PXD037009

PXD037009 is an original dataset announced via ProteomeXchange.

Title	Global, site-resolved analysis of ubiquitylation occupancy and turnover rate reveals systems properties
Description	Ubiquitylation regulates most proteins and biological processes in a eukaryotic cell. However, the site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have not been quantified. Here we present an integrated picture of the global ubiquitylation site occupancy and half-life. Ubiquitylation site occupancy spans over four orders of magnitude, but the median ubiquitylation site occupancy is three orders of magnitude lower than that of phosphorylation. The occupancy, turnover rate, and regulation of sites by proteasome inhibitors are strongly interrelated, and these attributes distinguish sites involved in proteasomal degradation and cellular signaling. Sites in structured protein regions exhibit longer half-lives and stronger upregulation by proteasome inhibitors than sites in unstructured regions. Importantly, we discovered a surveillance mechanism that rapidly and site-indiscriminately deubiquitylates all ubiquitin-specific E1 and E2 enzymes, protecting them against accumulation of bystander ubiquitylation. The work provides a systems-scale, quantitative view of ubiquitylation properties and reveals general principles of ubiquitylation-dependent governance.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:36:08.540.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gabriela Prus
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitination signature dipeptidyl lysine
Instrument	Q Exactive HF; Orbitrap Exploris 480; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-25 15:40:07	ID requested
1	2024-04-15 20:43:41	announced
⏵ 2	2024-10-22 06:36:09	announced	2024-10-22: Updated project metadata.

10.1016/J.CELL.2024.03.024;

submitter keyword: Human, ubiquitylation, dynamics, PTMs, stoichiometry, half-life

Chuna Choudhary
contact affiliation	Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
contact email	chuna.choudhary@cpr.ku.dk
lab head
Gabriela Prus
contact affiliation	Novo Nordisk Center for Protein Research
contact email	gabriela.prus@cpr.ku.dk
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/2024/04/PXD037009

PRIDE project URI

• PRIDE
  1. PXD037009
     1. Label: PRIDE project
     2. Name: Global, site-resolved analysis of ubiquitylation occupancy and turnover rate reveals systems properties