PDBsum entry 1pjk

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Transferase PDB id
Jmol PyMol
Protein chain
331 a.a. *
Waters ×98
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of a c-terminal deletion mutant of human p kinase ck2 catalytic subunit
Structure: Casein kinase ii, alpha chain. Chain: a. Fragment: residue 2-335. Synonym: ck ii. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: csnk2a1 or ck2a1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.50Å     R-factor:   0.188     R-free:   0.257
Authors: I.Ermakova,B.Boldyreff,O.-G.Issinger,K.Niefind
Key ref:
I.Ermakova et al. (2003). Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit. J Mol Biol, 330, 925-934. PubMed id: 12860116 DOI: 10.1016/S0022-2836(03)00638-7
03-Jun-03     Release date:   24-Jun-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P68400  (CSK21_HUMAN) -  Casein kinase II subunit alpha
391 a.a.
331 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Non-specific serine/threonine protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
+ protein
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein phosphorylation   1 term 
  Biochemical function     protein kinase activity     2 terms  


DOI no: 10.1016/S0022-2836(03)00638-7 J Mol Biol 330:925-934 (2003)
PubMed id: 12860116  
Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit.
I.Ermakova, B.Boldyreff, O.G.Issinger, K.Niefind.
Protein kinase CK2 (formerly called: casein kinase 2) is a heterotetrameric enzyme composed of two separate catalytic chains (CK2alpha) and a stable dimer of two non-catalytic subunits (CK2beta). CK2alpha is a highly conserved member of the superfamily of eukaryotic protein kinases. The crystal structure of a C-terminal deletion mutant of human CK2alpha was solved and refined to 2.5A resolution. In the crystal the CK2alpha mutant exists as a monomer in agreement with the organization of the subunits in the CK2 holoenzyme. The refined structure shows the helix alphaC and the activation segment, two main regions of conformational plasticity and regulatory importance in eukaryotic protein kinases, in active conformations stabilized by extensive contacts to the N-terminal segment. This arrangement is in accordance with the constitutive activity of the enzyme. By structural superimposition of human CK2alpha in isolated form and embedded in the human CK2 holoenzyme the loop connecting the strands beta4 and beta5 and the ATP-binding loop were identified as elements of structural variability. This structural comparison suggests that the ATP-binding loop may be the key region by which the non-catalytic CK2beta dimer modulates the activity of CK2alpha. The beta4/beta5 loop was found in a closed conformation in contrast to the open conformation observed for the CK2alpha subunits of the CK2 holoenzyme. CK2alpha monomers with this closed beta4/beta5 loop conformation are unable to bind CK2beta dimers in the common way for sterical reasons, suggesting a mechanism to protect CK2alpha from integration into CK2 holoenzyme complexes. This observation is consistent with the growing evidence that CK2alpha monomers and CK2beta dimers can exist in vivo independently from the CK2 holoenzyme and may possess physiological roles of their own.
  Selected figure(s)  
Figure 2.
Figure 2. Aspects of the rhCK2a^DC structure. (a) Folding of the monomer drawn in rainbow colors. A view was chosen that shows the attachment of the N-terminal segment to the activation segment and to helix aC. The equivalents of these regions and the b4/b5 loop as found in maize CK2a (PDB code 1LP4) are drawn in black. (b) Stereo picture of the cosubstrate-binding site. The AMPPNP molecule is covered with s[A]-weighted (F[o] -F[c]) OMIT density[30] colored in blue and drawn above a cutoff level of 2.7s above the average. The OMIT map was calculated with CNS [31] after a 2000 K simulated annealing run in which the AMPPNP molecule had been omitted. The surrounding protein is embedded in the final s[A]-weighted (2F[o] -F[c]) electron density (green color; cutoff level 1.4s above the average). ATP as bound to CAPK is drawn in black after superimposition of the protein matrices. (c) Stereo picture of the b4/b5 loop covered by s[A]-weighted (2F[o] -F[c]) electron density with a cutoff level of 1.0s above the average. For comparison, the equivalent region of rhCK2a^DC within the CK2 holoenzyme is drawn in black. Furthermore a part of the CK2b-dimer is shown in black to illustrate that the b4/b5-loop conformation in isolated rhCK2a^DC is not compatible with CK2b binding. All parts of the Figure were prepared with BOBSCRIPT[41] and RASTER3D. [42]
Figure 3.
