Human MKP-3 isoforms display differential structural and functional profiles

Mitogen-activated protein kinase (MAPK) phosphatases [MKPs, also known as dual-specificity phosphatases (DUSPs)] regulate MAPKs -key mediators of cellular processes such as proliferation, differentiation, and survival- by dephosphorylating the threonine and tyrosine residues required for MAPK activation. MKP-3/DUSP6 is an ERK-selective phosphatase that has also been reported to regulate the transcription factor FOXO1. The full-length MKP-3 transcript has been shown to encode the MKP-3L protein, whereas alternative splicing gives rise to the shorter isoform MKP-3S. However, the available information regarding the functional differences between these variants is limited. By combining biochemical and bioinformatic approaches, we demonstrate that these isoforms differ significantly in subcellular localization and enzymatic activity. Structural analysis and molecular docking reveal that while MKP-3S retains functional binding domains and recognizes ERK2 similarly to the full-length isoform. However, the absence of critical catalytic motifs in MKP-3S leads to a structural uncoupling where the protein retains its ability to bind ERK2 but fails to induce dephosphorylation, suggesting a non-canonical role as a molecular scaffold. The results obtained demonstrate significant variations in subcellular localization, enzymatic activity, and the capacity to modulate FOXO1 transcriptional activity. This, in turn, affects the expression of genes such as p21. In conclusion, the findings indicate that MKP-3 variants exhibit distinct functional behaviours, which may result in differential regulation of a wide range of cellular processes.