4V2K | pdb_00004v2k

Crystal structure of the thiosulfate dehydrogenase TsdA in complex with thiosulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 
    0.155 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.143 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.143 (Depositor) 

Starting Models: experimental
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This is version 2.2 of the entry. See complete history

Literature

Mechanism of Thiosulfate Oxidation in the Soxa Family of Cysteine-Ligated Cytochromes

Grabarczyk, D.B.Chappell, P.E.Eisel, B.Johnson, S.Lea, S.M.Berks, B.C.

(2015) J Biological Chem 290: 9209

  • DOI: https://doi.org/10.1074/jbc.M114.618025
  • Primary Citation Related Structures: 
    4V2K

  • PubMed Abstract: 

    Thiosulfate dehydrogenase (TsdA) catalyzes the oxidation of two thiosulfate molecules to form tetrathionate and is predicted to use an unusual cysteine-ligated heme as the catalytic cofactor. We have determined the structure of Allochromatium vinosum TsdA to a resolution of 1.3 Å. This structure confirms the active site heme ligation, identifies a thiosulfate binding site within the active site cavity, and reveals an electron transfer route from the catalytic heme, through a second heme group to the external electron acceptor. We provide multiple lines of evidence that the catalytic reaction proceeds through the intermediate formation of a S-thiosulfonate derivative of the heme cysteine ligand: the cysteine is reactive and is accessible to electrophilic attack; cysteine S-thiosulfonate is formed by the addition of thiosulfate or following the reverse reaction with tetrathionate; the S-thiosulfonate modification is removed through catalysis; and alkylating the cysteine blocks activity. Active site amino acid residues required for catalysis were identified by mutagenesis and are inferred to also play a role in stabilizing the S-thiosulfonate intermediate. The enzyme SoxAX, which catalyzes the first step in the bacterial Sox thiosulfate oxidation pathway, is homologous to TsdA and can be inferred to use a related catalytic mechanism.


  • Organizational Affiliation
    • From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom and.

Macromolecule Content 

  • Total Structure Weight: 28.41 kDa 
  • Atom Count: 2,080 
  • Modeled Residue Count: 235 
  • Deposited Residue Count: 253 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
THIOSULFATE DEHYDROGENASE253Allochromatium vinosumMutation(s): 0 
EC: 1.8.2.2
UniProt
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free:  0.155 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.143 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.143 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.28α = 90
b = 70.42β = 129.34
c = 57.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-07-22
    Changes: Database references
  • Version 2.0: 2019-09-25
    Changes: Atomic model, Data collection, Derived calculations, Experimental preparation, Non-polymer description, Other, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary