8OYP

Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic

Summary for 8OYP

• Entry DOI: 10.2210/pdb8oyp/pdb
• Descriptor: Ubiquitin carboxyl-terminal hydrolase 11,Response regulator FrzS, Polyubiquitin-B, CADMIUM ION, ... (8 entities in total)
• Functional Keywords: protease, ubiquitin, substrate complex, deubiquitinating enzyme, hydrolase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 128747.73

Authors

Maurer, S.K.,Caulton, S.G.,Ward, S.J.,Emsley, J.,Dreveny, I. (deposition date: 2023-05-05, release date: 2023-10-18, Last modification date: 2023-11-15)

Primary citation

Maurer, S.K.,Mayer, M.P.,Ward, S.J.,Boudjema, S.,Halawa, M.,Zhang, J.,Caulton, S.G.,Emsley, J.,Dreveny, I.
Ubiquitin-specific protease 11 structure in complex with an engineered substrate mimetic reveals a molecular feature for deubiquitination selectivity.
J.Biol.Chem., 299:105300-105300, 2023

PubMed Abstract: Ubiquitin-specific proteases (USPs) are crucial for controlling cellular proteostasis and signaling pathways but how deubiquitination is selective remains poorly understood, in particular between paralogues. Here, we developed a fusion tag method by mining the Protein Data Bank and trapped USP11, a key regulator of DNA double-strand break repair, in complex with a novel engineered substrate mimetic. Together, this enabled structure determination of USP11 as a Michaelis-like complex that revealed key S1 and S1' binding site interactions with a substrate. Combined mutational, enzymatic, and binding experiments identified Met in linear diubiquitin as a significant residue that leads to substrate discrimination. We identified an aspartate "gatekeeper" residue in the S1' site of USP11 as a contributing feature for discriminating against linear diubiquitin. When mutated to a glycine, the corresponding residue in paralog USP15, USP11 acquired elevated activity toward linear diubiquitin in-gel shift assays, but not controls. The reverse mutation in USP15 confirmed that this position confers paralog-specific differences impacting diubiquitin cleavage rates. The results advance our understanding of the molecular basis for the higher selectivity of USP11 compared to USP15 and may aid targeted inhibitor development. Moreover, the reported carrier-based crystallization strategy may be applicable to other challenging targets.

PubMed: 37777157
DOI: 10.1016/j.jbc.2023.105300

Experimental method

X-RAY DIFFRACTION (2.44 Å)