PXD022904

PXD022904 is an original dataset announced via ProteomeXchange.

Title	Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies
Description	Of the 16 non-structural proteins (Nsps) encoded by SARS CoV-2, Nsp3 is the largest and plays important roles in the viral life cycle. Being a large, multidomain, transmembrane protein, Nsp3 has been the most challenging to characterize. Encoded within the multidomain Nsp3 is the papain-like protease PLpro that cleaves not only the viral protein but also polyubiquitin and the ubiquitin-like modifier ISG15 from host cells. We here compare the interactors of PLpro and Nsp3 and find a largely overlapping interactome. Intriguingly, we find that near full length Nsp3 is a more active protease compared to the minimal PLpro. Using a MALDI-TOF based assay, we screen 7538 approved clinical compounds and identify five compounds that inhibit PLpro. Despite their ability to inhibit PLpro with IC50s in the low micromolar range, the inhibitors do not have any appreciable antiviral activity in cellular SARS-CoV2 infection assays. We therefore engineered nanobodies that bind to the S1 site of PLpro with nanomolar affinity and inhibit the enzyme. Our work highlights the importance of studying Nsp3 and provides tools and valuable insights to investigate Nsp3 biology.
HostingRepository	PRIDE
AnnounceDate	2021-09-15
AnnouncementXML	Submission_2021-09-15_07:41:14.813.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Raja Sekhar Nirujogi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-04 00:39:02	ID requested
⏵ 1	2021-09-15 07:41:15	announced

Armstrong LA, Lange SM, Dee Cesare V, Matthews SP, Nirujogi RS, Cole I, Hope A, Cunningham F, Toth R, Mukherjee R, Bojkova D, Gruber F, Gray D, Wyatt PG, Cinatl J, Dikic I, Davies P, Kulathu Y, Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies. PLoS One, 16(7):e0253364(2021) [pubmed]

ProteomeXchange project tag: Sars-cov-2, Covid-19

submitter keyword: SARS CoV-2, ISG15, Ubiqutylation

Yogesh Kulathu
contact affiliation	MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
contact email	y.kulathu@dundee.ac.uk
lab head
Raja Sekhar Nirujogi
contact affiliation	MRC Protein Phosphorylation Unit, university of Dundee
contact email	rnirujogi@dundee.ac.uk
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD022904

PRIDE project URI

• PRIDE
  1. PXD022904
     1. Label: PRIDE project
     2. Name: Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies