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PDBsum entry 1a6o

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protein ligands metals links
Transferase PDB id
1a6o
Jmol
Contents
Protein chain
327 a.a.
Ligands
ATP
Metals
_MG
Waters ×148
Superseded by: 1lr4
PDB id:
1a6o
Name: Transferase
Title: Protein kinase ck2 (catalytic subunit) from zea mays
Structure: Protein kinase ck2/alpha-subunit. Chain: null. Engineered: yes
Source: Zea mays. Maize. Expressed in: escherichia coli.
Resolution:
2.10Å     R-factor:   0.209     R-free:   0.272
Authors: K.Niefind,B.Guerra,L.A.Pinna,O.-G.Issinger,D.Schomburg
Key ref:
K.Niefind et al. (1998). Crystal structure of the catalytic subunit of protein kinase CK2 from Zea mays at 2.1 A resolution. EMBO J, 17, 2451-2462. PubMed id: 9564028 DOI: 10.1093/emboj/17.9.2451
Date:
26-Feb-98     Release date:   17-Jun-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 327 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.37  - Transferred entry: 2.7.11.1, 2.7.11.8, 2.7.11.9, 2.7.11.10, 2.7.11.11,
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein

+ a
=
+ a
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1093/emboj/17.9.2451 EMBO J 17:2451-2462 (1998)
PubMed id: 9564028  
 
 
Crystal structure of the catalytic subunit of protein kinase CK2 from Zea mays at 2.1 A resolution.
K.Niefind, B.Guerra, L.A.Pinna, O.G.Issinger, D.Schomburg.
 
  ABSTRACT  
 
CK2alpha is the catalytic subunit of protein kinase CK2, an acidophilic and constitutively active eukaryotic Ser/Thr kinase involved in cell proliferation. A crystal structure, at 2.1 A resolution, of recombinant maize CK2alpha (rmCK2alpha) in the presence of ATP and Mg2+, shows the enzyme in an active conformation stabilized by interactions of the N-terminal region with the activation segment and with a cluster of basic residues known as the substrate recognition site. The close interaction between the N-terminal region and the activation segment is unique among known protein kinase structures and probably contributes to the constitutively active nature of CK2. The active centre is occupied by a partially disordered ATP molecule with the adenine base attached to a novel binding site of low specificity. This finding explains the observation that CK2, unlike other protein kinases, can use both ATP and GTP as phosphorylating agents.
 
  Selected figure(s)  
 
