7UV5

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a Lys48-linked di-ubiquitin

Summary for 7UV5

• Entry DOI: 10.2210/pdb7uv5/pdb
• Related: 7rbr
• Descriptor: Papain-like protease nsp3, Ubiquitin, ZINC ION, ... (6 entities in total)
• Functional Keywords: covid-19, coronavirus, sars, cov-2, papain-like protease, ubiquitin, idp51000, idp52003, center for structural genomics of infectious diseases, csgid, hydrolase
• Biological source: Severe acute respiratory syndrome coronavirus 2; More
• Total number of polymer chains: 3
• Total formula weight: 53422.07

Authors

Osipiuk, J.,Tesar, C.,Endres, M.,Lanham, B.T.,Wydorski, P.,Fushman, D.,Joachimiak, L.,Joachimiak, A.,Center for Structural Genomics of Infectious Diseases (CSGID) (deposition date: 2022-04-29, release date: 2022-05-11, Last modification date: 2023-10-25)

Primary citation

Wydorski, P.M.,Osipiuk, J.,Lanham, B.T.,Tesar, C.,Endres, M.,Engle, E.,Jedrzejczak, R.,Mullapudi, V.,Michalska, K.,Fidelis, K.,Fushman, D.,Joachimiak, A.,Joachimiak, L.A.
Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin.
Nat Commun, 14:2366-2366, 2023

PubMed Abstract: The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.

PubMed: 37185902
DOI: 10.1038/s41467-023-38031-5

Experimental method

X-RAY DIFFRACTION (1.45 Å)