5D9V

Crystal structure of oxidized dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural understanding of the recycling of oxidized ascorbate by dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica

Do, H.Kim, I.S.Jeon, B.W.Lee, C.W.Park, A.K.Wi, A.R.Shin, S.C.Park, H.Kim, Y.S.Yoon, H.S.Kim, H.W.Lee, J.H.

(2016) Sci Rep 6: 19498-19498

  • DOI: https://doi.org/10.1038/srep19498
  • Primary Citation of Related Structures:  
    5D9T, 5D9V, 5D9W, 5D9X

  • PubMed Abstract: 

    Dehydroascorbate reductase (DHAR) is a key enzyme involved in the recycling of ascorbate, which catalyses the glutathione (GSH)-dependent reduction of oxidized ascorbate (dehydroascorbate, DHA). As a result, DHAR regenerates a pool of reduced ascorbate and detoxifies reactive oxygen species (ROS). In previous experiments involving transgenic rice, we observed that overexpression of DHAR enhanced grain yield and biomass. Since the structure of DHAR is not available, the enzymatic mechanism is not well-understood and remains poorly characterized. To elucidate the molecular basis of DHAR catalysis, we determined the crystal structures of DHAR from Oryza sativa L. japonica (OsDHAR) in the native, ascorbate-bound, and GSH-bound forms and refined their resolutions to 1.9, 1.7, and 1.7 Å, respectively. These complex structures provide the first information regarding the location of the ascorbate and GSH binding sites and their interacting residues. The location of the ascorbate-binding site overlaps with the GSH-binding site, suggesting a ping-pong kinetic mechanism for electron transfer at the common Cys20 active site. Our structural information and mutagenesis data provide useful insights into the reaction mechanism of OsDHAR against ROS-induced oxidative stress in rice.


  • Organizational Affiliation

    Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dehydroascorbate reductase230Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: P0496H07.8Os05g0116100OJ1654_B10.18
UniProt
Find proteins for Q65XA0 (Oryza sativa subsp. japonica)
Explore Q65XA0 
Go to UniProtKB:  Q65XA0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65XA0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.966α = 90
b = 47.905β = 107.24
c = 51.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Korea Polar Research InstituteKorea, Republic OfPE15070
Rural Development AdministrationKorea, Republic OfPJ011122

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release