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: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


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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
  • Primary Citation of Related Structures:  
    4IB5

  • 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 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 ...

    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

    Organizational Affiliation

    Kosan Biosciences, Inc., 3832 Bay Center Place, Hayward, CA 94545, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase II subunit alphaA, B, C335Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1CK2A1
EC: 2.7.11.1
Find proteins for P68400 (Homo sapiens)
Explore P68400 
Go to UniProtKB:  P68400
NIH Common Fund Data Resources
PHAROS:  P68400
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CK2beta-derived cyclic peptideD, E, F, G13N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.38α = 90
b = 105.42β = 90
c = 152.11γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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