4WQD

Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - K208G mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

  • 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 ...

    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.


    Related Citations: 
    • Production, crystallization and preliminary crystallographic analysis of Allochromatium vinosum thiosulfate dehydrogenase TsdA, an unusual acidophilic c-type cytochrome.
      Brito, J.A., Gutierres, A., Denkmann, K., Dahl, C., Archer, M.
      (2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 1424

    Organizational Affiliation

    the Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany ChDahl@uni-bonn.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thiosulfate dehydrogenaseA252Allochromatium vinosum DSM 180Mutation(s): 1 
Gene Names: tsdAAlvin_0091
EC: 1.8.2.2
Find proteins for D3RVD4 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D))
Explore D3RVD4 
Go to UniProtKB:  D3RVD4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
IOD
Query on IOD

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A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
GAI
Query on GAI

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A
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS
AL-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.093α = 90
b = 70.811β = 128.99
c = 57.873γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report



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--
BioStruct-X1493
Fundacao para a Ciencia e a TecnologiaPortugalSFRH/BPD/79224/2011

Revision History 

  • 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