[4Fe-4S]-dependent thiouracil desulfidase TudS (DUF523Vcz) solved by Fe-SAD phasing

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structural Evidence for a [4Fe-5S] Intermediate in the Non-Redox Desulfuration of Thiouracil.

Zhou, J.Pecqueur, L.Aucynaite, A.Fuchs, J.Rutkiene, R.Vaitekunas, J.Meskys, R.Boll, M.Fontecave, M.Urbonavicius, J.Golinelli-Pimpaneau, B.

(2021) Angew Chem Int Ed Engl 60: 424-431

  • DOI: https://doi.org/10.1002/anie.202011211
  • Primary Citation of Related Structures:  
    6Z92, 6Z93, 6Z94, 6Z96, 6ZW9

  • PubMed Abstract: 

    We recently discovered a [Fe-S]-containing protein with in vivo thiouracil desulfidase activity, dubbed TudS. The crystal structure of TudS refined at 1.5 Å resolution is reported; it harbors a [4Fe-4S] cluster bound by three cysteines only. Incubation of TudS crystals with 4-thiouracil trapped the cluster with a hydrosulfide ligand bound to the fourth non-protein-bonded iron, as established by the sulfur anomalous signal. This indicates that a [4Fe-5S] state of the cluster is a catalytic intermediate in the desulfuration reaction. Structural data and site-directed mutagenesis indicate that a water molecule is located next to the hydrosulfide ligand and to two catalytically important residues, Ser101 and Glu45. This information, together with modeling studies allow us to propose a mechanism for the unprecedented non-redox enzymatic desulfuration of thiouracil, in which a [4Fe-4S] cluster binds and activates the sulfur atom of the substrate.

  • Organizational Affiliation

    Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, Paris CEDEX 05, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF523 domain-containing protein
A, B
166uncultured bacteriumMutation(s): 0 
Find proteins for A0A2H4Z949 (uncultured bacterium)
Explore A0A2H4Z949 
Go to UniProtKB:  A0A2H4Z949
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2H4Z949
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
Fe4 S4
Query on PEG

Download Ideal Coordinates CCD File 
C4 H10 O3
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth B],
H [auth B],
J [auth B]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.28α = 90
b = 85.911β = 93.64
c = 39.565γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
STARANISOdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French National Research AgencyFranceLABEX DYNAMO, ANR-11-LABX-0011-01

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references