9BU4 image
Deposition Date 2024-05-16
Release Date 2025-05-28
Last Version Date 2025-08-13
Entry Detail
PDB ID:
9BU4
Title:
Crystal structure of an MKP5 mutant, Y435W, in complex with an allosteric inhibitor
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.90 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Dual specificity protein phosphatase 10
Gene (Uniprot):DUSP10
Mutagens:Y435W
Chain IDs:A, B, C, D, E, F, G, H, I, J, K, L
Chain Length:148
Number of Molecules:12
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Dynamic and structural insights into allosteric regulation on MKP5 a dual-specificity phosphatase.
Nat Commun 16 7011 7011 (2025)
PMID: 40745179 DOI: 10.1038/s41467-025-62150-w

Abstact

Dual-specificity mitogen-activated protein kinase (MAPK) phosphatases (MKPs) directly dephosphorylate and inactivate the MAPKs. Although the catalytic mechanism of dephosphorylation of the MAPKs by the MKPs is established, a complete molecular picture of the regulatory interplay between the MAPKs and MKPs still remains to be fully explored. Here, we sought to define the molecular mechanism of MKP5 regulation through an allosteric site within its catalytic domain. We demonstrate using crystallographic and NMR spectroscopy approaches that residue Y435 is required to maintain the structural integrity of the allosteric pocket. Along with molecular dynamics simulations, these data provide insight into how changes in the allosteric pocket propagate conformational flexibility in the surrounding loops to reorganize catalytically crucial residues in the active site. Furthermore, Y435 is required for the interaction with p38 MAPK and JNK, thereby promoting dephosphorylation. Collectively, these results demonstrate critical roles for the allosteric site in coordinating both MKP5 catalysis and MAPK binding.

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Primary Citation of related structures