3OFM

Structure of a human CK2alpha prime, the paralog isoform of the catalytic subunit of protein kinase CK2 from Homo sapiens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of the reduced affinity between the protein kinase CK2 subunits CK2alpha prime and CK2beta

Bischoff, N.Olsen, B.Raaf, J.Bretner, M.Issinger, O.G.Niefind, K.

(2011) J.Mol.Biol. 407: 1-12

  • DOI: 10.1016/j.jmb.2011.01.020
  • Also Cited By: 3RP0, 3RPS, 3U87, 5OOI

  • PubMed Abstract: 
  • Protein kinase CK2 (formerly "casein kinase 2") is composed of a central dimer of noncatalytic subunits (CK2β) binding two catalytic subunits. In humans, there are two isoforms of the catalytic subunit (and an additional splicing variant), one of whi ...

    Protein kinase CK2 (formerly "casein kinase 2") is composed of a central dimer of noncatalytic subunits (CK2β) binding two catalytic subunits. In humans, there are two isoforms of the catalytic subunit (and an additional splicing variant), one of which (CK2α) is well characterized. To supplement the limited biochemical knowledge about the second paralog (CK2α'), we developed a well-soluble catalytically active full-length mutant of human CK2α', characterized it by Michaelis-Menten kinetics and isothermal titration calorimetry, and determined its crystal structure to a resolution of 2 Å. The affinity of CK2α' for CK2β is about 12 times lower than that of CK2α and is less driven by enthalpy. This result fits the observation that the β4/β5 loop, a key element of the CK2α/CK2β interface, adopts an open conformation in CK2α', while in CK2α, it opens only after assembly with CK2β. The open β4/β5 loop in CK2α' is stabilized by two elements that are absent in CK2α: (1) the extension of the N-terminal β-sheet by an additional β-strand, and (2) the filling of a conserved hydrophobic cavity between the β4/β5 loop and helix αC by a tryptophan residue. Moreover, the interdomain hinge region of CK2α' adopts a fully functional conformation, while unbound CK2α is often found with a nonproductive hinge conformation that is overcome only by CK2β binding. Taken together, CK2α' exhibits a significantly lower affinity for CK2β than CK2α; moreover, in functionally critical regions, it is less dependent on CK2β to obtain a fully functional conformation.


    Related Citations: 
    • 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
    • Protein kinase CK2: from structures to insights
      Niefind, K.,Raaf, J.,Issinger, O.-G.
      (2009) CELL.MOL.LIFE SCI. 66: 1800
    • 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, Zülpicher Straße 47, D-50674 Köln, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha'
A
350Homo sapiensGene Names: CSNK2A2 (CK2A2)
EC: 2.7.11.1
Find proteins for P19784 (Homo sapiens)
Go to Gene View: CSNK2A2
Go to UniProtKB:  P19784
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4B0
Query on 4B0

Download SDF File 
Download CCD File 
A
3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol
C9 H7 Br4 N3 O
VXLNELSTYPRMEW-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 46.690α = 112.40
b = 47.570β = 89.49
c = 50.570γ = 91.30
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
HKL-2000data collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-06-19
    Type: Database references