PXD075565

PXD075565 is an original dataset announced via ProteomeXchange.

Title	Chemical proteomics reveal the inventory of pyrroloquinoline quinone binding proteins in bacteria
Description	Pyrroloquinoline quinone (PQQ) is a bacterial redox cofactor enabling enzyme catalysis in various sugar and alcohol dehydrogenases. However, its proposed additional role as a "longevity vitamin" lacks a clear molecular basis and is thus highly debated. Here, we applied chemical proteomics to identify so far unknown classes of PQQ-binding proteins. We designed and synthesized a structurally diverse suite of five PQQ probes equipped with a diazirine photocrosslinker and an alkyne handle for target identification. The fidelity of the probes was first evaluated for two well-characterized bacterial PQQ-dependent enzymes, demonstrating not only probe binding but also reconstitution of catalytic activity. We then commenced with proteome profiling of Escherichia coli and Pseudomonas putida cells and unraveled a distinct set of putative PQQ-binding proteins. Recombinant expression of selected hits including several chaperones validated PQQ binding. Notably, in some cases, PQQ even formed covalent adducts with selected lysine residues, for instance in the AAA+ ATPase RuvB involved in DNA remodeling. Overall, our work highlights the utility of PQQ probes to further unravel the complement of cofactor-binding proteins in whole cells. It also provides a basis for future mechanistic studies on PQQ functions beyond redox catalysis.
HostingRepository	PRIDE
AnnounceDate	2026-04-27
AnnouncementXML	Submission_2026-04-26_16:10:59.251.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tao Wang
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: NEWT:562;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2026-03-12 08:45:42	ID requested
⏵ 1	2026-04-26 16:11:00	announced

10.1021/jacs.6c03427;

Wang T, M, ü, hlhofer R, Lei E, Ding W, Klein AS, Zeymer C, Sieber SA, Chemical Proteomics Reveal the Inventory of Pyrroloquinoline Quinone Binding Proteins in Bacteria. J Am Chem Soc, 148(14):15306-15319(2026) [pubmed]

submitter keyword: proteomics, pyrroloquinoline quinone

Stephan A. Sieber
contact affiliation	Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich (TUM), Ernst-Otto-Fischer-Stra?e 8, 85748 Garching, Germany
contact email	stephan.sieber@tum.de
lab head
Tao Wang
contact affiliation	Technical University of Munich
contact email	tao.wang@tum.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD075565
     1. Label: PRIDE project
     2. Name: Chemical proteomics reveal the inventory of pyrroloquinoline quinone binding proteins in bacteria