4CZU

Crystal structure of the kinase domain of CIPK23 T190D mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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This is version 1.3 of the entry. See complete history


Literature

Structural Basis of the Regulatory Mechanism of the Plant Cipk Family of Protein Kinases Controlling Ion Homeostasis and Abiotic Stress

Chaves-Sanjuan, A.Sanchez-Barrena, M.J.Gonzalez-Rubio, J.M.Moreno, M.Ragel, P.Jimenez, M.Pardo, J.M.Martinez-Ripoll, M.Quintero, F.J.Albert, A.

(2014) Proc Natl Acad Sci U S A 111: E4532

  • DOI: 10.1073/pnas.1407610111
  • Primary Citation of Related Structures:  
    4D28, 4CZT, 4CZU

  • PubMed Abstract: 
  • Plant cells have developed specific protective molecular machinery against environmental stresses. The family of CBL-interacting protein kinases (CIPK) and their interacting activators, the calcium sensors calcineurin B-like (CBLs), work together to decode calcium signals elicited by stress situations ...

    Plant cells have developed specific protective molecular machinery against environmental stresses. The family of CBL-interacting protein kinases (CIPK) and their interacting activators, the calcium sensors calcineurin B-like (CBLs), work together to decode calcium signals elicited by stress situations. The molecular basis of biological activation of CIPKs relies on the calcium-dependent interaction of a self-inhibitory NAF motif with a particular CBL, the phosphorylation of the activation loop by upstream kinases, and the subsequent phosphorylation of the CBL by the CIPK. We present the crystal structures of the NAF-truncated and pseudophosphorylated kinase domains of CIPK23 and CIPK24/SOS2. In addition, we provide biochemical data showing that although CIPK23 is intrinsically inactive and requires an external stimulation, CIPK24/SOS2 displays basal activity. This data correlates well with the observed conformation of the respective activation loops: Although the loop of CIPK23 is folded into a well-ordered structure that blocks the active site access to substrates, the loop of CIPK24/SOS2 protrudes out of the active site and allows catalysis. These structures together with biochemical and biophysical data show that CIPK kinase activity necessarily requires the coordinated releases of the activation loop from the active site and of the NAF motif from the nucleotide-binding site. Taken all together, we postulate the basis for a conserved calcium-dependent NAF-mediated regulation of CIPKs and a variable regulation by upstream kinases.


    Organizational Affiliation

    Departamento de Cristalografía y Biología Estructural, Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Madrid E-28006, Spain; and xalbert@iqfr.csic.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 23A, B, C, D464Arabidopsis thalianaMutation(s): 1 
Gene Names: CIPK23LKS1PKS17SnRK3.23At1g30270F12P21.6
EC: 2.7.11.1
UniProt
Find proteins for Q93VD3 (Arabidopsis thaliana)
Explore Q93VD3 
Go to UniProtKB:  Q93VD3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPS (Subject of Investigation/LOI)
Query on CPS

Download Ideal Coordinates CCD File 
E [auth A], J [auth B], K [auth B], P [auth C], Q [auth C], W [auth D], X [auth D]3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D] , BA [auth D] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , L [auth B] , M [auth B] , 
AA [auth D],  BA [auth D],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  L [auth B],  M [auth B],  N [auth B],  O [auth B],  R [auth C],  S [auth C],  T [auth C],  U [auth C],  V [auth C],  Y [auth D],  Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.7α = 90
b = 91.73β = 90
c = 207.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references
  • Version 1.2: 2017-12-06
    Changes: Structure summary
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation