3U87

Structure of a chimeric construct of human CK2alpha and human CK2alpha' in complex with a non-hydrolysable ATP-analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Low-density crystal packing of human protein kinase CK2 catalytic subunit in complex with resorufin or other ligands: a tool to study the unique hinge-region plasticity of the enzyme without packing bias.

Klopffleisch, K.Issinger, O.G.Niefind, K.

(2012) Acta Crystallogr.,Sect.D 68: 883-892

  • DOI: 10.1107/S0907444912016587
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A low-resolution structure of the catalytic subunit CK2α of human protein kinase CK2 (formerly known as casein kinase 2) in complex with the ATP-competitive inhibitor resorufin is presented. The structure supplements previous human CK2α structures in ...

    A low-resolution structure of the catalytic subunit CK2α of human protein kinase CK2 (formerly known as casein kinase 2) in complex with the ATP-competitive inhibitor resorufin is presented. The structure supplements previous human CK2α structures in which the interdomain hinge/helix αD region adopts a closed conformation correlating to a canonically established catalytic spine as is typical for eukaryotic protein kinases. In the corresponding crystal packing the hinge/helix αD region is nearly unaffected by crystal contacts, so that largely unbiased conformational adaptions are possible. This is documented by published human CK2α structures with the same crystal packing but with an open hinge/helix αD region, one of which has been redetermined here with a higher symmetry. An overview of all published human CK2α crystal packings serves as the basis for a discussion of the factors that determine whether the open or the closed hinge/helix αD conformation is adopted. Lyotropic salts in crystallization support the closed conformation, in which the Phe121 side chain complements the hydrophobic catalytic spine ensemble. Consequently, genuine ligand effects on the hinge/helix αD conformation can be best studied under moderate salt conditions. Ligands that stabilize either the open or the closed conformation by hydrogen bonds are known, but a general rule is not yet apparent.


    Related Citations: 
    • Protein kinase CK2: from structures to insights
      Niefind, K.,Raaf, J.,Issinger, O.-G.
      (2009) Cell. Mol. Life Sci. 66: 1800
    • Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit.
      Ermakova, I.,Boldyreff, B.,Issinger, O.G.,Niefind, K.
      (2003) J.Mol.Biol. 330: 925
    • The catalytic subunit of human protein kinase CK2 structurally deviates from its maize homologue in complex with the mucleotide competitive inhibitor emodin
      Raaf, J.,Klopffleisch, K.,Issinger, O.-G.,Niefind, K.
      (2008) J.Mol.Biol. 377: 1
    • Structure of the human protein kinase CK2 catalytic subunit CK2alpha' and interaction thermodynamics with the regulatory subunit CK2beta
      Bischoff, N.,Olsen, B.,Raaf, J.,Bretner, M.,Issinger, O.G.,Niefind, K.
      (2011) J.Mol.Biol. 407: 1
    • Enzymatic activity with an incomplete catalytic spine - insights from a comparative structural analysis of human CK2alpha and its paralogous isoform CK2alpha'
      Bischoff, N.,Raaf, J.,Olsen, B.,Bretner, M.,Issinger, O.G.,Niefind, K.
      (2011) Mol.Cell.Biochem. 356: 57
    • First inactive conformation of CK2alpha, the catalytic subunit of protein kinase CK2
      Raaf, J.,Issinger, O.-G.,Niefind, K.
      (2009) J.Mol.Biol. 386: 1212
    • The CK2alpha/CK2beta interface of human protein kinase CK2 harbors a binding pocket for small molecules
      Raaf, J.,Brunstein, E.,Issinger, O.-G.,Niefind, K.
      (2008) Chem.Biol. 15: 111
    • Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate.
      Yde, C.W.,Ermakova, I.,Issinger, O.G.,Niefind, K.
      (2005) J.Mol.Biol. 347: 399
    • Evolved to be active: sulfate ions define substrate recognition sites of CK2alpha and emphasise its exceptional role within the CMGC family of eukaryotic protein kinases.
      Niefind, K.,Yde, C.W.,Ermakova, I.,Issinger, O.G.
      (2007) J.Mol.Biol. 370: 427
    • GTP plus water mimic ATP in the active site of protein kinase CK2.
      Niefind, K.,Putter, M.,Guerra, B.,Issinger, O.G.,Schomburg, D.
      (1999) Nat.Struct.Mol.Biol. 6: 1100
    • 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


    Organizational Affiliation

    Department für Chemie, Institut für Biochemie, Universität zu Köln, Otto-Fischer-Strasse 12-14, D-50674 Köln, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A, B
349Homo sapiensMutation(s): 0 
Gene Names: CSNK2A2 (CK2A2), CSNK2A1 (CK2A1)
EC: 2.7.11.1 2.7.11.1
Find proteins for P19784 (Homo sapiens)
Go to Gene View: CSNK2A2
Go to UniProtKB:  P19784
Find proteins for P68400 (Homo sapiens)
Go to Gene View: CSNK2A1
Go to UniProtKB:  P68400
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.186 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 127.821α = 90.00
b = 127.821β = 90.00
c = 125.333γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Source and taxonomy