PXD054175

PXD054175 is an original dataset announced via ProteomeXchange.

Title	Nucleoside diphosphate kinase A (NME1) catalyzes its own oligophosphorylation
Description	Protein phosphorylation is a central regulatory mechanism in eukaryotic cell signaling, and was recently expanded to include protein pyrophosphorylation and protein polyphosphorylation. Here, we report the discovery of yet another mode of phosphorylation – protein oligophosphorylation. Using site-specifically phosphorylated and pyrophosphorylated nucleoside diphosphate kinase A (NME1), the effects of these modifications on enzyme activity were investigated. Phosphorylation, and even more so pyrophosphorylation, on threonine 94 notably reduced the nucleoside diphosphate kinase activity. Nevertheless, both phosphoprotein and pyrophosphoprotein were able to catalyze their own oligophosphorylation – up to the formation of a hexaphosphate chain – using ATP as a co-factor. This reaction was critically dependent on the catalytic histidine residue (H118) and cryo-EM analysis of the differently modified proteins suggests an intramolecular phosphoryl transfer, likely via a phosphohistidine intermediate. Oligophosphorylation of NME1 in biochemical samples, as well as cell lysates, was further confirmed using mass spectrometry, and oligophophorylation promoted a new set of protein interactions. Our results highlight the complex nature of phosphoregulation, and the methods described here provide the opportunity to investigate the occurrence and the impact of this novel modification in the future.
HostingRepository	PRIDE
AnnounceDate	2025-08-21
AnnouncementXML	Submission_2025-08-21_06:23:56.887.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Max Ruwolt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-24 04:01:00	ID requested
⏵ 1	2025-08-21 06:23:57	announced

10.1038/S41557-025-01915-8;

submitter keyword: oligophosphorylation, open-search,phosphorylation

Dorothea Fiedler
contact affiliation	FMP Berlin
contact email	Fiedler@fmp-berlin.de
lab head
Max Ruwolt
contact affiliation	Leibniz-Forschungsinstitut for Molecular Pharmacology
contact email	ruwolt@fmp-berlin.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD054175
     1. Label: PRIDE project
     2. Name: Nucleoside diphosphate kinase A (NME1) catalyzes its own oligophosphorylation