PXD072107

PXD072107 is an original dataset announced via ProteomeXchange.

Title	A Proteolytic Switch: USP5 controls SDE2 function via UBL-directed cleavage
Description	Proteolytic processing is a critical regulatory mechanism in eukaryotic cells, yet the molecular identities and mechanisms underlying these events often remain elusive. Silencing Defective 2 (SDE2) is an essential human protein involved in multiple aspects of genome regulation, including DNA repair, ribosome biogenesis, and mRNA splicing. SDE2 is expressed with an N-terminal ubiquitin-like domain (SDE2UBL) which must be proteolytically cleaved to release the functional C-terminal domain (SDE2CT). This cleavage not only activates SDE2CT but also marks it for subsequent degradation, highlighting the importance of this tightly regulated processing. Despite the crucial role of this cleavage event, the human protease responsible has remained unknown. Here, we identify that the deubiquitinating enzyme, ubiquitin-specific protease 5 (USP5), catalyses the cleavage of SDE2. Using an integrated workflow combining biochemical assays, proteomic profiling, and mass spectrometry, we demonstrate that USP5 selectively processes SDE2 in vitro and in cell. To validate the specificity of this interaction, we engineered SDE2UBL into an activity-based probe, and developed a cellular reporter assay, both of which confirmed USP5 as the primary effector. Biophysical analysis further revealed that SDE2UBL binds to USP5 with similar characteristics to ubiquitin, albeit with reduced affinity, supporting a mechanism of substrate mimicry. Together, these findings uncover a novel regulatory axis for SDE2 function, highlighting an underappreciated role for DUBs in regulating protein maturation events. They also establish a versatile approach for identifying and validating substrate-protease interactions with broader implications for the study of post-translational regulation.
HostingRepository	PRIDE
AnnounceDate	2026-06-25
AnnouncementXML	Submission_2026-06-25_03:18:39.576.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Glenn Masson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	phosphorylated residue
Instrument	SELECT SERIES Cyclic IMS

Revision	Datetime	Status	ChangeLog Entry
0	2025-12-17 11:53:55	ID requested
⏵ 1	2026-06-25 03:18:40	announced

Dataset with its publication pending

ProteomeXchange project tag: Hydrogen Deuterium Exchange (HDX-MS)

submitter keyword: HDX-MS, SDE2, USP5, Ubiquitin

Glenn Masson
contact affiliation	University of Dundee
contact email	gmasson001@dundee.ac.uk
lab head
Glenn Masson
contact affiliation	University of Dundee
contact email	gmasson001@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/2026/06/PXD072107

PRIDE project URI

• PRIDE
  1. PXD072107
     1. Label: PRIDE project
     2. Name: A Proteolytic Switch: USP5 controls SDE2 function via UBL-directed cleavage