CysMP reveals metal ion–specific metalloproteomes and copper-regulated PGK1 activity in glycolysis

Metal ions are essential in regulating protein functions through interactions with residues such as cysteine, but comprehensive mapping of metal-specific metalloproteomes in mammals remains limited. Here, we introduce CysMP, a cysteine-centered metalloprotein profiling strategy to profile the metalloproteomes of 11 key metal ions. CysMP identified 8895 metal-binding sites across 4150 proteins, enabling quantitative comparisons between different metals and revealing both their binding promiscuity and preferences. Notably, zinc and copper ions exhibit the broadest protein interaction profiles. CysMP uncovers numerous potential metalloproteins. We demonstrate that copper and zinc bind to and inhibit 5′-methylthioadenosine phosphorylase, resulting in the accumulation of 5′-methylthioadenosine. Furthermore, copper binding suppresses phosphoglycerate kinase 1 activity, leading to a down-regulation of glycolysis. Our work not only establishes a valuable resource for a dual-specific metalloproteome database but also paves the way for understanding the molecular insights of metalloprotein functions.