5YRY | pdb_00005yry

Crystal structure of C-terminal redox domain of APR1 from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb5YRY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-11 Released: 2018-11-14 
• Deposition Author(s): Hsu, C.H.
• Funding Organization(s): National Science Council (Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.250 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

C-terminal Redox Domain ofArabidopsisAPR1 is a Non-Canonical Thioredoxin Domain with Glutaredoxin Function.

Chen, F.F., Chien, C.Y., Cho, C.C., Chang, Y.Y., Hsu, C.H.

(2019) Antioxidants (Basel) 8

• PubMed: 31597378 
• DOI: https://doi.org/10.3390/antiox8100461
• Primary Citation Related Structures: 
  5YRY


• PubMed Abstract: 
  

  Sulfur is an essential nutrient that can be converted into utilizable metabolic forms to produce sulfur-containing metabolites in plant. Adenosine 5'-phosphosulfate (APS) reductase (APR) plays a vital role in catalyzing the reduction of activated sulfate to sulfite, which requires glutathione. Previous studies have shown that the C-terminal domain of APR acts as a glutathione-dependent reductase. The crystal structure of the C-terminal redox domain of Arabidopsis APR1 (AtAPR1) shows a conserved α/β thioredoxin fold, but not a glutaredoxin fold. Further biochemical studies of the redox domain from AtAPR1 provided evidence to support the structural observation. Collectively, our results provide structural and biochemical information to explain how the thioredoxin fold exerts the glutaredoxin function in APR.

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Organizational Affiliation: 
• Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan. [e-mail].
Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan. [e-mail].
Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.
Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan.
Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan. [e-mail].
Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 14.13 kDa 
• Atom Count: 935 
• Modeled Residue Count: 116 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-adenylylsulfate reductase 1, chloroplastic	A	123	Arabidopsis thaliana	Mutation(s): 0  Gene Names: APR1, PRH19, At4g04610, F4H6.13 EC: 1.8.4.9
UniProt
Find proteins for P92979 (Arabidopsis thaliana) Explore P92979  Go to UniProtKB:  P92979

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.250 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.2	α = 90
b = 58.2	β = 90
c = 86.687	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-14 
Deposition Author(s): Hsu, C.H.

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Funding Organization	Location	Grant Number
National Science Council (Taiwan)	Taiwan	NSC102-2113-M-002-005

Revision History  

• Version 1.0: 2018-11-14
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references