3UGL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Characterization of an Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase Cdelta

Shanmugasundararaj, S.Das, J.Sandberg, W.S.Zhou, X.Wang, D.Messing, R.O.Bruzik, K.S.Stehle, T.Miller, K.W.

(2012) Biophys J 103: 2331-2340

  • DOI: 10.1016/j.bpj.2012.10.034
  • Primary Citation of Related Structures:  
    3UEY, 3UEJ, 3UGD, 3UFF, 3UGI, 3UGL

  • 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 ...

    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.


    Related Citations: 
    • Crystal structure of the cys2 activator binding domain of protein kinase C delta in complex with phorbol ester
      Zhang, G., Kazanietz, M.G., Blumberg, P.M., Hurley, J.H.
      (1995) Cell 81: 917

    Organizational Affiliation

    Department of Anesthesia and Critical Care, Massachusetts General Hospital, Boston, MA, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteine kinase C delta typeA, B65Mus musculusMutation(s): 0 
Gene Names: PrkcdPkcd
EC: 2.7.11.13 (PDB Primary Data), 2.7.10.2 (UniProt)
Find proteins for P28867 (Mus musculus)
Explore P28867 
Go to UniProtKB:  P28867
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.876α = 90
b = 32.522β = 94.02
c = 49.816γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description