X-ray structure of protein kinase ck2 alpha subunit H148S mutant

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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Hydration Structures of the Human Protein Kinase CK2 alpha Clarified by Joint Neutron and X-ray Crystallography.

Shibazaki, C.Arai, S.Shimizu, R.Saeki, M.Kinoshita, T.Ostermann, A.Schrader, T.E.Kurosaki, Y.Sunami, T.Kuroki, R.Adachi, M.

(2018) J Mol Biol 430: 5094-5104

  • DOI: https://doi.org/10.1016/j.jmb.2018.09.018
  • Primary Citation of Related Structures:  
    5ZN0, 5ZN1, 5ZN2, 5ZN3, 5ZN4, 5ZN5

  • PubMed Abstract: 

    Casein kinase 2 (CK2) has broad phosphorylation activity against various regulatory proteins, which are important survival factors in eukaryotic cells. To clarify the hydration structure and catalytic mechanism of CK2, we determined the crystal structure of the alpha subunit of human CK2 containing hydrogen and deuterium atoms using joint neutron (1.9 Å resolution) and X-ray (1.1 Å resolution) crystallography. The analysis revealed the structure of conserved water molecules at the active site and a long potential hydrogen bonding network originating from the catalytic Asp156 that is well known to enhance the nucleophilicity of the substrate OH group to the γ-phospho group of ATP by proton elimination. His148 and Asp214 conserved in the protein kinase family are located in the middle of the network. The water molecule forming a hydrogen bond with Asp214 appears to be deformed. In addition, mutational analysis of His148 in CK2 showed significant reductions by 40%-75% in the catalytic efficiency with similar affinity for ATP. Likewise, remarkable reductions to less than 5% were shown by corresponding mutations on His131 in death-associated protein kinase 1, which belongs to a group different from that of CK2. These findings shed new light on the catalytic mechanism of protein kinases in which the hydrogen bond network through the C-terminal domain may assist the general base catalyst to extract a proton with a link to the bulk solvent via intermediates of a pair of residues.

  • Organizational Affiliation

    National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha329Homo sapiensMutation(s): 3 
Gene Names: CSNK2A1CK2A1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens)
Explore P68400 
Go to UniProtKB:  P68400
PHAROS:  P68400
GTEx:  ENSG00000101266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68400
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.59α = 90
b = 45.371β = 111.92
c = 63.415γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanJP16KT0063

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references