Figure 7.
Figure 7 Stereo illustration of the adenine moiety in the hydrophobic purine binding pocket surrounded by the non-polar side chains contributing to the hydrophobic character. The net marks the hydrophobic surface of the protein matrix including water, with the intensity of the blue colour as an indicator of hydrophobicity. This surface was calculated with BRAGI (Schomburg and Reichelt, 1988). For comparison, the adenine moiety of cAPK-bound ATP is drawn (green) after global 3D-fit of the cAPK/ATP complex on rmCK2 .
Figure 8.
Figure 8 Helix D region with ATP ribose anchor in cAPK (yellow), CDK2 (green), protein kinase CK1 (red) and rmCK2 (grey) after global 3D-fits of the structures.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1998, 17, 2451-2462) copyright 1998.  
  Figures were 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.  
20824888 M.J.Hernández-López, J.A.Prieto, and F.Randez-Gil (2010).
Isolation and characterization of the carbon catabolite-derepressing protein kinase Snf1 from the stress tolerant yeast Torulaspora delbrueckii.
  Yeast, 27, 1061-1069.  
20976471 M.Montenarh (2010).
Cellular regulators of protein kinase CK2.
  Cell Tissue Res, 342, 139-146.  
19703660 K.J.Thomas, and M.R.Cookson (2009).
The role of PTEN-induced kinase 1 in mitochondrial dysfunction and dynamics.
  Int J Biochem Cell Biol, 41, 2025-2035.  
19470094 M.Lebska, J.Szczegielniak, G.Dobrowolska, G.Cozza, S.Moro, and G.MuszyƄska (2009).
A novel splicing variant encoding putative catalytic alpha subunit of maize protein kinase CK2.
  Physiol Plant, 136, 251-263.  
19039653 P.P.Kuntamalla, E.Kunttas-Tatli, U.Karandikar, C.P.Bishop, and A.P.Bidwai (2009).
Drosophila protein kinase CK2 is rendered temperature-sensitive by mutations of highly conserved residues flanking the activation segment.
  Mol Cell Biochem, 323, 49-60.  
19326076 S.H.Yoon, d.o. .S.Min, and Y.S.Bae (2009).
Over-expression of phospholipase D isozymes down-regulates protein kinase CKII activity via proteasome-dependent CKIIbeta degradation in NIH3T3 cells.
  Mol Cells, 27, 299-305.  
  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
18221368 R.D.Mills, C.H.Sim, S.S.Mok, T.D.Mulhern, J.G.Culvenor, and H.C.Cheng (2008).
Biochemical aspects of the neuroprotective mechanism of PTEN-induced kinase-1 (PINK1).
  J Neurochem, 105, 18-33.  
16606343 B.B.Olsen, J.Petersen, and O.G.Issinger (2006).
BID, an interaction partner of protein kinase CK2alpha.
  Biol Chem, 387, 441-449.  
16204220 M.A.Shakir, J.S.Gill, and E.A.Lundquist (2006).
Interactions of UNC-34 Enabled with Rac GTPases and the NIK kinase MIG-15 in Caenorhabditis elegans axon pathfinding and neuronal migration.
  Genetics, 172, 893-913.  
15979847 S.Grewal, D.M.Molina, and L.Bardwell (2006).
Mitogen-activated protein kinase (MAPK)-docking sites in MAPK kinases function as tethers that are crucial for MAPK regulation in vivo.
  Cell Signal, 18, 123-134.  
16505477 Y.Liu, N.V.Belkina, C.Graham, and S.Shaw (2006).
Independence of protein kinase C-delta activity from activation loop phosphorylation: structural basis and altered functions in cells.
  J Biol Chem, 281, 12102-12111.  
16244704 E.D.Scheeff, and P.E.Bourne (2005).
Structural evolution of the protein kinase-like superfamily.
  PLoS Comput Biol, 1, e49.  
16335529 F.Llorens, S.Sarno, E.Sarró, A.Duarri, N.Roher, F.Meggio, M.Plana, L.A.Pinna, and E.Itarte (2005).
Cross talk between protein kinase CK2 and eukaryotic translation initiation factor eIF2beta subunit.
  Mol Cell Biochem, 274, 53-61.  
15525646 K.C.Qian, L.Wang, E.R.Hickey, J.Studts, K.Barringer, C.Peng, A.Kronkaitis, J.Li, A.White, S.Mische, and B.Farmer (2005).
