5YRY

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.250
R-Value Work: 0.179
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.3390/antiox8100461
Primary Citation of 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.

Organizational Affiliation

Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan. fun_0108@hotmail.com.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P92979
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.250
R-Value Work: 0.179
R-Value Observed: 0.186
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-11-14

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.