3UGL

Structural and functional characterization of an anesthetic binding site in the second cysteine-rich domain of protein kinase C delta

Summary for 3UGL

• Entry DOI: 10.2210/pdb3ugl/pdb
• Related: 1PTQ 1PTR 3UEJ 3UEY 3UFF 3UGD 3UGI
• Descriptor: Proteine kinase C delta type, ZINC ION, cyclopropylmethanol, ... (5 entities in total)
• Functional Keywords: proteine kinase c delta, phosphotransferase, anesthetic binding site, metal binding protein
• Biological source: Mus musculus (mouse)
• Cellular location: Cytoplasm : P28867
• Total number of polymer chains: 2
• Total formula weight: 15443.87

Authors

Shanmugasundararaj, S.,Stehle, T.,Miller, K.W. (deposition date: 2011-11-02, release date: 2012-12-12, Last modification date: 2023-09-13)

Primary citation

Shanmugasundararaj, S.,Das, J.,Sandberg, W.S.,Zhou, X.,Wang, D.,Messing, R.O.,Bruzik, K.S.,Stehle, T.,Miller, K.W.
Structural and Functional Characterization of an Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase Cdelta
Biophys.J., 103:2331-2340, 2012

PubMed Abstract: Elucidating the principles governing anesthetic-protein interactions requires structural determinations at high resolutions not yet achieved with ion channels. Protein kinase C (PKC) activity is modulated by general anesthetics. We solved the structure of the phorbol-binding domain (C1B) of PKCδ complexed with an ether (methoxymethylcycloprane) and with an alcohol (cyclopropylmethanol) at 1.36-Å resolution. The cyclopropane rings of both agents displace a single water molecule in a surface pocket adjacent to the phorbol-binding site, making van der Waals contacts with the backbone and/or side chains of residues Asn-237 to Ser-240. Surprisingly, two water molecules anchored in a hydrogen-bonded chain between Thr-242 and Lys-260 impart elasticity to one side of the binding pocket. The cyclopropane ring takes part in π-acceptor hydrogen bonds with the amide of Met-239. There is a crucial hydrogen bond between the oxygen atoms of the anesthetics and the hydroxyl of Tyr-236. A Tyr-236-Phe mutation results in loss of binding. Thus, both van der Waals interactions and hydrogen-bonding are essential for binding to occur. Ethanol failed to bind because it is too short to benefit from both interactions. Cyclopropylmethanol inhibited phorbol-ester-induced PKCδ activity, but failed to do so in PKCδ containing the Tyr-236-Phe mutation.

PubMed: 23283232
DOI: 10.1016/j.bpj.2012.10.034

Experimental method

X-RAY DIFFRACTION (1.357 Å)