8P1Z

Arabidopsis thaliana cytosolic seryl-tRNA synthetase in addition of dithiothreitol (DTT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.226 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Evolutionarily conserved cysteines in plant cytosolic seryl-tRNA synthetase are important for its resistance to oxidation.

Evic, V.Soic, R.Mocibob, M.Kekez, M.Houser, J.Wimmerova, M.Matkovic-Calogovic, D.Gruic-Sovulj, I.Kekez, I.Rokov-Plavec, J.

(2023) FEBS Lett 597: 2975-2992

  • DOI: https://doi.org/10.1002/1873-3468.14748
  • Primary Citation of Related Structures:  
    8P1Y, 8P1Z

  • PubMed Abstract: 

    We have previously identified a unique disulfide bond in the crystal structure of Arabidopsis cytosolic seryl-tRNA synthetase involving cysteines evolutionarily conserved in all green plants. Here, we discovered that both cysteines are important for protein stability, but with opposite effects, and that their microenvironment may promote disulfide bond formation in oxidizing conditions. The crystal structure of the C244S mutant exhibited higher rigidity and an extensive network of noncovalent interactions correlating with its higher thermal stability. The activity of the wild-type showed resistance to oxidation with H 2 O 2 , while the activities of cysteine-to-serine mutants were impaired, indicating that the disulfide link may enable the protein to function under oxidative stress conditions which can be beneficial for an efficient plant stress response.


  • Organizational Affiliation

    Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine--tRNA ligase, cytoplasmicA [auth AAA]456Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g27470F21A20_180
EC: 6.1.1.11
UniProt
Find proteins for Q39230 (Arabidopsis thaliana)
Explore Q39230 
Go to UniProtKB:  Q39230
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39230
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.226 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.41α = 90
b = 45.889β = 93.942
c = 107.068γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
AMoREphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Croatian Science FoundationCroatiaIP-2014-09-4274

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2024-12-04
    Changes: Database references