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PDBsum entry 1lpu

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Transferase PDB id
1lpu
Jmol
Contents
Protein chain
327 a.a. *
Ligands
BEN
Waters ×331
* Residue conservation analysis
PDB id:
1lpu
Name: Transferase
Title: Low temperature crystal structure of the apo-form of the catalytic subunit of protein kinase ck2 from zea mays
Structure: Protein kinase ck2. Chain: a. Synonym: casein kinase ii, alpha chain. Engineered: yes
Source: Zea mays. Organism_taxid: 4577. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.86Å     R-factor:   0.206     R-free:   0.248
Authors: K.Niefind,M.Puetter,B.Guerra,O.-G.Issinger,D.Schomburg
Key ref:
C.W.Yde et al. (2005). Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate. J Mol Biol, 347, 399-414. PubMed id: 15740749 DOI: 10.1016/j.jmb.2005.01.003
Date:
08-May-02     Release date:   29-May-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P28523  (CSK2A_MAIZE) -  Casein kinase II subunit alpha
Seq:
Struc:
332 a.a.
327 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.11.1  - Non-specific serine/threonine protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
= ADP
+ 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     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2005.01.003 J Mol Biol 347:399-414 (2005)
PubMed id: 15740749  
 
 
Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate.
C.W.Yde, I.Ermakova, O.G.Issinger, K.Niefind.
 
