9EOY

Structure of Thr354Asn, Glu355Gln, Thr412Asn, Ile414Met, Ile464His, and Phe467Met mutant human CaMKII alpha hub bound to PIPA

This is a non-PDB format compatible entry.

Summary for 9EOY

• Entry DOI: 10.2210/pdb9eoy/pdb
• Descriptor: Calcium/calmodulin-dependent protein kinase type II subunit alpha, ACETATE ION, 2-[6-(4-chlorophenyl)imidazo[1,2-b]pyridazin-2-yl]ethanoic acid, ... (5 entities in total)
• Functional Keywords: camkii hub, oligomer, signaling protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 7
• Total formula weight: 109984.94

Authors

Narayanan, D.,Larsen, A.S.G.,Solbak, S.M.O.,Wellendorph, P.,Gee, C.L.,Kastrup, J.S. (deposition date: 2024-03-15, release date: 2024-09-25)

Primary citation

Narayanan, D.,Larsen, A.S.G.,Gauger, S.J.,Adafia, R.,Hammershoi, R.B.,Hamborg, L.,Bruus-Jensen, J.,Griem-Krey, N.,Gee, C.L.,Frolund, B.,Stratton, M.M.,Kuriyan, J.,Kastrup, J.S.,Langkilde, A.E.,Wellendorph, P.,Solbak, S.M.O.
Ligand-induced CaMKII alpha hub Trp403 flip, hub domain stacking, and modulation of kinase activity.
Protein Sci., 33:e5152-e5152, 2024

PubMed Abstract: γ-Hydroxybutyric acid (GHB) analogs are small molecules that bind competitively to a specific cavity in the oligomeric CaMKIIα hub domain. Binding affects conformation and stability of the hub domain, which may explain the neuroprotective action of some of these compounds. Here, we describe molecular details of interaction of the larger-type GHB analog 2-(6-(4-chlorophenyl)imidazo[1,2-b]pyridazine-2-yl)acetic acid (PIPA). Like smaller-type analogs, PIPA binding to the CaMKIIα hub domain promoted thermal stability. PIPA additionally modulated CaMKIIα activity under sub-maximal CaM concentrations and ultimately led to reduced substrate phosphorylation. A high-resolution X-ray crystal structure of a stabilized CaMKIIα (6x mutant) hub construct revealed details of the binding mode of PIPA, which involved outward placement of tryptophan 403 (Trp403), a central residue in a flexible loop close to the upper hub cavity. Small-angle X-ray scattering (SAXS) solution structures and mass photometry of the CaMKIIα wild-type hub domain in the presence of PIPA revealed a high degree of ordered self-association (stacks of CaMKIIα hub domains). This stacking neither occurred with the smaller compound 3-hydroxycyclopent-1-enecarboxylic acid (HOCPCA), nor when Trp403 was replaced with leucine (W403L). Additionally, CaMKIIα W403L hub was stabilized to a larger extent by PIPA compared to CaMKIIα hub wild type, indicating that loop flexibility is important for holoenzyme stability. Thus, we propose that ligand-induced outward placement of Trp403 by PIPA, which promotes an unforeseen mechanism of hub domain stacking, may be involved in the observed reduction in CaMKIIα kinase activity. Altogether, this sheds new light on allosteric regulation of CaMKIIα activity via the hub domain.

PubMed: 39275999
DOI: 10.1002/pro.5152

Experimental method

X-RAY DIFFRACTION (2.1 Å)