Structural and functional insights into Ubl domain-mediated regulation of SARS-CoV-2 PLpro
Rimanshee Arya, Janani Ganesh, Vishal Prashar, Mukesh Kumar
Biology Direct, doi:10.1186/s13062-025-00690-3
domain that hydrolyzes peptide and isopeptide bonds of viral and cellular substrates. PLpro cleaves viral polyproteins to release Nsp1, Nsp2, and Nsp3 which is essential for viral replication [1, 2]. In addition, PLpro removes ubiquitin (Ub) and interferon-stimulated gene product 15 (ISG15) from the cellular protein substrates-a process known as deubiquitination (DUB) and deISGylation, respectively [2-4]. By acting as both a deubiquitinase and a deISGylase, PLpro enables SARS-CoV-2 to evade host immune responses. It impairs the interferon signalling pathway by removing Ub and ISG15 from key signalling proteins, thereby disrupting innate immunity [5-7]. Furthermore, PLpro-mediated deISGylation of the viral nucleocapsid protein enhances viral replication [8].
Supplementary Information The online version contains supplementary material available at h t t p s : / / d o i . o r g / 1 0 . 1 1 8 6 / s 1 3 0 6 2 -0 2 5 -0 0 6 9 0 -3.
Supplementary Material 1. Author contributions R.A.: Planned and performed experiments, analyzed data and written the manuscript, J.G.: Performed experiments, analyzed data and written the manuscript, V.P.: Supervised the research work, analyzed data and written the manuscript, M.K.: Supervised the research work, analyzed data and written the manuscript.
Declarations
Competing interests The authors declare no competing interests.
Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
References
Adams, Grosse-Kunstleve, Hung, Ioerger, Mccoy et al., PHENIX: building new software for automated crystallographic structure determination, Acta Crystallogr D Biol Crystallogr,
doi:10.1107/S0907444902016657
Al-Homoudi, Engel, Muczynski, Brunzelle, Gavande et al., Human structural homologues of SARS-CoV-2 PLpro as anti-targets: a strategic panel analysis, MicroPubl Biol,
doi:10.17912/micropub.biology.001418
Armstrong, Lange, Cesare, Matthews, Nirujogi et al., Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its Inhibition by nanobodies, PLoS ONE,
doi:10.1371/journal.pone.0253364
Arya, Prashar, Kumar, Evaluating stability and activity of SARS-CoV-2 PLpro for High-throughput screening of inhibitors, Mol Biotechnol,
doi:10.1007/s12033-021-00383-y
Arya, Prashar, Kumar, Identification and characterization of aurintricarboxylic acid as a potential inhibitor of SARS-CoV-2 PLpro, Int J Biol Macromol,
doi:10.1016/j.ijbiomac.2023.123347
Báez-Santos, Mielech, Deng, Baker, Mesecar, Catalytic function and substrate specificity of the Papain-like protease domain of nsp3 from the middle East respiratory syndrome coronavirus, J Virol,
doi:10.1128/JVI.01294-14
Békés, Van Der Heden Van Noort, Ekkebus, Ovaa, Huang et al., Recognition of Lys48-Linked Di-ubiquitin and deubiquitinating activities of the SARS coronavirus Papain-like protease, Mol Cell,
doi:10.1016/j.molcel.2016.04.016
Clasman, Báez-Santos, Mettelman, 'brien, Baker et al., X-ray structure and enzymatic activity profile of a core Papain-like protease of MERS coronavirus with utility for structure-based drug design, Sci Rep,
doi:10.1038/srep40292
Clerici, Vargas, Faesen, Sixma, The DUSP-Ubl domain of USP4 enhances its catalytic efficiency by promoting ubiquitin exchange, Nat Commun,
doi:10.1038/ncomms6399
Comeau, Gatchell, Vajda, Camacho, ClusPro: an automated Docking and discrimination method for the prediction of protein complexes, Bioinformatics,
doi:10.1093/bioinformatics/btg371
Faesen, Vargas, Sixma, The role of UBL domains in ubiquitinspecific proteases, Biochem Soc Trans,
doi:10.1042/BST20120004
Ferreira, Pillaiyar, Hirata, Poso, Kronenberger, Inhibitor induced conformational changes in SARS-COV-2 papain-like protease, Sci Rep,
doi:10.1038/s41598-022-15181-y
Ferreira, Villanueva, Adem, Fadl, Alzyoud et al., Identification of novel allosteric sites of SARS-CoV-2 papain-like protease (PLpro) for the development of COVID-19 antivirals, J Biol Chem,
doi:10.1016/j.jbc.2024.107821
Frieman, Ratia, Johnston, Mesecar, Baric, Severe acute respiratory syndrome coronavirus Papain-like protease Ubiquitin-like domain and catalytic domain regulate antagonism of IRF3 and NF-κB signaling, J Virol,
doi:10.1128/JVI.02220-08
Hu, Li, Song, Jeffrey, Chenova et al., Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14, EMBO J,
doi:10.1038/sj.emboj.7600832
Huang, Wang, Zhong, Zhang, Zhang et al., Molecular architecture of coronavirus double-membrane vesicle pore complex, Nature,
doi:10.1038/s41586-024-07817-y
Klemm, Ebert, Calleja, Allison, Richardson et al., Mechanism and inhibition of the papain-like protease, plpro, of SARS-CoV-2, EMBO J,
doi:10.15252/embj.2020106275
Komander, Clague, Urbé, Breaking the chains: structure and function of the deubiquitinases, Nat Rev Mol Cell Biol,
doi:10.1038/nrm2731
Kozakov, Hall, Xia, Porter, Padhorny et al., The cluspro web server for protein-protein Docking, Nat Protoc,
doi:10.1038/nprot.2016.169
Lee, Lei, Santarsiero, Gatuz, Cao et al., Inhibitor recognition specificity of MERS-CoV papain-like protease may differ from that of SARS-CoV, ACS Chem Biol,
doi:10.1021/cb500917m
Liu, Lee, Parker, Acharya, Chiang et al., ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity, Nat Microbiol,
doi:10.1038/s41564-021-00884-1
Lu, Zhao, Yu, Kang, Yang, Targeting ubiquitin-specific protease 7 (USP7) in cancer: a new insight to overcome drug resistance, Front Pharmacol,
doi:10.3389/fphar.2021.648491
Munnur, Teo, Eggermont, Lee, Thery et al., Altered isgylation drives aberrant macrophagedependent immune responses during SARS-CoV-2 infection, Nat Immunol,
doi:10.1038/s41590-021-01035-8
Osipiuk, Azizi, Dvorkin, Endres, Jedrzejczak et al., Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors, Nat Commun,
doi:10.1038/s41467-021-21060-3
Patchett, Lv, Rut, Békés, Drag et al., A molecular sensor determines the ubiquitin substrate specificity of SARS-CoV-2 papainlike protease, Cell Rep,
doi:10.1016/j.celrep.2021.109754
Peth, Besche, Goldberg, Ubiquitinated proteins activate the proteasome by binding to Usp14/Ubp6 which causes 20s gate opening, Mol Cell,
doi:10.1016/j.molcel.2009.11.015
Ran, Zhu, Chen, Ni, Mu, Papain-like protease of SARS-CoV-2 inhibits RLR signaling in a deubiquitination-dependent and deubiquitination-independent manner, Front Immunol,
doi:10.3389/fimmu.2022.947272
Rehman, Armstrong, Lange, Kristariyanto, Gräwert et al., Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2, Mol Cell,
doi:10.1016/j.molcel.2021.08.024
Rhamadianti, Abe, Tanaka, Ono, Katayama et al., SARS-CoV-2 papain-like protease inhibits isgylation of the viral nucleocapsid protein to evade host anti-viral immunity, J Virol. n.d,
doi:10.1128/jvi.00855-24
Shin, Mukherjee, Grewe, Bojkova, Baek et al., Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity, Nature,
doi:10.1038/s41586-020-2601-5
Srinivasan, Brognaro, Prabhu, De Souza, Günther et al., Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papainlike protease, Commun Biol,
doi:10.1038/s42003-022-03737-7
Sulea, Lindner, Purisima, Ménard, Deubiquitination, a new function of the severe acute respiratory syndrome coronavirus Papain-like protease?, J Virol,
doi:10.1128/jvi.79.7.4550-4551.2005
Vliet, Huynh, Palà, Patel, Singer et al., Ubiquitin variants potently inhibit SARS-CoV-2 PLpro and viral replication via a novel site distal to the protease active site, PLoS Pathog,
doi:10.1371/journal.ppat.1011065
Wydorski, Osipiuk, Lanham, Tesar, Endres et al., Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin, Nat Commun,
doi:10.1038/s41467-023-38031-5
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