1S6I | pdb_00001s6i

Ca2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence of Ca2+ and the junction domain (JD)

• PDB DOI: https://doi.org/10.2210/pdb1S6I/pdb
• BMRB: 6104

• Classification: TRANSFERASE, PLANT PROTEIN
• Organism(s): Glycine max
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-01-23 Released: 2004-06-15 
• Deposition Author(s): Weljie, A.M., Vogel, H.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 15 
• Selection Criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations 

Literature

Unexpected structure of the Ca2+-regulatory region from soybean calcium-dependent protein kinase-alpha

Weljie, A.M., Vogel, H.J.

(2004) J Biological Chem 279: 35494-35502

• PubMed: 15155727 
• DOI: https://doi.org/10.1074/jbc.M311520200
• Primary Citation Related Structures: 
  1S6I


• PubMed 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.

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Organizational Affiliation: 
• Structural Biology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. N. W., Calgary, Alberta T2N 1N4, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.42 kDa 
• Atom Count: 1,432 
• Modeled Residue Count: 182 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-dependent protein kinase SK5	A	188	Glycine max	Mutation(s): 0  Gene Names: CDPK SK5 EC: 2.7.1 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt
Find proteins for P28583 (Glycine max) Explore P28583  Go to UniProtKB:  P28583

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 15 
• Selection Criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-15 
Deposition Author(s): Weljie, A.M., Vogel, H.J.

Revision History  

• Version 1.0: 2004-06-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection