PXD054748-1

PXD054748 is an original dataset announced via ProteomeXchange.

Title	Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53
Description	Ubiquitin-specific proteases (USPs) are the largest class of human deubiquitinases (DUBs) and comprise its phylogenetically most distant members USP53 and USP54, which are annotated as catalytically inactive pseudo-enzymes. Conspicuously, mutations in the USP domain of USP53 cause progressive familial intrahepatic cholestasis. Here we report the discovery that USP53 and USP54 are active DUBs with high specificity for K63-linked polyubiquitin. We demonstrate how USP53 patient mutations abrogate catalytic activity, implicating loss of DUB activity in USP53-mediated pathology. Depletion of USP53 increases K63-linked ubiquitination of tricellular junction components. Assays with substrate-bound polyubiquitin reveal that USP54 cleaves within K63-linked chains, whereas USP53 can en bloc deubiquitinate substrate proteins in a K63-linkage-dependent manner. Biochemical and structural analyses uncover underlying K63-specific S2-ubiquitin-binding sites within their catalytic domains. Collectively, our work revises the annotation of USP53 and USP54, provides reagents and a mechanistic framework to investigate K63-polyubiquitin decoding, and establishes K63-linkage-directed deubiquitination as novel DUB activity.
HostingRepository	PRIDE
AnnounceDate	2024-11-11
AnnouncementXML	Submission_2024-11-11_00:13:44.247.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jeroen Demmers
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitination signature dipeptidyl lysine
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-09 03:52:11	ID requested
⏵ 1	2024-11-11 00:13:44	announced

Dataset with its publication pending

submitter keyword: ubiquitin chain length,DUBs, ubiquitin signaling, K63 linkage, x-ray crystallography, cholestasis, deubiquitinating enzymes, protease mechanism, ubiquitin probes, ubiquitin, polyubiquitin specificity, USP54, USP53

Jeroen Demmers
contact affiliation	Erasmus MC
contact email	j.demmers@erasmusmc.nl
lab head
Jeroen Demmers
contact affiliation	Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
contact email	j.demmers@erasmusmc.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD054748
     1. Label: PRIDE project
     2. Name: Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53