3UEJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.301 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.142 

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:  

  • 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 structu ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein kinase C delta type
A, B
65Mus musculusMutation(s): 0 
Gene Names: Prkcd (Pkcd)
EC: 2.7.11.13
Find proteins for P28867 (Mus musculus)
Go to UniProtKB:  P28867
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.301 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.142 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.598α = 90.00
b = 32.475β = 94.10
c = 49.965γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
ADSCdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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