6G62 | pdb_00006g62

Crystal structure of thioredoxin O2 from Arabidopsis thaliana in oxidized state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.179 (Depositor), 0.182 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6G62

This is version 1.1 of the entry. See complete history

Literature

MitochondrialArabidopsis thalianaTRXo Isoforms Bind an Iron−Sulfur Cluster and Reduce NFU Proteins In Vitro.

Zannini, F.Roret, T.Przybyla-Toscano, J.Dhalleine, T.Rouhier, N.Couturier, J.

(2018) Antioxidants (Basel) 7

  • DOI: https://doi.org/10.3390/antiox7100142
  • Primary Citation Related Structures: 
    6G61, 6G62

  • PubMed Abstract: 

    In plants, the mitochondrial thioredoxin (TRX) system generally comprises only one or two isoforms belonging to the TRX h or o classes, being less well developed compared to the numerous isoforms found in chloroplasts. Unlike most other plant species, Arabidopsis thaliana possesses two TRXo isoforms whose physiological functions remain unclear. Here, we performed a structure⁻function analysis to unravel the respective properties of the duplicated TRXo1 and TRXo2 isoforms. Surprisingly, when expressed in Escherichia coli , both recombinant proteins existed in an apo-monomeric form and in a homodimeric iron⁻sulfur (Fe-S) cluster-bridged form. In TRXo2, the [4Fe-4S] cluster is likely ligated in by the usual catalytic cysteines present in the conserved Trp-Cys-Gly-Pro-Cys signature. Solving the three-dimensional structure of both TRXo apo-forms pointed to marked differences in the surface charge distribution, notably in some area usually participating to protein⁻protein interactions with partners. However, we could not detect a difference in their capacity to reduce nitrogen-fixation-subunit-U (NFU)-like proteins, NFU4 or NFU5, two proteins participating in the maturation of certain mitochondrial Fe-S proteins and previously isolated as putative TRXo1 partners. Altogether, these results suggest that a novel regulation mechanism may prevail for mitochondrial TRXs o, possibly existing as a redox-inactive Fe-S cluster-bound form that could be rapidly converted in a redox-active form upon cluster degradation in specific physiological conditions.


  • Organizational Affiliation
    • Université de Lorraine, Inra, IAM, F-54000 Nancy, France. flavien.zannini@univ-lorraine.fr.

Macromolecule Content 

  • Total Structure Weight: 14.52 kDa 
  • Atom Count: 976 
  • Modeled Residue Count: 115 
  • Deposited Residue Count: 133 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thioredoxin O2, mitochondrial133Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g31020F17F8.6
UniProt
Find proteins for Q93VQ9 (Arabidopsis thaliana)
Explore Q93VQ9 
Go to UniProtKB:  Q93VQ9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93VQ9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.179 (Depositor), 0.182 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.806α = 90
b = 70.806β = 90
c = 35.755γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
ARP/wARPmodel building
Cootmodel building
MolProbitymodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary