4PDE

Crystal structure of FdhD in complex with GDP

Summary for 4PDE

• Entry DOI: 10.2210/pdb4pde/pdb
• Descriptor: Protein FdhD, GUANOSINE-5'-DIPHOSPHATE (3 entities in total)
• Functional Keywords: hydrolase, gdp, mo-bispgd sulfuration
• Biological source: Escherichia coli
• Cellular location: Cytoplasm : J7QY30
• Total number of polymer chains: 1
• Total formula weight: 32111.34

Authors

Arnoux, P.,Walburger, A.,Magalon, A.,Pignol, D. (deposition date: 2014-04-18, release date: 2015-05-20, Last modification date: 2023-12-20)

Primary citation

Arnoux, P.,Ruppelt, C.,Oudouhou, F.,Lavergne, J.,Siponen, M.I.,Toci, R.,Mendel, R.R.,Bittner, F.,Pignol, D.,Magalon, A.,Walburger, A.
Sulphur shuttling across a chaperone during molybdenum cofactor maturation.
Nat Commun, 6:6148-6148, 2015

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 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.

PubMed: 25649206
DOI: 10.1038/ncomms7148

Experimental method

X-RAY DIFFRACTION (2.8 Å)