4IB5

Structure of human protein kinase CK2 catalytic subunit in complex with a CK2beta-competitive cyclic peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

First structure of protein kinase CK2 catalytic subunit with an effective CK2 beta-competitive ligand

Raaf, J.Guerra, B.Neundorf, I.Bopp, B.Issinger, O.G.Jose, J.Pietsch, M.Niefind, K.

(2013) Acs Chem.Biol. 8: 901-907

  • DOI: 10.1021/cb3007133

  • PubMed Abstract: 
  • The constitutively active Ser/Thr kinase CK2 (casein kinase 2) is used by tumor cells to acquire apoptosis resistance. CK2 exists as a heterotetrameric holoenzyme with two catalytic chains (CK2α) attached to a dimer of noncatalytic subunits (CK2β). A ...

    The constitutively active Ser/Thr kinase CK2 (casein kinase 2) is used by tumor cells to acquire apoptosis resistance. CK2 exists as a heterotetrameric holoenzyme with two catalytic chains (CK2α) attached to a dimer of noncatalytic subunits (CK2β). A druggable cavity at the CK2β interface of CK2α allows the design of small molecules disturbing the CK2α/CK2β interaction and thus affecting activity, stability, and substrate specificity. We describe here the first structure of CK2α with an effective CK2β-competitive compound, namely, a 13-meric cyclic peptide derived from the C-terminal CK2β segment. Some well-ordered water molecules not visible in CK2 holoenzyme structures were detected at the interface. Driven mainly by enthalpy, the peptide binds with submicromolar affinity to CK2α, stimulates its catalytic activity, and reduces effectively the CK2α/CK2β affinity. The results provide a thermodynamic and structural rationalization of the peptide's CK2β-competitive functionality and pave thus the way to a peptidomimetic drug addressing the CK2α/CK2β interaction.


    Related Citations: 
    • Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme
      Niefind, K.,Guerra, B.,Ermakowa, I.,Issinger, O.G.
      (2001) Embo J. 20: 5320
    • Structure-based design of small peptide inhibitors of protein kinase CK2 subunit interaction.
      Laudet, B.,Barette, C.,Dulery, V.,Renaudet, O.,Dumy, P.,Metz, A.,Prudent, R.,Deshiere, A.,Dideberg, O.,Filhol, O.,Cochet, C.
      (2007) Biochem.J. 408: 363



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A, B, C
335Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1 (CK2A1)
EC: 2.7.11.1
Find proteins for P68400 (Homo sapiens)
Go to Gene View: CSNK2A1
Go to UniProtKB:  P68400
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CK2beta-derived cyclic peptide
D, E, F, G
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.380α = 90.00
b = 105.420β = 90.00
c = 152.110γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references