8P1Y | pdb_00008p1y

Arabidopsis thaliana mutated variant C244S of seryl-tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb8P1Y/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-05-13 Released: 2024-05-22 
• Deposition Author(s): Kekez, I., Soic, R., Rokov-Plavec, J., Matkovic-Calogovic, D.
• Funding Organization(s): Croatian Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.266 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.212 (DCC) 

Starting Model: experimental

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

• PubMed: 37804069 
• DOI: https://doi.org/10.1002/1873-3468.14748
• Primary Citation 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.

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Organizational Affiliation: 
• Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia.
Division of General and Inorganic Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia.
Central European Institute of Technology (CEITEC), Brno, Czech Republic.
National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.13 kDa 
• Atom Count: 3,338 
• Modeled Residue Count: 416 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine--tRNA ligase, cytoplasmic	A [auth AAA]	456	Arabidopsis thaliana	Mutation(s): 1  Gene Names: At5g27470, F21A20_180 EC: 6.1.1.11
UniProt
Find proteins for Q39230 (Arabidopsis thaliana) Explore Q39230  Go to UniProtKB:  Q39230

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.266 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.212 (DCC) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.385	α = 90
b = 46.154	β = 93.791
c = 107.605	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
AMoRE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Kekez, I., Soic, R., Rokov-Plavec, J., Matkovic-Calogovic, D.

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Funding Organization	Location	Grant Number
Croatian Science Foundation	Croatia	IP-2014-09-4274

Revision History  

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