PDBsum entry 2aao

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protein metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
147 a.a. *
140 a.a. *
_CA ×9
Waters ×153
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Regulatory apparatus of calcium dependent protein kinase fro arabidopsis thaliana
Structure: Calcium-dependent protein kinase, isoform ak1. Chain: a, b. Synonym: cdpk. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: ak1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
2.00Å     R-factor:   0.278     R-free:   0.254
Authors: V.Chandran,E.J.Stollar,K.Lindorff-Larsen,J.F.Harper,W.J.Chaz C.M.Dobson,B.F.Luisi,J.Christodoulou
Key ref:
V.Chandran et al. (2006). Structure of the regulatory apparatus of a calcium-dependent protein kinase (CDPK): a novel mode of calmodulin-target recognition. J Mol Biol, 357, 400-410. PubMed id: 16430916 DOI: 10.1016/j.jmb.2005.11.093
13-Jul-05     Release date:   27-Dec-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q06850  (CDPK1_ARATH) -  Calcium-dependent protein kinase 1
610 a.a.
147 a.a.
Protein chain
Pfam   ArchSchema ?
Q06850  (CDPK1_ARATH) -  Calcium-dependent protein kinase 1
610 a.a.
140 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains A, B: 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!
  Biochemical function     calcium ion binding     1 term  


DOI no: 10.1016/j.jmb.2005.11.093 J Mol Biol 357:400-410 (2006)
PubMed id: 16430916  
Structure of the regulatory apparatus of a calcium-dependent protein kinase (CDPK): a novel mode of calmodulin-target recognition.
V.Chandran, E.J.Stollar, K.Lindorff-Larsen, J.F.Harper, W.J.Chazin, C.M.Dobson, B.F.Luisi, J.Christodoulou.
Calcium-dependent protein kinases (CDPKs) are a class of calcium-binding sensory proteins that are found in plants and certain protozoa, including the causative agent of malaria, Plasmodium falciparum. CDPKs have diverse regulatory functions, including involvement in the triggering of the lytic cycle of malarial infection. CDPKs contain an autoinhibitory junction (J) region whose calcium-dependent interaction with the tethered regulatory calmodulin-like domain (CaM-LD) activates the catalytic kinase domain. We report here the X-ray crystal structure of the J-CaM-LD region of CDPK from Arabidopsis thaliana (AtCPK1), determined to 2.0 A resolution using multiple-wavelength anomalous dispersion (MAD). The structure reveals a symmetric dimer of calcium-bound J-CaM-LD with domain-swap interactions, in which the J region of one protomer interacts extensively with the carboxy-terminal EF-hand domain (C-lobe) of the partner protomer. However, as the J-CaM-LD is monomeric in solution, the activated monomer was modelled to account for the intra-molecular recognition of the two domains. While the J-CaM-LD segment mimics certain aspects of target motif recognition by CaM other features are specific to CDPKs, in particular the combination of the strong interaction between the N and C-lobes of the CaM-LD and the exclusive use of only the C-lobe in the recognition of the covalently tethered target region. Combined with our previous observations showing that there is likely to be strong interactions between this tethered J region and the CaM-LD even at basal Ca(2+) concentrations, the new structural data indicate that the response to calcium of CDPKs is clearly unique among the CaM family.
  Selected figure(s)  
Figure 1.
Figure 1. (a) Schematic of the domain structure of CDPK. The regulatory apparatus is comprised of the Junction region (J) and the calmodulin-like domain (CaM-LD). (b) Ribbon diagram of the crystal structure of the regulatory apparatus of CDPK showing the homodimeric organization observed. The two molecules are coloured in red and blue, respectively. The J region of each monomer depicted in a darker colour is observed interacting with the partner molecule in a domain swap interaction. The inset depicts these interactions schematically. (c) Overlay of the amino-terminal and carboxyl-terminal calcium-binding sub-domains of the CaM-LD (N-lobe and C-lobe, respectively). The root-mean-square deviation (RMSD) of C^α atoms for the overlay is 0.9 Å. The models are complete except for residues 428–432, 556–562, 588–591 from protomer A and residues 428–432, 551–566, 588–591 from protomer B.
Figure 3.
Figure 3. (a) Stereo view of the interaction of the J region with the C-lobe of the CaM-LD. The J region is shown in red and the C-lobe in blue. (b) A schematic summary of the key interactions of the helical J region with the CaM-LD (boxed). The J region interacts exclusively with the C-lobe.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 400-410) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287613 A.K.Wernimont, M.Amani, W.Qiu, J.C.Pizarro, J.D.Artz, Y.H.Lin, J.Lew, A.Hutchinson, and R.Hui (2011).
Structures of parasitic CDPK domains point to a common mechanism of activation.
  Proteins, 79, 803-820.
PDB codes: 3k21 3khe
20436473 A.K.Wernimont, J.D.Artz, P.Finerty, Y.H.Lin, M.Amani, A.Allali-Hassani, G.Senisterra, M.Vedadi, W.Tempel, F.Mackenzie, I.Chau, S.Lourido, L.D.Sibley, and R.Hui (2010).
Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium.
  Nat Struct Mol Biol, 17, 596-601.
PDB codes: 3hx4 3hzt 3igo 3ku2
20001960 T.A.DeFalco, K.W.Bender, and W.A.Snedden (2010).
Breaking the code: Ca2+ sensors in plant signalling.
  Biochem J, 425, 27-40.  
19307175 R.Ranjan, A.Ahmed, S.Gourinath, and P.Sharma (2009).
Dissection of Mechanisms Involved in the Regulation of Plasmodium falciparum Calcium-dependent Protein Kinase 4.
  J Biol Chem, 284, 15267-15276.  
18768477 J.L.Green, R.R.Rees-Channer, S.A.Howell, S.R.Martin, E.Knuepfer, H.M.Taylor, M.Grainger, and A.A.Holder (2008).
  J Biol Chem, 283, 30980-30989.  
16947054 E.W.Chehab, O.R.Patharkar, and J.C.Cushman (2007).
Isolation and characterization of a novel v-SNARE family protein that interacts with a calcium-dependent protein kinase from the common ice plant, Mesembryanthemum crystallinum.
  Planta, 225, 783-799.  
16957918 F.Capozzi, F.Casadei, and C.Luchinat (2006).
EF-hand protein dynamics and evolution of calcium signal transduction: an NMR view.
  J Biol Inorg Chem, 11, 949-962.  
16773372 O.R.Patharkar, and J.C.Cushman (2006).
A novel coiled-coil protein co-localizes and interacts with a calcium-dependent protein kinase in the common ice plant during low-humidity stress.
  Planta, 225, 57-73.  
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.