PXD047866 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Substrate identification and specificity profiling of deubiquitylases against endogenously-generated ubiquitin-protein conjugates |
Description | Deubiquitylating enzymes (DUBs) remove ubiquitin from proteins thereby regulating their stability or activity. Our understanding of DUB-substrate specificity is limited because DUBs are typically not compared to each other against many physiological substrates. By broadly inhibiting DUBs in Xenopus egg extract, we generated hundreds of ubiquitylated proteins and compared the ability of 30 DUBs to deubiquitylate them using quantitative proteomics. We identified five high impact DUBs (USP7, USP9X, USP36, USP15 and USP24) that each reduced ubiquitylation of over ten percent of the isolated proteins. Candidate substrates of high impact DUBs showed substantial overlap and were enriched for disordered regions, suggesting this feature may promote substrate recognition. Other DUBs showed lower impact and non-overlapping specificity, targeting distinct non-disordered proteins including complexes such as the ribosome or the proteasome. Altogether our study identifies candidate DUB substrates and defines patterns of functional redundancy and specificity, revealing substrate characteristics that may influence DUB-substrate recognition. |
HostingRepository | PRIDE |
AnnounceDate | 2024-04-26 |
AnnouncementXML | Submission_2024-04-26_11:26:01.156.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Joao Paulo |
SpeciesList | scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Eclipse; Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-12-16 06:01:35 | ID requested | |
⏵ 1 | 2024-04-26 11:26:01 | announced | |
2 | 2024-10-22 06:37:31 | announced | 2024-10-22: Updated project metadata. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: DUB substrates, Xenopus,Deubiquitylating enzymes, ubiquitin, TMT-proteomics |
Contact List
Randall W. King |
contact affiliation | Department of Cell Biology Blavatnik Institute at Harvard Medical School Boston, MA 02115, USA |
contact email | randy_king@hms.harvard.edu |
lab head | |
Joao Paulo |
contact affiliation | Harvard Medical School |
contact email | joao_paulo@post.harvard.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD047866
- Label: PRIDE project
- Name: Substrate identification and specificity profiling of deubiquitylases against endogenously-generated ubiquitin-protein conjugates