Deubiquitinating enzyme amino acid profiling reveals a class of ubiquitin esterases

De Cesare, V., Carbajo Lopez, D., Mabbitt, P. D., Fletcher, A. J., Soetens, M., Antico, O., Wood, N. T. and Virdee, S. (2021) Deubiquitinating enzyme amino acid profiling reveals a class of ubiquitin esterases. Proceedings of the National Academy of Sciences, 118(4), e200694711. (doi: 10.1073/pnas.2006947118) (PMID:33479176) (PMCID:PMC7848729)

Abstract

The reversibility of ubiquitination by the action of deubiquitinating enzymes (DUBs) serves as an important regulatory layer within the ubiquitin system. Approximately 100 DUBs are encoded by the human genome, and many have been implicated with pathologies, including neurodegeneration and cancer. Non-lysine ubiquitination is chemically distinct, and its physiological importance is emerging. Here, we couple chemically and chemoenzymatically synthesized ubiquitinated lysine and threonine model substrates to a mass spectrometry-based DUB assay. Using this platform, we profile two-thirds of known catalytically active DUBs for threonine esterase and lysine isopeptidase activity and find that most DUBs demonstrate dual selectivity. However, with two anomalous exceptions, the ovarian tumor domain DUB class demonstrates specific (iso)peptidase activity. Strikingly, we find the Machado–Joseph disease (MJD) class to be unappreciated non-lysine DUBs with highly specific ubiquitin esterase activity rivaling the efficiency of the most active isopeptidases. Esterase activity is dependent on the canonical catalytic triad, but proximal hydrophobic residues appear to be general determinants of non-lysine activity. Our findings also suggest that ubiquitin esters have appreciable cellular stability and that non-lysine ubiquitination is an integral component of the ubiquitin system. Its regulatory sophistication is likely to rival that of canonical ubiquitination.

• Item Type: Articles
• Additional Information: This work was funded by the United Kingdom MRC (MC_UU_12016/8), the Biotechnology and Biological Sciences Research Council (BB/P003982/1), and The Michael J. Fox Foundation (12756).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Fletcher, Dr Adam
• Authors: De Cesare, V., Carbajo Lopez, D., Mabbitt, P. D., Fletcher, A. J., Soetens, M., Antico, O., Wood, N. T., and Virdee, S.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Proceedings of the National Academy of Sciences
• Publisher: National Academy of Sciences
• ISSN: 0027-8424
• ISSN (Online): 1091-6490
• Copyright Holders: Copyright © De Cesare et al. 2021
• First Published: First published in Proceedings of the National Academy of Sciences 118(4):e2006947118
• Publisher Policy: Reproduced under a Creative Commons licence