3UGL image
Deposition Date 2011-11-02
Release Date 2012-12-12
Last Version Date 2023-09-13
Entry Detail
PDB ID:
3UGL
Title:
Structural and functional characterization of an anesthetic binding site in the second cysteine-rich domain of protein kinase C delta
Biological Source:
Source Organism:
Mus musculus (Taxon ID: 10090)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.36 Å
R-Value Free:
0.17
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 1 21 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteine kinase C delta type
Gene (Uniprot):Prkcd
Chain IDs:A, B
Chain Length:65
Number of Molecules:2
Biological Source:Mus musculus
Primary Citation
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)
PMID: 23283232 DOI: 10.1016/j.bpj.2012.10.034

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures