PXD063080-1

PXD063080 is an original dataset announced via ProteomeXchange.

Title	Engineering a Cell-Based Orthogonal Ubiquitin Transfer Cascade for Profiling the Substrates of RBR E3 Parkin
Description	The E3 ubiquitin (UB) ligase Parkin utilizes a Ring-Between-Ring (RBR) domain to mediate UB transfer to substrate proteins, and mutations affecting Parkin catalysis promote cancer and are associated with Parkinson’s disease. An essential role of Parkin is to initiate mitophagy by ubiquitinating mitochondrial proteins. Still, it is unclear how Parkin carries out other cellular functions, such as the regulation of the cell cycle, metabolism, and the neuronal synapse. Here, we used phage display to engineer the RBR domain of Parkin and assembled an orthogonal ubiquitin transfer (OUT) cascade to profile Parkin substrates in living cells. Guided by the substate profile from the OUT screen, we verified a panel of Rab GTPases and CDK5 as Parkin substrates. We also showed mitophagy stimulation enhanced Parkin-mediated ubiquitination of Rab proteins. Our work demonstrates that the Parkin OUT cascade can be an empowering tool for identifying Parkin substrates to elucidate its multifaceted cellular functions.
HostingRepository	PRIDE
AnnounceDate	2025-07-28
AnnouncementXML	Submission_2025-07-27_16:07:19.540.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Duc Duong
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitinylated lysine
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-17 12:23:38	ID requested
⏵ 1	2025-07-27 16:07:20	announced

10.1016/j.isci.2025.112913;

Fang S, Zhou L, Chen G, Zhang J, Wang X, Jeong IH, Jacobs SE, Kossmann BR, Wei W, Liu S, Jeong GH, Xie Y, Duong D, Seyfried NT, Ivanov I, Mabb AM, Kiyokawa H, Zhao B, Yin J, Engineering a cell-based orthogonal ubiquitin transfer cascade for profiling the substrates of RBR E3 Parkin. iScience, 28(7):112913(2025) [pubmed]

submitter keyword: Ubiquitin, Parkin, Mass spectrometry, E3

Jun Yin
contact affiliation	Ph.D. and Professor Department of Chemistry and Center for Diagnostics & Therapeutics (CDT) Georgia State University
contact email	junyin@gsu.edu
lab head
Duc Duong
contact affiliation	Center of Neurodegenerative Diseases
contact email	dduong@emory.edu
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/2025/07/PXD063080

PRIDE project URI

• PRIDE
  1. PXD063080
     1. Label: PRIDE project
     2. Name: Engineering a Cell-Based Orthogonal Ubiquitin Transfer Cascade for Profiling the Substrates of RBR E3 Parkin