3DML | pdb_00003dml

Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus (reduced form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.201 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The structure of the periplasmic thiol-disulfide oxidoreductase SoxS from Paracoccus pantotrophus indicates a triple Trx/Grx/DsbC functionality in chemotrophic sulfur oxidation.

Carius, Y.Rother, D.Friedrich, C.G.Scheidig, A.J.

(2009) Acta Crystallogr D Biol Crystallogr 65: 229-240

  • DOI: https://doi.org/10.1107/S0907444908043023
  • Primary Citation of Related Structures:  
    3D4T, 3DML

  • PubMed Abstract: 

    The periplasmic thiol-disulfide oxidoreductase SoxS is beneficial for the sulfur-oxidizing (Sox) phenotype of the facultative chemotrophic bacterium Paracoccus pantotrophus and is not part of the Sox enzyme system. SoxS combines features of thioredoxins, glutaredoxins and the thiol-disulfide oxidoreductases of the Dsb family in structure, target specificity and reaction. The structure of SoxS was solved in oxidized and reduced forms at 2.1 and 1.9 A resolution, respectively. SoxS revealed high structural homology to typical cytoplasmic bacterial thioredoxins. In contrast, SoxS contained the active-site motif Pro-Gly-Cys-Leu-Tyr-Cys that is not present in other thioredoxins. Interestingly, the sequence of this motif is closely related to the Pro-Gly-Cys-Pro-Tyr-Cys sequence of some glutaredoxins and to the Pro-Xaa-Cys-Xaa-Tyr-Cys sequences of some members of the DsbC and DsbG subfamilies of thiol-disulfide oxidoreductases. Furthermore, the proposed substrate of SoxS, the interprotein disulfide of SoxY, Cys110(Y)-Cys110(Y), is structurally similar to oxidized glutathione. However, SoxS is proposed to specifically reduce the interprotein disulfide between two SoxY subunits, releasing a heterodimeric SoxYZ as an active part of the sulfur-oxidation cycle.


  • Organizational Affiliation
    • Abteilung für Strukturbiologie, Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein116Paracoccus denitrificansMutation(s): 0 
Gene Names: soxS
EC: 1.8.4
UniProt
Find proteins for Q8KM22 (Paracoccus denitrificans)
Explore Q8KM22 
Go to UniProtKB:  Q8KM22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KM22
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.201 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.909α = 90
b = 80.909β = 90
c = 33.212γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2025-08-06
    Changes: Database references