9NXE

Crystal Structure of Calcineurin Clinical Variant E282K

Summary for 9NXE

• Entry DOI: 10.2210/pdb9nxe/pdb
• Descriptor: Protein phosphatase 3 catalytic subunit alpha, Calcineurin subunit B type 1, Sodium/hydrogen exchanger 1, ... (8 entities in total)
• Functional Keywords: cn e282k, cn, clinical variant, hydrolase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 66070.79

Authors

Parikh, T.,Shirakawa, K.T.,Page, R.,Peti, W. (deposition date: 2025-03-25, release date: 2025-12-17, Last modification date: 2026-07-01)

Primary citation

Shirakawa, K.T.,Parikh, T.,Machado, L.E.S.F.,Poimenidou, G.,Nguyen, H.T.,Dell'Acqua, M.L.,Kettenbach, A.N.,Page, R.,Peti, W.
The clinical missense variant E282K in PPP3CA/calcineurin shifts substrate dephosphorylation by altering active site recruitment.
Nat Commun, 17:-, 2026

PubMed Abstract: Recently, de novo heterozygous variants of Calcineurin (CN) were reported as the cause of a neurodevelopmental disorder that presents with epileptic encephalopathy and dysmorphism (DEE91), with the largest group of patients harboring the CN missense mutation E282K (glutamate → lysine). Here, we use molecular and cellular techniques to define how this mutation alters CN activity. We discover that basophilic substrates use an arginine residue to bind to CN via an acidic substrate recruitment pocket adjacent to the CN active site, the E282 pocket. Furthermore, we show that basic residues in the i-1 position of the substrate relative to the substrate phosphosite enhance CN-mediated dephosphorylation. While the CN structure shows that the overall conformation is unchanged, the E282 pocket transforms from acidic to basic, with pocket access blocked by the formation of a E282K-E237 salt bridge. Finally, in vitro assays and in cell phosphoproteomics show that CN shifts CN substrate dephosphorylation profiles from basic to acidic, thereby altering CN-mediated dephosphorylation signaling. Together, these data define the molecular impact of the CN variant in cells and development, providing a key step for developing strategies to treat this disorder and its accompanying complications.

PubMed: 41698888
DOI: 10.1038/s41467-026-69535-5

Experimental method

X-RAY DIFFRACTION (2.09 Å)