PXD055530-1

PXD055530 is an original dataset announced via ProteomeXchange.

Title	CysMP reveals metal ion-specific metalloproteomes and copper-regulated PGK1 activity in glycolysis
Description	Metal ions are crucial in regulating protein functions by coordinating with specific residues, such as cysteine. However, a comprehensive map of metal-specific metalloproteomes in mammals remains elusive, hindering our understanding of their intricate effects. We address this gap by introducing CysMP, a cysteine-centered metalloprotein profiling strategy that uses a cysteine-reactive probe to profile the metalloproteomes of eleven key metal ions. CysMP identified 8895 metal-binding sites across 4150 proteins, enabling quantitative comparisons of cysteine residue interactions with different metals and revealing binding preferences. Notably, zinc and copper ions displayed the broadest protein interaction profiles. Furthermore, CysMP uncovered numerous potential novel metalloproteins. We demonstrate that copper and zinc bind and inhibit 5′-Methylthioadenosine phosphorylase (MTAP), leading to the accumulation of 5’-methylthioadenosine (MTA). Similarly, copper binding inhibits phosphoglycerate kinase 1 (PGK1) activity, downregulating glycolysis. CysMP establishes a rich resource for a dual-specific metalloproteome database, encompassing interactions between metal ions and cysteine residues. Our data not only pave the way for understanding the molecular basis of metalloprotein functions but also hold promise for guiding the development of related therapeutics.
HostingRepository	iProX
AnnounceDate	2024-09-04
AnnouncementXML	Submission_2025-09-17_03:56:08.852.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yamei Yuan
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF; Q Exactive HF-X; timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-03 20:07:53	ID requested
⏵ 1	2025-09-17 03:56:09	announced
2	2025-09-18 02:00:25	announced	2025-09-18: Updata dataset information.

Dataset with its publication pending

submitter keyword: Metal binding proteins, cysteine-reactive probes, chemical proteomics, PGK1, glycolysis

Yaoyang Zhang
contact affiliation	Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., Shanghai 201210, China
contact email	zyy@sioc.ac.cn
lab head
Yamei Yuan
contact affiliation	Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., Shanghai 201210, China
contact email	yuanym@sioc.ac.cn
dataset submitter

iProX dataset URI