6G50

The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus as isolated.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.147 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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 1.8.2.7) 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

    Research Centre of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B, C, D
467Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
H [auth A]
M [auth B]
Q [auth C]
R [auth C]
AA [auth D],
H [auth A],
M [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU
Query on CU

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
P [auth C],
W [auth D],
X [auth D],
Y [auth D]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth D],
CA [auth D],
U [auth C],
V [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.63α = 90
b = 162.28β = 119.51
c = 90.57γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian FederationGrant 14-24-00172

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Advisory, Data collection
  • Version 1.2: 2020-07-22
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description