PDBsum entry 1jam

Go to PDB code: 
protein links
Transferase PDB id
Jmol PyMol
Protein chain
327 a.a. *
Waters ×97
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of apo-form of z. Mays ck2 protein kinase alpha subunit
Structure: Casein kinase ii, alpha chain. Chain: a. Synonym: ck ii, ck2-alpha. Engineered: yes
Source: Zea mays. Organism_taxid: 4577. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
2.18Å     R-factor:   0.217     R-free:   0.248
Authors: R.Battistutta,E.De Moliner,S.Sarno,G.Zanotti,L.A.Pinna
Key ref:
R.Battistutta et al. (2001). Structural features underlying selective inhibition of protein kinase CK2 by ATP site-directed tetrabromo-2-benzotriazole. Protein Sci, 10, 2200-2206. PubMed id: 11604527 DOI: 10.1110/ps.19601
31-May-01     Release date:   31-May-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P28523  (CSK2A_MAIZE) -  Casein kinase II subunit alpha
332 a.a.
327 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
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   2 terms 
  Biochemical function     nucleotide binding     6 terms  


DOI no: 10.1110/ps.19601 Protein Sci 10:2200-2206 (2001)
PubMed id: 11604527  
Structural features underlying selective inhibition of protein kinase CK2 by ATP site-directed tetrabromo-2-benzotriazole.
R.Battistutta, E.De Moliner, S.Sarno, G.Zanotti, L.A.Pinna.
Two novel crystal structures of Zea mays protein kinase CK2alpha catalytic subunit, one in complex with the specific inhibitor 4,5,6,7-tetrabromobenzotriazole (TBB) and another in the apo-form, were solved at 2.2 A resolution. These structures were compared with those of the enzyme in presence of ATP and GTP (the natural cosubstrates) and the inhibitor emodin. Interaction of TBB with the active site of CK2alpha is mainly due to van der Waals contacts, with the ligand fitting almost perfectly the cavity. One nitrogen of the five-membered ring interacts with two charged residues, Glu 81 and Lys 68, in the depth of the cavity, through two water molecules. These are buried in the active site and are also generally found in the structures of CK2alpha enzyme analyzed so far, with the exception of the complex with emodin. In the N-terminal lobe, the position of helix alphaC is particularly well preserved in all the structures examined; the Gly-rich loop is displaced from the intermediate position it has in the apo-form and in the presence of the natural cosubstrates (ATP/GTP) to either an upper (with TBB) or a lower position (with emodin). The selectivity of TBB for CK2 appears to be mainly dictated by the reduced size of the active site which in most other protein kinases is too large for making stable interactions with this inhibitor.
  Selected figure(s)  
Figure 3.
Fig. 3. (A) Two clipped views of the active site showing the inhibitor (as cpk model) fitting the cavity are shown. The molecular surface of the protein is represented as a white mesh. Bromine atoms are in red, carbon atoms in green, and nitrogen atoms in blue. (B) Position of TBB with respect to that of ATP (cyan) and emodin (green) in the catalytic site is shown from different points of view. Inhibitor rings lay practically in the same plane of the purine moiety of the natural cosubstrates (bottom).
  The above figure is reprinted by permission from the Protein Society: Protein Sci (2001, 10, 2200-2206) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19526464 G.Cozza, A.Bortolato, and S.Moro (2010).
How druggable is protein kinase CK2?
  Med Res Rev, 30, 419-462.  
19821123 N.Zhang, and R.Zhong (2010).
Structural basis for decreased affinity of Emodin binding to Val66-mutated human CK2 alpha as determined by molecular dynamics.
  J Mol Model, 16, 771-780.  
19460754 M.Nojiri, K.M.Loyet, V.A.Klenchin, G.Kabachinski, and T.F.Martin (2009).
CAPS Activity in Priming Vesicle Exocytosis Requires CK2 Phosphorylation.
  J Biol Chem, 284, 18707-18714.  
  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
18563535 R.Prudent, V.Moucadel, M.López-Ramos, S.Aci, B.Laudet, L.Mouawad, C.Barette, J.Einhorn, C.Einhorn, J.N.Denis, G.Bisson, F.Schmidt, S.Roy, L.Lafanechere, J.C.Florent, and C.Cochet (2008).
Expanding the chemical diversity of CK2 inhibitors.
  Mol Cell Biochem, 316, 71-85.  
18763715 Y.Suzuki, J.Cluzeau, T.Hara, A.Hirasawa, G.Tsujimoto, S.Oishi, H.Ohno, and N.Fujii (2008).
Structure-activity relationships of pyrazine-based CK2 inhibitors: synthesis and evaluation of 2,6-disubstituted pyrazines and 4,6-disubstituted pyrimidines.