Figure 3. Structures for comparison. (a) The CK2 holoenzyme (PDB file 1JWH). The complex is formed by a central CK2b dimer (blue and red) with a Zn2+-containing interface and by two rhCK2a^DC subunits composed of an N-terminal (green) and a C-terminal (yellow) domain, respectively. The activation segment and the helix aC are indicated by black color. (b) Active CDK2[35] (PDB code 1FIN) in complex with a cyclin A fragment (gray). The activation segment in active CDK2 is drawn in magenta. To illustrate the structural changes upon cyclin A-mediated activation the activation segment, the helix aC and the ATP-binding loop of inactive, cyclin-free CDK2 [34] (PDB code 1HCL) are added in blue color.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 330, 925-934) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19177021 I.S.Sandholt, B.B.Olsen, B.Guerra, and O.G.Issinger (2009).
Resorufin: a lead for a new protein kinase CK2 inhibitor.
  Anticancer Drugs, 20, 238-248.  
  19193990 T.Nakaniwa, T.Kinoshita, Y.Sekiguchi, T.Tada, I.Nakanishi, K.Kitaura, Y.Suzuki, H.Ohno, A.Hirasawa, and G.Tsujimoto (2009).
Structure of human protein kinase CK2 alpha 2 with a potent indazole-derivative inhibitor.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 75-79.
PDB code: 3e3b
18574672 B.B.Olsen, T.Rasmussen, K.Niefind, and O.G.Issinger (2008).
Biochemical characterization of CK2alpha and alpha' paralogues and their derived holoenzymes: evidence for the existence of a heterotrimeric CK2alpha'-holoenzyme forming trimeric complexes.
  Mol Cell Biochem, 316, 37-47.  
18824508 J.Raaf, E.Brunstein, O.G.Issinger, and K.Niefind (2008).
The interaction of CK2alpha and CK2beta, the subunits of protein kinase CK2, requires CK2beta in a preformed conformation and is enthalpically driven.
  Protein Sci, 17, 2180-2186.
PDB code: 3eed
16606343 B.B.Olsen, J.Petersen, and O.G.Issinger (2006).
BID, an interaction partner of protein kinase CK2alpha.
  Biol Chem, 387, 441-449.  
  15951851 A.C.Bibby, and D.W.Litchfield (2005).
The multiple personalities of the regulatory subunit of protein kinase CK2: CK2 dependent and CK2 independent roles reveal a secret identity for CK2beta.
  Int J Biol Sci, 1, 67-79.  
16335523 K.Niefind, and O.G.Issinger (2005).
Primary and secondary interactions between CK2alpha and CK2beta lead to ring-like structures in the crystals of the CK2 holoenzyme.
  Mol Cell Biochem, 274, 3.  
16335535 T.Rasmussen, I.H.Skjøth, H.H.Jensen, K.Niefind, B.Boldyreff, and O.G.Issinger (2005).
Biochemical characterization of the recombinant human Drosophila homologues Timekeeper and Andante involved in the Drosophila circadian oscillator.
  Mol Cell Biochem, 274, 151-161.  
15036861 E.Pechkova, and C.Nicolini (2004).
Protein nanocrystallography: a new approach to structural proteomics.
  Trends Biotechnol, 22, 117-122.  
15273306 N.Kannan, and A.F.Neuwald (2004).
Evolutionary constraints associated with functional specificity of the CMGC protein kinases MAPK, CDK, GSK, SRPK, DYRK, and CK2alpha.
  Protein Sci, 13, 2059-2077.  
15060571 O.Filhol, J.L.Martiel, and C.Cochet (2004).
Protein kinase CK2: a new view of an old molecular complex.
  EMBO Rep, 5, 351-355.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.