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PDBsum entry 1s6i

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protein metals links
Transferase, plant protein PDB id
1s6i
Jmol
Contents
Protein chain
182 a.a. *
Metals
_CA ×4
* Residue conservation analysis
PDB id:
1s6i
Name: Transferase, plant protein
Title: Ca2+-regulatory region (cld) from soybean calcium-dependent protein kinase-alpha (cdpk) in the presence of ca2+ and the junction domain (jd)
Structure: Calcium-dependent protein kinase sk5. Chain: a. Fragment: calmodulin-like domain (cld) and c-terminal tail. Synonym: cdpk. Calcium-dependent protein kinase-alpha. Engineered: yes
Source: Glycine max. Soybean. Organism_taxid: 3847. Gene: cdpk sk5. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: ca2+-binding region and c-terminal tail, along with his(6) at c-terminus
NMR struc: 15 models
Authors: A.M.Weljie,H.J.Vogel
Key ref:
A.M.Weljie and H.J.Vogel (2004). Unexpected structure of the Ca2+-regulatory region from soybean calcium-dependent protein kinase-alpha. J Biol Chem, 279, 35494-35502. PubMed id: 15155727 DOI: 10.1074/jbc.M311520200
Date:
23-Jan-04     Release date:   15-Jun-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P28583  (CDPK_SOYBN) -  Calcium-dependent protein kinase SK5
Seq:
Struc:
508 a.a.
182 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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!
  Biochemical function     calcium ion binding     1 term  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M311520200 J Biol Chem 279:35494-35502 (2004)
PubMed id: 15155727  
 
 
Unexpected structure of the Ca2+-regulatory region from soybean calcium-dependent protein kinase-alpha.
A.M.Weljie, H.J.Vogel.
 
  ABSTRACT  
 
Calcium-dependent protein kinases (CDPKs) are an extensive class of multidomain Ca(2+)-regulated enzymes from plants and protozoa. In vivo the so-called calmodulin-like domain (CLD) of CDPK binds intramolecularly to the junction domain (JD), which exhibits both kinase-inhibitory and CLD binding properties. Here we report the high resolution solution structure of the calcium-regulatory region from soybean CDPK-alpha determined in the presence of a peptide encompassing the JD. The structure of both lobes of CLD resembles that of related helix-loop-helix Ca(2+)-binding proteins. NMR chemical shift mapping studies demonstrate that the JD induces significant structural changes in isolated Ca(2+)-CLD, particularly the C-terminal domain, although a stable complex is not formed. A CLD solution structure calculated on the basis of NMR data and long range fluorescence resonance energy transfer distances reveals an activated state with both lobes positioned side by side, similar to calcineurin B rather than calmodulin, highlighting the possible pitfall of assigning function purely from sequence information.
 
  Selected figure(s)  
 
Figure 5.
FIG. 5. Comparison of the activated forms of calmodulin (Protein Data Bank code 1CDM [PDB] , CaM·CaMKII peptide complex), calcineurin B (Protein Data Bank code 1TCO [PDB] ), and the Ca^2+-saturated JD-CLD molecule from this study with the two domains positioned in a manner consistent with FRET-derived distance restraints. The N-terminal domains are shown in red along the y axis.
Figure 6.
FIG. 6. Schematic diagram of JD-CLD interaction. Structural evidence suggests that in the absence of JD peptide there are multiple conformations of the C-terminal lobe, while NMR diffusion and FRET-derived long range data show that the protein is collapsed although not necessarily into a single stable conformation. In this situation, the tether region also has significant flexibility as depicted by the dashed lines. Subsequently the C-terminal lobe of the CLD interacts most significantly on addition of JD peptide to Ca^2+-CLD as the evidence from the current study indicates. The N-terminal lobe likely acts as a scaffold that allows the tether region to position the JD. In the current study where a bimolecular system was used, the tether retains its flexibility, although presumably in the intact protein it would remain less mobile since it is directly attached to the JD. It is not clear to what extent the tether region, linker region, and flexible regions of the C-terminal lobe of the CLD act in concert on binding the JD.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 35494-35502) copyright 2004.  
  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
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.  
19546223 F.Schumann, H.Hoffmeister, R.Bader, M.Schmidt, R.Witzgall, and H.R.Kalbitzer (2009).
Ca2+-dependent conformational changes in a C-terminal cytosolic domain of polycystin-2.
  J Biol Chem, 284, 24372-24383.  
16758442 A.D.Hegeman, M.Rodriguez, B.W.Han, Y.Uno, G.N.Phillips, E.M.Hrabak, J.C.Cushman, J.F.Harper, A.C.Harmon, and M.R.Sussman (2006).
A phyloproteomic characterization of in vitro autophosphorylation in calcium-dependent protein kinases.
  Proteomics, 6, 3649-3664.  
16765896 E.Babini, I.Bertini, F.Capozzi, E.Chirivino, and C.Luchinat (2006).
A structural and dynamic characterization of the EF-hand protein CLSP.
  Structure, 14, 1029-1038.
PDB code: 2b1u
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.  
16885238 J.M.Yang, and C.H.Tung (2006).
Protein structure database search and evolutionary classification.
  Nucleic Acids Res, 34, 3646-3659.  
16072038 J.F.Harper, and A.Harmon (2005).
Plants, symbiosis and parasites: a calcium signalling connection.
  Nat Rev Mol Cell Biol, 6, 555-566.  
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.