Tetrathionate hydrolase from Acidithiobacillus ferrooxidans

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Reaction mechanism of tetrathionate hydrolysis based on the crystal structure of tetrathionate hydrolase from Acidithiobacillus ferrooxidans.

Kanao, T.Hase, N.Nakayama, H.Yoshida, K.Nishiura, K.Kosaka, M.Kamimura, K.Hirano, Y.Tamada, T.

(2020) Protein Sci 30: 328-338

  • DOI: https://doi.org/10.1002/pro.3984
  • Primary Citation of Related Structures:  
    6L8A, 7CQY

  • PubMed Abstract: 

    Tetrathionate hydrolase (4THase) plays an important role in dissimilatory sulfur oxidation in the acidophilic iron- and sulfur-oxidizing bacterium Acidithiobacillus ferrooxidans. The structure of recombinant 4THase from A. ferrooxidans (Af-Tth) was determined by X-ray crystallography to a resolution of 1.95 Å. Af-Tth is a homodimer, and its monomer structure exhibits an eight-bladed β-propeller motif. Two insertion loops participate in dimerization, and one loop forms a cavity with the β-propeller region. We observed unexplained electron densities in this cavity of the substrate-soaked structure. The anomalous difference map generated using diffraction data collected at a wavelength of 1.9 Å indicated the presence of polymerized sulfur atoms. Asp325, a highly conserved residue among 4THases, was located near the polymerized sulfur atoms. 4THase activity was completely abolished in the site-specific Af-Tth D325N variant, suggesting that Asp325 plays a crucial role in the first step of tetrathionate hydrolysis. Considering that the Af-Tth reaction occurs only under acidic pH, Asp325 acts as an acid for the tetrathionate hydrolysis reaction. The polymerized sulfur atoms in the active site cavity may represent the intermediate product in the subsequent step.

  • Organizational Affiliation

    Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tetrathionate hydrolase
A, B, C, D, E
A, B, C, D, E, F
470Acidithiobacillus ferrooxidansMutation(s): 0 
EC: 3.12.1
Find proteins for B7J3C9 (Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455))
Explore B7J3C9 
Go to UniProtKB:  B7J3C9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7J3C9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
G [auth A],
H [auth A],
HA [auth E],
I [auth A],
IA [auth E],
J [auth A],
K [auth A],
L [auth A],
LA [auth F],
M [auth A],
MA [auth F],
N [auth B],
NA [auth F],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth C],
X [auth C],
Y [auth C]
O4 S
Query on BAL

Download Ideal Coordinates CCD File 
GA [auth D],
JA [auth E],
Z [auth C]
C3 H7 N O2
Query on GLY

Download Ideal Coordinates CCD File 
KA [auth E],
OA [auth F]
C2 H5 N O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.026α = 90
b = 91.026β = 90
c = 231.845γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Derived calculations