  ABSTRACT  
 
Protein kinase CK2 (casein kinase 2) is a highly conserved and ubiquitously found eukaryotic serine/threonine kinase that plays a role in various cellular key processes like proliferation, apoptosis and circadian rhythm. One of its prominent biochemical properties is its ability to use GTP as well as ATP as a cosubstrate (dual-cosubstrate specificity). This feature is exceptional among eukaryotic protein kinases, and its biological significance is unknown. We describe here a mutant of the catalytic subunit of protein kinase CK2 (CK2alpha) from Homo sapiens (hsCK2alpha) with a clear and CK2-atypical preference for ATP compared to GTP. This mutant was designed on the basis of several structures of CK2alpha from Zea mays (zmCK2alpha) in complex with various ATP-competitive ligands. A structural overlay revealed the existence of a "purine base binding plane" harbouring the planar moiety of the respective ligand like the purine base of ATP and GTP. This purine base binding plane is sandwiched between the side-chains of Ile66 (Val66 in hsCK2alpha) and Met163, and it adopts a significantly different orientation than in prominent homologues like cAMP-dependent protein kinase (CAPK). By exchanging these two flanking amino acids (Val66Ala, Met163Leu) in hsCK2alpha(1-335), a C-terminally truncated variant of hsCK2alpha, the cosubstrate specificity shifted in the expected direction so that the mutant strongly favours ATP. A structure determination of the mutant in complex with an ATP-analogue confirmed the predicted change of the purine base binding plane orientation. An unexpected but in retrospect plausible consequence of the mutagenesis was, that the helix alpha D region, which is in the direct neighbourhood of the ATP-binding site, has adopted a conformation that is more similar to CAPK and less favourable for binding of GTP. These findings demonstrate that CK2alpha possesses sophisticated structural adaptations in favour of dual-cosubstrate specificity, suggesting that this property could be of biological significance.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo pictures of selected sections of zmCK2a. (a) The hypothetical benzamidine molecule (covered by blue s[a]-weighted 2F[o] -F[c] electron density; no. 2 in Table 2) within its protein environment (green electron density). The corresponding room temperature structure (no. 1 in Table 2) looks essentially identical (not shown). For comparision equivalent parts of the zmCK2a/AMPPNP complex (no. 3 in Table 2) are drawn in black. The hypothetical benzamidine molecule and the adenine group of the bound AMPPNP molecule are almost co-planar but do not overlap. Two alternative side-chain conformations of Met163 are found in structure 2 of Table 2 but only one of these is selected when AMPPNP is bound (black bonds; black electron density). For comparison two further side-chain conformations of Met163 are displayed as observed in apo-zmCK2a^21 (brown) and in a zmCK2a complex with 4,5,6,7-tetrabromo-2-benzotriazole21 (magenta colour). All pieces of electron density are drawn with a 1s contour level. Some hydrogen bonds are indicated with pink broken lines. (b) The divalent sulphur atom of Met163 (structure 3 of Table 2) attached simultaneously to two p-systems, namely the adenine group of AMPPNP and the terminal amide group of Asn118. The final electron density is drawn in green with a contour level of 1s.
Figure 4.
Figure 4. Structural characterisation of the mutant hsCK2a^1-335-V66A/M163L. (a) Stereo picture of the AMPPNP molecule (covered by blue s[a]-weighted 2F[o] -F[c] electron density contoured at 1s) and a part of its protein environment (green density). For comparision the equivalent sections of the zmCK2a/AMPPNP structure (structure no. 3 in Table 2) are drawn with black carbon atoms. (b) The adenine group of AMPPNP and its flanking side-chains in hsCK2a^1-335-V66A/M163L (covered by green electron density), in hsCK2a^1-335 (blue bonds), in zmCK2a (structure no. 3 of Table 2; black bonds) and in CAPK (magenta bonds). (c) Main chain atom RMS deviations after superimposition of the structures of hsCK2a^1-335 and hsCK2a^1-335-V66A/M163L. (d) Stereo picture to illustrate the structural variation in the helix aD region. While zmCK2a (black trace) and hsCK2a^1-335 (blue trace) deviate strongly from CAPK (magenta trace) in this region, hsCK2a^1-335-V66A/M163L (yellow trace) is much more similar to it. As a consequence the space at the entrance to the purine base binding plane is restricted and the binding of GMPPNP (and GTP) is hampered.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 347, 399-414) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19942586 D.Huang, T.Zhou, K.Lafleur, C.Nevado, and A.Caflisch (2010).
Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis.
  Bioinformatics, 26, 198-204.  
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.  
20162627 O.Doppelt-Azeroual, F.Delfaud, F.Moriaud, and A.G.de Brevern (2010).
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.
  Protein Sci, 19, 847-867.  
20091237 T.A.Binkowski, M.Cuff, B.Nocek, C.Chang, and A.Joachimiak (2010).
Assisted assignment of ligands corresponding to unknown electron density.
  J Struct Funct Genomics, 11, 21-30.  
19450520 A.Mehra, M.Shi, C.L.Baker, H.V.Colot, J.J.Loros, and J.C.Dunlap (2009).
A role for casein kinase 2 in the mechanism underlying circadian temperature compensation.
  Cell, 137, 749-760.  
  19920922 O.Doppelt-Azeroual, F.Moriaud, F.Delfaud, and A.G.de Brevern (2009).
Analysis of HSP90-related folds with MED-SuMo classification approach.
  Drug Des Devel Ther, 3, 59-72.  
19857459 S.L.Bostrom, J.Dore, and L.C.Griffith (2009).
CaMKII uses GTP as a phosphate donor for both substrate and autophosphorylation.
  Biochem Biophys Res Commun, 390, 1154-1159.  
19029291 Y.W.Tan, J.A.Hanson, and H.Yang (2009).
Direct Mg2+ Binding Activates Adenylate Kinase from Escherichia coli.
  J Biol Chem, 284, 3306-3313.  
18291315 J.Raaf, E.Brunstein, O.G.Issinger, and K.Niefind (2008).
The CK2 alpha/CK2 beta interface of human protein kinase CK2 harbors a binding pocket for small molecules.
  Chem Biol, 15, 111-117.
PDB codes: 2rkp 3bw5 3h30
18954462 T.A.Binkowski, and A.Joachimiak (2008).
Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites.
  BMC Struct Biol, 8, 45.  
17097160 B.C.Jensen, C.T.Kifer, D.L.Brekken, A.C.Randall, Q.Wang, B.L.Drees, and M.Parsons (2007).
Characterization of protein kinase CK2 from Trypanosoma brucei.
  Mol Biochem Parasitol, 151, 28-40.  
17912359 J.D.Knight, B.Qian, D.Baker, and R.Kothary (2007).
Conservation, variability and the modeling of active protein kinases.
  PLoS ONE, 2, e982.  
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
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 codes are shown on the right.