8oyp
Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic
Structural highlights
FunctionQ1D4U9_MYXXD UBP11_HUMAN Protease that can remove conjugated ubiquitin from target proteins and polyubiquitin chains. Inhibits the degradation of target proteins by the proteasome. Plays a role in the regulation of pathways leading to NF-kappa-B activation. Plays a role in the regulation of DNA repair after double-stranded DNA breaks.[1] [2] [3] [4] [5] Publication Abstract from PubMedUbiquitin 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(77) in linear di-ubiquitin 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 di-ubiquitin. When mutated to a glycine, the corresponding residue in paralogue USP15, USP11 acquired elevated activity towards linear di-ubiquitin in gel shift assays, but not controls. The reverse mutation in USP15 confirmed that this position confers paralogue-specific differences impacting di-ubiquitin 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. Ubiquitin specific protease 11 structure in complex with an engineered substrate mimetic reveals a molecular feature for deubiquitination selectivity.,Maurer SK, Mayer MP, Ward SJ, Boudjema S, Halawa M, Zhang J, Caulton SG, Emsley J, Dreveny I J Biol Chem. 2023 Sep 28:105300. doi: 10.1016/j.jbc.2023.105300. PMID:37777157[6] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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