5LO9

Thiosulfate dehydrogenase (TsdBA) from Marichromatium purpuratum - "as isolated" form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Electron Accepting Units of the Diheme Cytochrome c TsdA, a Bifunctional Thiosulfate Dehydrogenase/Tetrathionate Reductase.

Kurth, J.M.Brito, J.A.Reuter, J.Flegler, A.Koch, T.Franke, T.Klein, E.M.Rowe, S.F.Butt, J.N.Denkmann, K.Pereira, I.A.Archer, M.Dahl, C.

(2016) J Biol Chem 291: 24804-24818

  • DOI: 10.1074/jbc.M116.753863
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The enzymes of the thiosulfate dehydrogenase (TsdA) family are wide-spread diheme c-type cytochromes. Here, redox carriers were studied mediating the flow of electrons arising from thiosulfate oxidation into respiratory or photosynthetic electron cha ...

    The enzymes of the thiosulfate dehydrogenase (TsdA) family are wide-spread diheme c-type cytochromes. Here, redox carriers were studied mediating the flow of electrons arising from thiosulfate oxidation into respiratory or photosynthetic electron chains. In a number of organisms, including Thiomonas intermedia and Sideroxydans lithotrophicus, the tsdA gene is immediately preceded by tsdB encoding for another diheme cytochrome. Spectrophotometric experiments in combination with enzymatic assays in solution showed that TsdB acts as an effective electron acceptor of TsdA in vitro when TsdA and TsdB originate from the same source organism. Although TsdA covers a range from -300 to +150 mV, TsdB is redox active between -100 and +300 mV, thus enabling electron transfer between these hemoproteins. The three-dimensional structure of the TsdB-TsdA fusion protein from the purple sulfur bacterium Marichromatium purpuratum was solved by X-ray crystallography to 2.75 Å resolution providing insights into internal electron transfer. In the oxidized state, this tetraheme cytochrome c contains three hemes with axial His/Met ligation, whereas heme 3 exhibits the His/Cys coordination typical for TsdA active sites. Interestingly, thiosulfate is covalently bound to Cys 330 on heme 3. In several bacteria, including Allochromatium vinosum, TsdB is not present, precluding a general and essential role for electron flow. Both AvTsdA and the MpTsdBA fusion react efficiently in vitro with high potential iron-sulfur protein from A. vinosum (E m +350 mV). High potential iron-sulfur protein not only acts as direct electron donor to the reaction center in anoxygenic phototrophs but can also be involved in aerobic respiratory chains.


    Related Citations: 
    • The more the merrier: de novo phasing of Marichromatium purpuratum thiosulfate dehydrogenase TsdBA by high multiplicity Fe-SAD
      Brito, J.A., Gutierres, A., Kurth, J.M., Reuter, J., Dahl, C., Archer, M.
      () To be published --: --

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome C
A, B
526Marichromatium purpuratum 984Mutation(s): 0 
Gene Names: MARPU_02550
Find proteins for W0DW89 (Marichromatium purpuratum 984)
Go to UniProtKB:  W0DW89
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

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

Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
THJ
Query on THJ

Download CCD File 
A, B
THIOSULFATE
O3 S2
DHCDFWKWKRSZHF-UHFFFAOYSA-L
 Ligand Interaction
PGO
Query on PGO

Download CCD File 
A, B
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.753α = 90
b = 159.753β = 90
c = 393.086γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
BUCCANEERmodel building
PHENIXrefinement
Cootmodel building
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalPEst-OE/EQB/LA0004/2011
Conselho de Reitores das Universidades PortuguesasPortugal--
German Research FoundationGermanyDA 351/7-2
German Academic Exchange ServiceGermany--
BioStruct-X1494

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2016-12-07
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Derived calculations