PXD015802

PXD015802 is an original dataset announced via ProteomeXchange.

Title	Molecular characterization of the eukaryotic Uba4/Urm1 system
Description	Ubiquitin-like protein activator 4 (Uba4) is required for the thiolation of uridine bases in eukaryotic transfer RNA. Uba4 catalyzes the sequential adenylation and thiocarboxylation of the C-terminus of Ubiquitin related modifier 1 (Urm1), acting as a hybrid between an E1-like activating enzyme and a sulfur-transferase. Structural and mechanistic details of the eukaryotic Uba4 protein and its respective reaction intermediates remained elusive. Here, we report the high-resolution crystal structures of full length Uba4 from Chaetomium thermophilum and its heterodimeric complex with Urm1. The structures show, how the aligned adenylation and rhodanese-like domains of Uba4 orchestrate substrate binding and specifically recognize and activate Urm1 at its C-terminus. We use complementary assays in vitro and in vivo to functionally validate all our structural findings. Furthermore, we uncover that under oxidative stress the specific relay of catalytic cysteines, similar to E1-E2 cascades, protects Uba4 from covalent conjugation by its own product, namely thiocarboxylated Urm1.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:09:00.945.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Urszula Jankowska
SpeciesList	scientific name: Chaetomium thermophilum; NCBI TaxID: 209285;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-14 02:04:16	ID requested
1	2020-07-14 05:43:45	announced
2	2020-09-13 22:27:58	announced	2020-09-14: Updated publication reference for PubMed record(s): 32901956.
⏵ 3	2024-10-22 05:09:03	announced	2024-10-22: Updated project metadata.

Pabis M, Termathe M, Ravichandran KE, Kienast SD, Krutyho, ł, owa R, Soko, ł, owski M, Jankowska U, Grudnik P, Leidel SA, Glatt S, Molecular basis for the bifunctional Uba4-Urm1 sulfur-relay system in tRNA thiolation and ubiquitin-like conjugation. EMBO J, 39(19):e105087(2020) [pubmed]

10.15252/embj.2020105087;

curator keyword: Biological

submitter keyword: Uba4, urmylation, Urm1

Urszula Jankowska
contact affiliation	Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
contact email	urszula.jankowska@uj.edu.pl
lab head
Urszula Jankowska
contact affiliation	Proteomics and Mass Spectrometry Core Facility, Malopolska Centre of Biotechnology, Jagiellonian University
contact email	urszula.jankowska@uj.edu.pl
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/2020/07/PXD015802

PRIDE project URI

• PRIDE
  1. PXD015802
     1. Label: PRIDE project
     2. Name: Molecular characterization of the eukaryotic Uba4/Urm1 system