1LPU

Low Temperature Crystal Structure of the Apo-form of the catalytic subunit of protein kinase CK2 from Zea mays


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 399-414

  • DOI: 10.1016/j.jmb.2005.01.003
  • Primary Citation of Related Structures:  1LP4, 1LR4, 1YMI, 3JUH
  • Also Cited By: 3BW5, 3FWQ, 3U87, 3U9C

  • PubMed Abstract: 
  • Protein kinase CK2 (casein kinase 2) is a highly conserved and ubiquitously found eukaryotic serine/threonine kinase that plays a role in various cellular key processes like proliferation, apoptosis and circadian rhythm. One of its prominent biochemi ...

    Protein kinase CK2 (casein kinase 2) is a highly conserved and ubiquitously found eukaryotic serine/threonine kinase that plays a role in various cellular key processes like proliferation, apoptosis and circadian rhythm. One of its prominent biochemical properties is its ability to use GTP as well as ATP as a cosubstrate (dual-cosubstrate specificity). This feature is exceptional among eukaryotic protein kinases, and its biological significance is unknown. We describe here a mutant of the catalytic subunit of protein kinase CK2 (CK2alpha) from Homo sapiens (hsCK2alpha) with a clear and CK2-atypical preference for ATP compared to GTP. This mutant was designed on the basis of several structures of CK2alpha from Zea mays (zmCK2alpha) in complex with various ATP-competitive ligands. A structural overlay revealed the existence of a "purine base binding plane" harbouring the planar moiety of the respective ligand like the purine base of ATP and GTP. This purine base binding plane is sandwiched between the side-chains of Ile66 (Val66 in hsCK2alpha) and Met163, and it adopts a significantly different orientation than in prominent homologues like cAMP-dependent protein kinase (CAPK). By exchanging these two flanking amino acids (Val66Ala, Met163Leu) in hsCK2alpha(1-335), a C-terminally truncated variant of hsCK2alpha, the cosubstrate specificity shifted in the expected direction so that the mutant strongly favours ATP. A structure determination of the mutant in complex with an ATP-analogue confirmed the predicted change of the purine base binding plane orientation. An unexpected but in retrospect plausible consequence of the mutagenesis was, that the helix alpha D region, which is in the direct neighbourhood of the ATP-binding site, has adopted a conformation that is more similar to CAPK and less favourable for binding of GTP. These findings demonstrate that CK2alpha possesses sophisticated structural adaptations in favour of dual-cosubstrate specificity, suggesting that this property could be of biological significance.


    Related Citations: 
    • 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
    • Expression and characterization of a recombinant maize CK-2 alpha subunit
      Boldyreff, B.,Meggio, F.,Dobrowolska, G.,Pinna, L.A.,Issinger, O.-G.
      (1993) BIOCHIM.BIOPHYS.ACTA 1173: 32
    • Crystallization and preliminary characterization of crystals of human protein kinase CK2
      Niefind, K.,Guerra, B.,Ermakowa, I.,Issinger, O.-G.
      (2000) Acta Crystallogr.,Sect.D 56: 1680
    • Expression, purification and crystallization of the catalytic subunit of protein kinase CK2 from Zea mays
      Guerra, B.,Niefind, K.,Pinna, L.A.,Schomburg, D.,Issinger, O.-G.
      (1998) Acta Crystallogr.,Sect.D 54: 143
    • Cloning and sequencing of the casein kinase 2 alpha subunit from Zea mays
      Dobrowolska, G.,Boldyreff, B.,Issinger, O.-G.
      (1991) BIOCHIM.BIOPHYS.ACTA 1129: 139
    • 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
    • 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


    Organizational Affiliation

    Syddansk Universitet, Institut for Biokemi og Molekylaerbiologi, Campusvej 55, DK-5230 Odense, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein kinase CK2
A
332Zea maysGene Names: ACK2
EC: 2.7.11.1
Find proteins for P28523 (Zea mays)
Go to UniProtKB:  P28523
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEN
Query on BEN

Download SDF File 
Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.190α = 90.00
b = 59.758β = 103.41
c = 45.082γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-29
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance