PXD072953

PXD072953 is an original dataset announced via ProteomeXchange.

Title	Structural and mechanistic basis of ubiquitous bacterial kinase signaling reveals PorX as a noncanonical substrate in Porphyromonas gingivalis
Description	Protein phosphorylation enables bacteria to coordinate regulatory networks underlying virulence and environmental adaptation. The ubiquitous bacterial kinase family comprises atypical kinases with dual serine threonine and tyrosine specificity, yet their structural organization, catalytic mechanisms, and physiological roles remain incompletely defined. In the anaerobic oral pathogen Porphyromonas gingivalis, the sole UbK homolog, UbK1, was previously shown to phosphorylate the orphan response regulator RprY, linking UbK1 to virulence-associated pathways. Here, we present the crystal structure of UbK1, revealing the conserved Walker A, HxDxYR, SPT/S, and EW motifs arranged around the ATP-binding site. Structure-guided mutagenesis establishes essential roles for these motifs in ATP hydrolysis and kinase activity. Phosphosite mapping identifies multiple autophosphorylation sites, with the flexible SPT/S loop showing the strongest occupancy and supporting a model in which loop centered autophosphorylation is a major feature of UbK1 cycling while additional sites arise through intermolecular phosphotransfer in trans. Consistent with this, biochemical assays demonstrate that UbK1 undergoes autophosphorylation both in cis and in trans, arguing against a strictly intramolecular autokinase mechanism. Using conserved gene neighborhood analysis, we identified the orphan response regulator PorX as a previously unrecognized UbK1 substrate, consistent with the relaxed substrate specificity reported for UbK homologs. UbK1 catalyzes PorX transphosphorylation in vitro at a single tyrosine residue within the receiver domain, independent of PorX oligomeric state. In vivo, ubk1 deletion causes a modest reduction in gingipain secretion, whereas mutation of the UbK1 dependent PorX phosphosite does not measurably affect T9SS mediated cargo export, indicating that UbK1-PorX signaling is separable from PorX canonical gingipain secretion output. Together, these findings establish a structural and mechanistic framework for UbK1 function, expand the UbK substrate repertoire, and support a model in which UbK1 contributes to regulatory pathways in P. gingivalis that extend beyond canonical secretion associated outputs.
HostingRepository	PRIDE
AnnounceDate	2026-06-15
AnnouncementXML	Submission_2026-06-14_16:10:45.859.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vincent Richard
SpeciesList	scientific name: Escherichia coli (strain K12); NCBI TaxID: NEWT:83333; scientific name: Porphyromonas gingivalis; NCBI TaxID: NEWT:837;
ModificationList	phosphorylated residue; iodoacetamide derivatized residue
Instrument	Bruker Daltonics timsTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2026-01-12 06:35:25	ID requested
⏵ 1	2026-06-14 16:10:46	announced

10.1016/j.jbc.2026.113088;

Saran A, Yang Z, Wang Z, Harris JNC, Vahidi S, Zeytuni N, Structural and mechanistic basis of ubiquitous bacterial kinase signaling identifies PorX as a noncanonical substrate in Porphyromonas gingivalis. J Biol Chem, 302(6):113088(2026) [pubmed]

submitter keyword: response regulator, transphosphorylation, Ubk1, autophosphorylation, Type IX Secretion System (T9SS),Ubiquitous bacterial Kinase (UbK), PorX, Porphyromonas gingivalis

Christoph H Borchers
contact affiliation	Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital,McGill University, Montréal, Québec,Canada
contact email	christoph.borchers@mcgill.ca
lab head
Vincent Richard
contact affiliation	Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University
contact email	vincentroyrichard@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD072953
     1. Label: PRIDE project
     2. Name: Structural and mechanistic basis of ubiquitous bacterial kinase signaling reveals PorX as a noncanonical substrate in Porphyromonas gingivalis