PXD049797

PXD049797 is an original dataset announced via ProteomeXchange.

Title	Development of covalent probes to capture Legionella pneumophila effector enzymes
Description	Upon infection of host cells Legionella pneumophila releases a multitude of effector enzymes into the hosts cytoplasm that hijack a plethora of cellular activities, including the hosts ubiquitination pathways. Effectors belonging to the SidE-family are involved in non-canonical serine phosphoribosyl ubiquitination of host substrate proteins contributing to the formation of a Legionella-containing vacuole which is crucial in the onset of legionnaires disease. This dynamic process is reversed by effectors called Dups that hydrolyse the phosphodiester in the phosphoribosyl ubiquitinated protein. We installed reactive warheads on chemically prepared ribosylated ubiquitin to generate a set of probes targetting these Legionella enzymes. In vitro tests on recombinant DupA revealed that a vinyl sulfonate warhead was most efficient in covalent complex formation. Mutagenesis and x-ray crystallography approaches were used to identify the site of covalent crosslinking to be an allosteric cysteine residue and subsequent application of this probe highlight the potential to selective enrich Dup enzymes from Legionella infected cell lysates.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_13:29:10.530.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rayman Tjokrodirijo
SpeciesList	scientific name: Legionella pneumophila subsp. pneumophila Lp02; NCBI TaxID: 1080311; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-20 03:29:58	ID requested
⏵ 1	2025-05-06 13:29:11	announced

10.1021/acs.bioconjchem.4c00541;

Kloet MS, Mukhopadhyay R, Mukherjee R, Misra M, Talavera Orme, ñ, o CMP, Tjokrodirijo RTN, Hensbergen PJ, van Veelen PA, Đ, iki, ć I, Sapmaz A, van der Heden van Noort GJ, Dup Enzymes. Bioconjug Chem, 36(3):457-463(2025) [pubmed]

submitter keyword: Legionella pneumophila,Activity-based probe, Ubiquitylation, ADP-ribosylation, Bacterial infection

Peter A. van Veelen
contact affiliation	Head Proteomics Group , Leiden University Medical Center, Center for Proteomics and Metabolomics, PO Box 9600, Postal zone P1-Q, 2300 RC Leiden, The Netherlands
contact email	P.A.van_Veelen@lumc.nl
lab head
Rayman Tjokrodirijo
contact affiliation	Leiden University Medical Center, Proteomics group
contact email	R.T.N.Tjokrodirijo@lumc.nl
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/2025/05/PXD049797

PRIDE project URI

• PRIDE
  1. PXD049797
     1. Label: PRIDE project
     2. Name: Development of covalent probes to capture Legionella pneumophila effector enzymes