The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus mutant with His 482 replaced by Gln

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.159 

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Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase.

Tikhonova, T.V.Sorokin, D.Y.Hagen, W.R.Khrenova, M.G.Muyzer, G.Rakitina, T.V.Shabalin, I.G.Trofimov, A.A.Tsallagov, S.I.Popov, V.O.

(2020) Proc Natl Acad Sci U S A 117: 5280-5290

  • DOI: https://doi.org/10.1073/pnas.1922133117
  • Primary Citation of Related Structures:  
    6G50, 6I3Q, 6SJI, 6UWE

  • PubMed Abstract: 

    Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC that was purified from the haloalkaliphilic sulfur-oxidizing bacterium of the genus Thioalkalivibrio ubiquitous in saline alkaline soda lakes. The copper cluster is formed by three copper ions located at the corners of a near-isosceles triangle and facilitates a direct thiocyanate conversion into cyanate, elemental sulfur, and two reducing equivalents without involvement of molecular oxygen. A molecular mechanism of catalysis is suggested based on high-resolution three-dimensional structures, electron paramagnetic resonance (EPR) spectroscopy, quantum mechanics/molecular mechanics (QM/MM) simulations, kinetic studies, and the results of site-directed mutagenesis.

  • Organizational Affiliation

    Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
thiocyanate dehydrogenaseA,
C [auth J],
D [auth K]
470Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
Gene Names: THITH_13335
Find proteins for W0DP94 (Thioalkalivibrio paradoxus ARh 1)
Explore W0DP94 
Go to UniProtKB:  W0DP94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0DP94
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
P [auth K]
O4 S
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
I [auth B]
J [auth B]
K [auth J]
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth J],
L [auth J],
M [auth K],
N [auth K],
O [auth K]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.08α = 90
b = 160.41β = 98.114
c = 90.88γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2020-03-18
    Changes: Database references