Structural basis of constitutive activity and a unique nucleotide binding mode of human Pim-1 kinase.
  J Biol Chem, 280, 6130-6137.
PDB codes: 1xqz 1xr1
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.  
16335534 R.Allada, and R.A.Meissner (2005).
Casein kinase 2, circadian clocks, and the flight from mutagenic light.
  Mol Cell Biochem, 274, 141-149.  
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.  
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.  
15108354 E.Grasselli, V.Tomati, M.V.Bernasconi, C.Nicolini, and L.Vergani (2004).
C-terminal region of protein kinase CK2 alpha: How the structure can affect function and stability of the catalytic subunit.
  J Cell Biochem, 92, 270-284.  
15036861 E.Pechkova, and C.Nicolini (2004).
Protein nanocrystallography: a new approach to structural proteomics.
  Trends Biotechnol, 22, 117-122.  
15388915 L.Bertrand, M.F.Sayed, X.Y.Pei, E.Parisini, V.Dhanaraj, V.M.Bolanos-Garcia, J.E.Allende, and T.L.Blundell (2004).
Structure of the regulatory subunit of CK2 in the presence of a p21WAF1 peptide demonstrates flexibility of the acidic loop.
  Acta Crystallogr D Biol Crystallogr, 60, 1698-1704.
PDB code: 1rqf
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.  
12522135 A.P.Chopra, S.A.Boone, X.Liang, and N.S.Duesbery (2003).
Anthrax lethal factor proteolysis and inactivation of MAPK kinase.
  J Biol Chem, 278, 9402-9406.  
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
14646071 E.Pechkova, G.Zanotti, and C.Nicolini (2003).
Three-dimensional atomic structure of a catalytic subunit mutant of human protein kinase CK2.
  Acta Crystallogr D Biol Crystallogr, 59, 2133-2139.
PDB code: 1na7
12626119 G.Link (2003).
Redox regulation of chloroplast transcription.
  Antioxid Redox Signal, 5, 79-87.  
12634389 M.D.Koffa, J.Kean, G.Zachos, S.A.Rice, and J.B.Clements (2003).
CK2 protein kinase is stimulated and redistributed by functional herpes simplex virus ICP27 protein.
  J Virol, 77, 4315-4325.  
12748192 Y.S.Kim, J.Y.Lee, M.Y.Son, W.Park, and Y.S.Bae (2003).
Phosphorylation of threonine 10 on CKBBP1/SAG/ROC2/Rbx2 by protein kinase CKII promotes the degradation of IkappaBalpha and p27Kip1.
  J Biol Chem, 278, 28462-28469.  
11948680 E.Pechkova, and C.Nicolini (2002).
Protein nucleation and crystallization by homologous protein thin film template.
  J Cell Biochem, 85, 243-251.  
12447397 J.M.Lin, V.L.Kilman, K.Keegan, B.Paddock, M.Emery-Le, M.Rosbash, and R.Allada (2002).
A role for casein kinase 2alpha in the Drosophila circadian clock.
  Nature, 420, 816-820.  
12084075 K.Ogrzewalla, M.Piotrowski, S.Reinbothe, and G.Link (2002).
The plastid transcription kinase from mustard (Sinapis alba L.). A nuclear-encoded CK2-type chloroplast enzyme with redox-sensitive function.
  Eur J Biochem, 269, 3329-3337.  
12191603 R.A.Engh, and D.Bossemeyer (2002).
Structural aspects of protein kinase control-role of conformational flexibility.
  Pharmacol Ther, 93, 99.  
11956194 S.Sarno, P.Ghisellini, and L.A.Pinna (2002).
Unique activation mechanism of protein kinase CK2. The N-terminal segment is essential for constitutive activity of the catalytic subunit but not of the holoenzyme.
  J Biol Chem, 277, 22509-22514.  
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.  
11574463 K.Niefind, B.Guerra, I.Ermakowa, and O.G.Issinger (2001).
Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme.
  EMBO J, 20, 5320-5331.
PDB code: 1jwh
11260493 M.Riera, G.Peracchia, E.de Nadal, J.Ariño, and M.Pagès (2001).
Maize protein kinase CK2: regulation and functionality of three beta regulatory subunits.
  Plant J, 25, 365-374.  
11604527 R.Battistutta, E.De Moliner, S.Sarno, G.Zanotti, and L.A.Pinna (2001).
