3SV0

Crystal structure of casein kinase-1 like protein in plant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and functional studies of casein kinase I-like protein from rice

Park, Y.I.Do, K.H.Kim, I.S.Park, H.H.

(2012) Plant Cell Physiol 53: 304-311

  • DOI: https://doi.org/10.1093/pcp/pcr175
  • Primary Citation of Related Structures:  
    3SV0

  • PubMed Abstract: 

    Casein kinase I (CKI) is a protein serine/threonine kinase that is highly conserved from plants to animals. It performs various functions in both the cytoplasm and nucleus, such as DNA repair, cell cycle, cytokinesis, vesicular trafficking, morphogenesis and circadian rhythm. CKI proteins contain a highly conserved kinase domain responsible for catalytic activity at the N-terminus and a highly diverse regulatory domain responsible for determining substrate specificity at the C-terminus. CKI-like protein has been identified in plants, including in rice, but its function and structure have not been reported. Here, we report the 2.0 Å crystal structure of the kinase domain of CKI-like protein from rice. Although the structure adopts the typical bi-lobal kinase architecture, the length and orientation of the glycine-rich ATP-binding motif are dynamic within the CKI family. A loop between α5 and α6 (the α5-α6 loop), which was previously not detected in the CKI family because of flexibility, was clearly detected in our structure. In addition, we identified a lipase as a substrate of CKI-like protein from rice. Phosphorylation of the lipase dramatically reduced its catalytic activity, suggesting that CKI may play a role in the regulation of lipase activity.


  • Organizational Affiliation

    School of Life Science and Biotechnology at Kyungpook National University, Daegu, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase I-like483Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q8LR51 (Oryza sativa subsp. japonica)
Explore Q8LR51 
Go to UniProtKB:  Q8LR51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8LR51
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.828α = 90
b = 69.604β = 109.47
c = 55.849γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references