Polyubiquitin binding and cross-reactivity in the USP domain deubiquitinase USP21

• Published in: EMBO reports Vol. 12; no. 4; pp. 350 - 357
• Main Authors: Ye, Yu, Akutsu, Masato, Reyes-Turcu, Francisca, Enchev, Radoslav I, Wilkinson, Keith D, Komander, David
• Format: Journal Article
• Language: English
• Published: Chichester, UK John Wiley & Sons, Ltd 01-04-2011; Nature Publishing Group UK; Blackwell Publishing Ltd; Nature Publishing Group
• Subjects: Binding Sites - physiology; Cellular biology; cross-reactivity; Crystallography, X-Ray; Cytokines - chemistry; Cytokines - metabolism; EMBO31; EMBO40; Enzymes; Humans; ISG15; linkage specificity; Molecular biology; NEDD8; NEDD8 Protein; Polymers; Polyubiquitin - metabolism; Proteases; Protein Binding; Proteins; Scientific Report; Scientific Reports; Ubiquitin Thiolesterase - chemistry; Ubiquitin Thiolesterase - metabolism; ubiquitin-specific protease; Ubiquitins - chemistry; Ubiquitins - metabolism; ISG15; NEDD8; ubiquitin‐specific protease; linkage specificity; cross‐reactivity
• ISSN: 1469-221X; 1469-3178
• DOI: 10.1038/embor.2011.17

Modification of proteins by ubiquitin (Ub) and Ub‐like (Ubl) modifiers regulates a variety of cellular functions. The ability of Ub to form chains of eight structurally and functionally distinct types adds further complexity to the system. Ub‐specific proteases (USPs) hydrolyse polyUb chains, and some have been suggested to be cross‐reactive with Ubl modifiers, such as neural precursor cell expressed, developmentally downregulated 8 (NEDD8) and interferon‐stimulated gene 15 (ISG15). Here, we report that USP21 cleaves Ub polymers, and with reduced activity also targets ISG15, but is inactive against NEDD8. A crystal structure of USP21 in complex with linear diUb aldehyde shows how USP21 interacts with polyUb through a previously unidentified second Ub‐ and ISG15‐binding surface on the USP domain core. We also rationalize the inability of USP21 to target NEDD8 and identify differences that allow USPs to distinguish between structurally related modifications.
The crystal structure of the ubiquitin‐specific protease USP21 bound to linear diubiquitin‐aldehyde reveals a second S2 ubiquitin/ISG15‐binding site. The structure reveals why USP21 cannot hydrolyze NEDD8 modifications.