Structural features underlying selective inhibition of protein kinase CK2 by ATP site-directed tetrabromo-2-benzotriazole.
  Protein Sci, 10, 2200-2206.
PDB codes: 1j91 1jam
11092945 K.Niefind, B.Guerra, I.Ermakowa, and O.G.Issinger (2000).
Crystallization and preliminary characterization of crystals of human protein kinase CK2.
  Acta Crystallogr D Biol Crystallogr, 56, 1680-1684.  
10806407 M.Ruzzene, A.M.Brunati, S.Sarno, O.Marin, A.Donella-Deana, and L.A.Pinna (2000).
Ser/Thr phosphorylation of hematopoietic specific protein 1 (HS1): implication of protein kinase CK2.
  Eur J Biochem, 267, 3065-3072.  
10658642 P.R.Blanquet (2000).
Casein kinase 2 as a potentially important enzyme in the nervous system.
  Prog Neurobiol, 60, 211-246.  
10931203 R.Battistutta, S.Sarno, E.De Moliner, O.Marin, O.G.Issinger, G.Zanotti, and L.A.Pinna (2000).
The crystal structure of the complex of Zea mays alpha subunit with a fragment of human beta subunit provides the clue to the architecture of protein kinase CK2 holoenzyme.
  Eur J Biochem, 267, 5184-5190.
PDB code: 1ds5
11015211 S.Sarno, O.Marin, M.Boschetti, M.A.Pagano, F.Meggio, and L.A.Pinna (2000).
Cooperative modulation of protein kinase CK2 by separate domains of its regulatory beta-subunit.
  Biochemistry, 39, 12324-12329.  
11076027 T.L.Blundell, D.F.Burke, D.Chirgadze, V.Dhanaraj, M.Hyvönen, C.A.Innis, E.Parisini, L.Pellegrini, M.Sayed, and B.L.Sibanda (2000).
Protein-protein interactions in receptor activation and intracellular signalling.
  Biol Chem, 381, 955-959.  
10197447 B.Guerra, and O.G.Issinger (1999).
Protein kinase CK2 and its role in cellular proliferation, development and pathology.
  Electrophoresis, 20, 391-408.  
15012205 D.G.Hardie (1999).
PLANT PROTEIN SERINE/THREONINE KINASES: Classification and Functions.
  Annu Rev Plant Physiol Plant Mol Biol, 50, 97.  
10551866 D.Li, G.Dobrowolska, L.D.Aicher, M.Chen, J.H.Wright, P.Drueckes, E.L.Dunphy, E.S.Munar, and E.G.Krebs (1999).
Expression of the casein kinase 2 subunits in Chinese hamster ovary and 3T3 L1 cells provides information on the role of the enzyme in cell proliferation and the cell cycle.
  J Biol Chem, 274, 32988-32996.  
10446360 F.O'Farrell, M.Loog, I.M.Janson, and P.Ek (1999).
Kinetic study of the inhibition of CK2 by heparin fragments of different length.
  Biochim Biophys Acta, 1433, 68-75.  
10454194 J.M.Sowadski, L.F.Epstein, L.Lankiewicz, and R.Karlsson (1999).
Conformational diversity of catalytic cores of protein kinases.
  Pharmacol Ther, 82, 157-164.  
10357806 L.Chantalat, D.Leroy, O.Filhol, A.Nueda, M.J.Benitez, E.M.Chambaz, C.Cochet, and O.Dideberg (1999).
Crystal structure of the human protein kinase CK2 regulatory subunit reveals its zinc finger-mediated dimerization.
  EMBO J, 18, 2930-2940.
PDB code: 1qf8
10089327 L.Chantalat, D.Leroy, O.Filhol, N.Quitaine, E.M.Chambaz, C.Cochet, and O.Dideberg (1999).
Crystallization and preliminary x-ray diffraction analysis of the regulatory subunit of human protein kinase CK2.
  Acta Crystallogr D Biol Crystallogr, 55, 895-897.  
10506183 O.Marin, F.Meggio, S.Sarno, L.Cesaro, M.A.Pagano, and L.A.Pinna (1999).
Tyrosine versus serine/threonine phosphorylation by protein kinase casein kinase-2. A study with peptide substrates derived from immunophilin Fpr3.
  J Biol Chem, 274, 29260-29265.  
10404639 S.Siemer, D.Ornskov, B.Guerra, B.Boldyreff, and O.G.Issinger (1999).
Determination of mRNA, and protein levels of p53, MDM2 and protein kinase CK2 subunits in F9 cells after treatment with the apoptosis-inducing drugs cisplatin and carboplatin.
  Int J Biochem Cell Biol, 31, 661-670.  
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.