PXD024464

PXD024464 is an original dataset announced via ProteomeXchange.

Title	Proximity proteomics identifies PAK4 as a component of Afadin–Nectin junctions.
Description	Human PAK4 is an ubiquitously expressed p21-activated kinase which acts downstream of Cdc42. Since PAK4 is demonstrably enriched in cell-cell junctions, we probed the local protein environment around the kinase with a view to understanding its location and substrates. In U2OS cells expressing PAK4-BirA-GFP the resultant SILAC proximity analyses revealed a subset of 28 proteins that are primarily cell-cell junction components. The protein with highest relative biotin labelling was Afadin/AF6, which associates with the nectin family of homophilic junctional proteins. Reciprocally >50% of the PAK4-proximal proteins were identified by Afadin BioID. Pull-down experiments failed to identify junctional proteins, emphasizing the advantage of the BioID method. Mechanistically PAK4 depended on Afadin for its junctional localization, which is similar to the situation in Drosophila. A highly ranked PAK4-proximal protein LZTS2 was immuno-localized with Afadin at cell-cell junctions. Though PAK4 and Cdc42 are junctional, BioID analysis did not yield conventional cadherins, indicating their spatial segregation. To identify cellular PAK4 substrates we then assessed changes in phospho-proteome after 12 min PF-3758309 treatment. Among the PAK4-proximal junctional proteins 17 PAK4 sites were identified. Thus we show PAK4 is selective for the mammalian Afadin/nectin sub-compartment, with a demonstrably distinct localization from tight and cadherin junctions.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_13:37:50.793.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sheena Wee
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	6x(13)C; 6x(13)C; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-02 09:13:59	ID requested
⏵ 1	2024-10-07 13:37:51	announced

Baskaran Y, Tay FP, Ng EYW, Swa CLF, Wee S, Gunaratne J, Manser E, Proximity proteomics identifies PAK4 as a component of Afadin-Nectin junctions. Nat Commun, 12(1):5315(2021) [pubmed]

10.1038/s41467-021-25011-w;

submitter keyword: LZTS2, PAK4, Cdc42, BioID, epithelial cells,protein kinase, cell junctions

Jayantha Gunaratne
contact affiliation	Translational Biomedical Proteomics Institute of Molecular and Cell Biology 61 Biopolis Drive, #7-12/13, Proteos, Singapore 138673
contact email	jayanthag@imcb.a-star.edu.sg
lab head
Sheena Wee
contact affiliation	IMCB
contact email	swee@imcb.a-star.edu.sg
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/2021/11/PXD024464

PRIDE project URI

• PRIDE
  1. PXD024464
     1. Label: PRIDE project
     2. Name: Proximity proteomics identifies PAK4 as a component of Afadin–Nectin junctions.