PXD032822 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Deubiquitinases that digest Met1 chains in Rice |
Description | Met1 type ubiquitination and deubiquitination are involved in the regulation of many fundamental processes such as inflammation and innate immunity, and their interference by pathogens can suppress immune responses in human cells. However, few plant-derived deubiquitinases (DUBs) against Met1 ubiquitin chains has been reported, and the selection mechanism for linkage-type of ubiquitin chains remains elusive, which greatly limits our understanding of the functions of plant-derived DUBs. Using a dehydroalanine (DHA)-bearing Met1 diubiquitin (Met1-diUb) suicide probe, synthesized in one-pot, we captured OTUB1 from Oryza sativa (OsOTUB1) and uncovered its ability to hydrolyze Met1 ubiquitin chains (Met1 activity). Further, by resolving the apo structure of OsOTUB1 and its complex with Met1-diUb, we found that Met1-specific motifs (N-handle motif and C-handle motif) in the S1’ pocket of OsOTUB1 confers its Met1 activity. Through large-scale sequence alignment and hydrolysis experiments, Met1-specific motifs in the S1' pocket of the OTUB subfamily (OTUBs) were found to determine the Met1 ability of OTUBs, regardless of species. Furthermore, by analyzing the species distribution of OTUBs capable of hydrolyzing Met1 ubiquitin chains, we found that whereas this activity does not exist in metazoans, it is conserved in green plants (Viridiplantae). This discovery may inform studies of the differentiation between primitive plants and animals. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:25:10.728.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD032822 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Li-Ning Lu |
SpeciesList | scientific name: Oryza sativa (Rice); NCBI TaxID: 4530; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | LTQ Orbitrap Elite |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-03-26 14:16:09 | ID requested | |
1 | 2022-10-14 19:36:06 | announced | |
⏵ 2 | 2023-11-14 08:25:12 | announced | 2023-11-14: Updated project metadata. |
Publication List
Lu L, Zhai X, Li X, Wang S, Zhang L, Wang L, Jin X, Liang L, Deng Z, Li Z, Wang Y, Fu X, Hu H, Wang J, Mei Z, He Z, Wang F, Met1-specific motifs conserved in OTUB subfamily of green plants enable rice OTUB1 to hydrolyse Met1 ubiquitin chains. Nat Commun, 13(1):4672(2022) [pubmed] |
10.6019/PXD032822; |
Keyword List
submitter keyword: Deubiquitinase, Met1 chains,Rice |
Contact List
Lining Lu |
contact affiliation | College of life sciences and technology,Guangxi University |
contact email | thu20151@sina.com |
lab head | |
Li-Ning Lu |
contact affiliation | Guangxi University |
contact email | thu20151@sina.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD032822
- Label: PRIDE project
- Name: Deubiquitinases that digest Met1 chains in Rice