4PDE

Crystal structure of FdhD in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Sulphur shuttling across a chaperone during molybdenum cofactor maturation.

Arnoux, P.Ruppelt, C.Oudouhou, F.Lavergne, J.Siponen, M.I.Toci, R.Mendel, R.R.Bittner, F.Pignol, D.Magalon, A.Walburger, A.

(2015) Nat Commun 6: 6148-6148

  • DOI: 10.1038/ncomms7148

  • PubMed Abstract: 
  • Formate dehydrogenases (FDHs) are of interest as they are natural catalysts that sequester atmospheric CO2, generating reduced carbon compounds with possible uses as fuel. FDHs activity in Escherichia coli strictly requires the sulphurtransferase EcF ...

    Formate dehydrogenases (FDHs) are of interest as they are natural catalysts that sequester atmospheric CO2, generating reduced carbon compounds with possible uses as fuel. FDHs activity in Escherichia coli strictly requires the sulphurtransferase EcFdhD, which likely transfers sulphur from IscS to the molybdenum cofactor (Mo-bisPGD) of FDHs. Here we show that EcFdhD binds Mo-bisPGD in vivo and has submicromolar affinity for GDP-used as a surrogate of the molybdenum cofactor's nucleotide moieties. The crystal structure of EcFdhD in complex with GDP shows two symmetrical binding sites located on the same face of the dimer. These binding sites are connected via a tunnel-like cavity to the opposite face of the dimer where two dynamic loops, each harbouring two functionally important cysteine residues, are present. On the basis of structure-guided mutagenesis, we propose a model for the sulphuration mechanism of Mo-bisPGD where the sulphur atom shuttles across the chaperone dimer.


    Organizational Affiliation

    1] Laboratoire de Bioénergétique Cellulaire, CEA, DSV, IBEB, 13108, Saint-Paul-lez-Durance, France [2] CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, 13108 Saint-Paul-lez-Durance, France [3] Aix Marseille Université, CEA, CNRS, Biologie Végétale et Microbiologie Environnementales UMR 7265, 13108 Saint-Paul-lez-Durance, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein FdhD
A
285Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: fdhD
Find proteins for P32177 (Escherichia coli (strain K12))
Go to UniProtKB:  P32177
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.190 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 98.430α = 90.00
b = 98.430β = 90.00
c = 120.411γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-20
    Type: Initial release