Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - K208N mutant

Experimental Data Snapshot

  • Resolution: 1.56 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 

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This is version 2.0 of the entry. See complete history


Thiosulfate Dehydrogenase (TsdA) from Allochromatium vinosum: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO THIOSULFATE OXIDATION.

Brito, J.A.Denkmann, K.Pereira, I.A.Archer, M.Dahl, C.

(2015) J Biol Chem 290: 9222-9238

  • DOI: https://doi.org/10.1074/jbc.M114.623397
  • Primary Citation of Related Structures:  
    4WQ7, 4WQ8, 4WQ9, 4WQA, 4WQB, 4WQC, 4WQD, 4WQE

  • PubMed Abstract: 

    Although the oxidative condensation of two thiosulfate anions to tetrathionate constitutes a well documented and significant part of the natural sulfur cycle, little is known about the enzymes catalyzing this reaction. In the purple sulfur bacterium Allochromatium vinosum, the reaction is catalyzed by the periplasmic diheme c-type cytochrome thiosulfate dehydrogenase (TsdA). Here, we report the crystal structure of the "as isolated" form of A. vinosum TsdA to 1.98 Å resolution and those of several redox states of the enzyme to different resolutions. The protein contains two typical class I c-type cytochrome domains wrapped around two hemes axially coordinated by His(53)/Cys(96) and His(164)/Lys(208). These domains are very similar, suggesting a gene duplication event during evolution. A ligand switch from Lys(208) to Met(209) is observed upon reduction of the enzyme. Cys(96) is an essential residue for catalysis, with the specific activity of the enzyme being completely abolished in several TsdA-Cys(96) variants. TsdA-K208N, K208G, and M209G variants were catalytically active in thiosulfate oxidation as well as in tetrathionate reduction, pointing to heme 2 as the electron exit point. In this study, we provide spectroscopic and structural evidence that the TsdA reaction cycle involves the transient presence of heme 1 in the high-spin state caused by movement of the Sγ atom of Cys(96) out of the iron coordination sphere. Based on the presented data, we draw important conclusions about the enzyme and propose a possible reaction mechanism for TsdA.

  • Organizational Affiliation

    From the Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Avenida da República, 2780-157 Oeiras, Portugal and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiosulfate dehydrogenase252Allochromatium vinosum DSM 180Mutation(s): 1 
Gene Names: tsdAAlvin_0091
Find proteins for D3RVD4 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D))
Explore D3RVD4 
Go to UniProtKB:  D3RVD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3RVD4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.56 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.054α = 90
b = 71.034β = 129.1
c = 57.811γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalPTDC/QUI-BIQ/100591/2008
Fundacao para a Ciencia e a TecnologiaPortugalPTDC/BIA-PRO/118535/2010
Fundacao para a Ciencia e a TecnologiaPortugalPEst-OE/EQB/LA0004/2011
German Academic Exchange ServiceGermany--
Conselho de Reitores das Universidades PortuguesasPortugal--
Fundacao para a Ciencia e a TecnologiaPortugalSFRH/BPD/79224/2011

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2015-04-15
    Changes: Database references
  • Version 2.0: 2024-05-08
    Changes: Atomic model, Data collection, Database references