals structural basis for specific inhibition of the mitophagy regulator USP30.
Nat.Struct.Mol.Biol., 2025

PubMed Abstract: The mitochondrial deubiquitinase ubiquitin-specific protease (USP) 30 negatively regulates PINK1-parkin-driven mitophagy. Whether enhanced mitochondrial quality control through inhibition of USP30 can protect dopaminergic neurons is currently being explored in a clinical trial for Parkinson's disease. However, the molecular basis for specific inhibition of USP30 by small molecules has remained elusive. Here we report the crystal structure of human USP30 in complex with a specific inhibitor, enabled by chimeric protein engineering. Our study uncovers how the inhibitor extends into a cryptic pocket facilitated by a compound-induced conformation of the USP30 switching loop. Our work underscores the potential of exploring induced pockets and conformational dynamics to obtain deubiquitinase inhibitors and identifies residues facilitating specific inhibition of USP30. More broadly, we delineate a conceptual framework for specific USP deubiquitinase inhibition based on a common ligandability hotspot in the Leu73 ubiquitin binding site and on diverse compound extensions. Collectively, our work establishes a generalizable chimeric protein-engineering strategy to aid deubiquitinase crystallization and enables structure-based drug design with relevance to neurodegeneration.

PubMed: 40325251
DOI: 10.1038/s41594-025-01534-4

Experimental method

X-RAY DIFFRACTION (1.5 Å)