A molecular sensor determines the ubiquitin substrate specificity of SARS-CoV-2 papain-like protease
Stephanie Patchett,
Zongyang Lv,
Wioletta Rut,
Miklos Békés,
Marcin Drag,
Shaun K. Olsen,
Tony T. Huang
Affiliations
Stephanie Patchett
Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
Zongyang Lv
Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
Wioletta Rut
Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
Miklos Békés
Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
Marcin Drag
Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
Shaun K. Olsen
Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Corresponding author
Tony T. Huang
Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Corresponding author
Summary: The SARS-CoV-2 papain-like protease (PLpro) is a target for antiviral drug development. It is essential for processing viral polyproteins for replication and functions in host immune evasion by cleaving ubiquitin (Ub) and ubiquitin-like protein (Ubl) conjugates. While highly conserved, SARS-CoV-2 and SARS-CoV PLpro have contrasting Ub/Ubl substrate preferences. Using a combination of structural analyses and functional assays, we identify a molecular sensor within the S1 Ub-binding site of PLpro that serves as a key determinant of substrate specificity. Variations within the S1 sensor specifically alter cleavage of Ub substrates but not of the Ubl interferon-stimulated gene 15 protein (ISG15). Significantly, a variant of concern associated with immune evasion carries a mutation in the S1 sensor that enhances PLpro activity on Ub substrates. Collectively, our data identify the S1 sensor region as a potential hotspot of variability that could alter host antiviral immune responses to newly emerging SARS-CoV-2 lineages.
