3FWQ

Inactive conformation of human protein kinase CK2 catalytic subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

First inactive conformation of CK2 alpha, the catalytic subunit of protein kinase CK2

Raaf, J.Issinger, O.G.Niefind, K.

(2009) J.Mol.Biol. 386: 1212-1221

  • DOI: 10.1016/j.jmb.2009.01.033
  • Also Cited By: 3U87

  • PubMed Abstract: 
  • The Ser/Thr kinase casein kinase 2 (CK2) is a heterotetrameric enzyme composed of two catalytic chains (CK2alpha, catalytic subunit of CK2) attached to a dimer of two noncatalytic subunits (CK2beta, noncatalytic subunit of CK2). CK2alpha belongs to t ...

    The Ser/Thr kinase casein kinase 2 (CK2) is a heterotetrameric enzyme composed of two catalytic chains (CK2alpha, catalytic subunit of CK2) attached to a dimer of two noncatalytic subunits (CK2beta, noncatalytic subunit of CK2). CK2alpha belongs to the superfamily of eukaryotic protein kinases (EPKs). To function as regulatory key components, EPKs normally exist in inactive ground states and are activated only upon specific signals. Typically, this activation is accompanied by large conformational changes in helix alpha C and in the activation segment, leading to a characteristic arrangement of catalytic key elements. For CK2alpha, however, no strict physiological control of activity is known. Accordingly, CK2alpha was found so far exclusively in the characteristic conformation of active EPKs, which is, in this case, additionally stabilized by a unique intramolecular contact between the N-terminal segment on one side, and helix alpha C and the activation segment on the other side. We report here the structure of a C-terminally truncated variant of human CK2alpha in which the enzyme adopts a decidedly inactive conformation for the first time. In this CK2alpha structure, those regulatory key regions still are in their active positions. Yet the glycine-rich ATP-binding loop, which is normally part of the canonical anti-parallel beta-sheet, has collapsed into the ATP-binding site so that ATP is excluded from binding; specifically, the side chain of Arg47 occupies the ribose region of the ATP site and Tyr50, the space required by the triphospho moiety. We discuss some factors that may support or disfavor this inactive conformation, among them coordination of small molecules at a remote cavity at the CK2alpha/CK2beta interaction region and binding of a CK2beta dimer. The latter stabilizes the glycine-rich loop in the extended active conformation known from the majority of CK2alpha structures. Thus, the novel inactive conformation for the first time provides a structural basis for the stimulatory impact of CK2beta on CK2alpha.


    Related Citations: 
    • 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
    • The CK2 alpha/CK2 beta 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
    • 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
    • Crystal structure of the catalytic subunit of protein kinase CK2 from Zea mays at 2.1 A resolution
      Niefind, K.,Guerra, B.,Pinna, L.A.,Issinger, O.G.,Schomburg, D.
      (1998) Embo J. 17: 2451
    • Primary and secondary interactions between CK2alpha and CK2beta lead to ring-like structures in the crystals of the CK2 holoenzyme
      Niefind, K.,Issinger, O.G.
      (2005) Mol.Cell.Biochem. 274: 3
    • The catalytic subunit of human protein kinase CK2 structurally deviates from its maize homologue in complex with the nucleotide competitive inhibitor emodin
      Raaf, J.,Klopffleisch, K.,Issinger, O.G.,Niefind, K.
      (2008) J.Mol.Biol. 377: 1
    • 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
    • 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


    Organizational Affiliation

    Universität zu Köln, Institut für Biochemie, Zülpicher Str. 47, D-50674 Köln, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A, B
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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.170 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 71.324α = 90.00
b = 71.324β = 90.00
c = 125.681γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2012-04-04
    Type: Database references