  Arch Pharm (Weinheim), 341, 554-561.  
17019678 G.Srinivas, S.Babykutty, P.P.Sathiadevan, and P.Srinivas (2007).
Molecular mechanism of emodin action: transition from laxative ingredient to an antitumor agent.
  Med Res Rev, 27, 591-608.  
17133643 M.A.Pagano, G.Poletto, G.Di Maira, G.Cozza, M.Ruzzene, S.Sarno, J.Bain, M.Elliott, S.Moro, G.Zagotto, F.Meggio, and L.A.Pinna (2007).
Tetrabromocinnamic acid (TBCA) and related compounds represent a new class of specific protein kinase CK2 inhibitors.
  Chembiochem, 8, 129-139.  
17344282 M.T.Nogalski, J.P.Podduturi, I.B.DeMeritt, L.E.Milford, and A.D.Yurochko (2007).
The human cytomegalovirus virion possesses an activated casein kinase II that allows for the rapid phosphorylation of the inhibitor of NF-kappaB, IkappaBalpha.
  J Virol, 81, 5305-5314.  
17768728 R.Battistutta, M.Mazzorana, L.Cendron, A.Bortolato, S.Sarno, Z.Kazimierczuk, G.Zanotti, S.Moro, and L.A.Pinna (2007).
The ATP-binding site of protein kinase CK2 holds a positive electrostatic area and conserved water molecules.
  Chembiochem, 8, 1804-1809.
PDB codes: 2oxd 2oxx 2oxy
16971462 C.Y.Lin, S.Navarro, S.Reddy, and L.Comai (2006).
CK2-mediated stimulation of Pol I transcription by stabilization of UBF-SL1 interaction.
  Nucleic Acids Res, 34, 4752-4766.  
16298300 R.Battistutta, M.Mazzorana, S.Sarno, Z.Kazimierczuk, G.Zanotti, and L.A.Pinna (2005).
Inspecting the structure-activity relationship of protein kinase CK2 inhibitors derived from tetrabromo-benzimidazole.
  Chem Biol, 12, 1211-1219.
PDB codes: 1zoe 1zog 1zoh
16335530 S.Sarno, M.Ruzzene, P.Frascella, M.A.Pagano, F.Meggio, A.Zambon, M.Mazzorana, G.Di Maira, V.Lucchini, and L.A.Pinna (2005).
Development and exploitation of CK2 inhibitors.
  Mol Cell Biochem, 274, 69-76.  
15557471 A.V.Ljubimov, S.Caballero, A.M.Aoki, L.A.Pinna, M.B.Grant, and R.Castellon (2004).
Involvement of protein kinase CK2 in angiogenesis and retinal neovascularization.
  Invest Ophthalmol Vis Sci, 45, 4583-4591.  
15485924 E.I.Schwartz, R.V.Intine, and R.J.Maraia (2004).
CK2 is responsible for phosphorylation of human La protein serine-366 and can modulate rpL37 5'-terminal oligopyrimidine mRNA metabolism.
  Mol Cell Biol, 24, 9580-9591.  
15034935 E.Pechkova, and C.Nicolini (2004).
Atomic structure of a CK2alpha human kinase by microfocus diffraction of extra-small microcrystals grown with nanobiofilm template.
  J Cell Biochem, 91, 1010-1020.  
15066279 J.I.Loizou, S.F.El-Khamisy, A.Zlatanou, D.J.Moore, D.W.Chan, J.Qin, S.Sarno, F.Meggio, L.A.Pinna, and K.W.Caldecott (2004).
The protein kinase CK2 facilitates repair of chromosomal DNA single-strand breaks.
  Cell, 117, 17-28.  
12869192 E.De Moliner, N.R.Brown, and L.N.Johnson (2003).
Alternative binding modes of an inhibitor to two different kinases.
  Eur J Biochem, 270, 3174-3181.
PDB code: 1p5e
12694177 P.Borowski, J.Deinert, S.Schalinski, M.Bretner, K.Ginalski, T.Kulikowski, and D.Shugar (2003).
Halogenated benzimidazoles and benzotriazoles as inhibitors of the NTPase/helicase activities of hepatitis C and related viruses.
  Eur J Biochem, 270, 1645-1653.  
12191608 S.Sarno, S.Moro, F.Meggio, G.Zagotto, D.Dal Ben, P.Ghisellini, R.Battistutta, G.Zanotti, and L.A.Pinna (2002).
Toward the rational design of protein kinase casein kinase-2 inhibitors.
  Pharmacol Ther, 93, 159-168.  
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.