PXD065625

PXD065625 is an original dataset announced via ProteomeXchange.

Title	Periplasmic Protein Quality Control at Atomic Level in Live Cells
Description	The periplasm of gram-negative bacteria facilitates critical functions, including nutrient uptake, cell wall metabolism, antibiotic resistance, and virulence. Efficient quality control of proteins involved in these processes is crucial for bacterial fitness and survival. The limited size of the periplasm has hindered high-resolution mechanistic investigations of complex processes within this compartment. Using in-cell NMR spectroscopy, we dissected the mechanism of periplasmic quality control of the metallo-β-lactamase NDM-1 under conditions of zinc starvation, which destabilizes its native structure promoting its degradation. We show that the protease Prc targets membrane-bound NDM-1 at specific residues and secondary structure motifs, while DegP processes peptides generated by Prc. This approach discloses the concerted mechanism of these proteases at atomic resolution in the periplasm of live cells.
HostingRepository	PRIDE
AnnounceDate	2025-07-10
AnnouncementXML	Submission_2025-07-09_17:07:40.081.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andres Binolfi
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-30 08:43:36	ID requested
⏵ 1	2025-07-09 17:07:40	announced

Dataset with its publication pending

submitter keyword: E. coli, periplasm, DegP, proteolysis,NDM1, Prc

Andres Binolfi
contact affiliation	Cellular-Structural Biology Lab. IBR-CONICET
contact email	binolfi@ibr-conicet.gov.ar
lab head
Andres Binolfi
contact affiliation	IBR-CONICET
contact email	binolfi@ibr-conicet.gov.ar
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/2025/07/PXD065625

PRIDE project URI

• PRIDE
  1. PXD065625
     1. Label: PRIDE project
     2. Name: Periplasmic Protein Quality Control at Atomic Level in Live Cells