Structural insights into the mechanism of the radical SAM carbide synthase NifB, a key nitrogenase cofactor maturating enzyme - Université Grenoble Alpes Accéder directement au contenu
Article Dans Une Revue Journal of the American Chemical Society Année : 2020

Structural insights into the mechanism of the radical SAM carbide synthase NifB, a key nitrogenase cofactor maturating enzyme

Ana Sosa Fajardo
  • Fonction : Auteur
Pierre Legrand
Lucía Payá-Tormo
  • Fonction : Auteur
Maria Teresa Pellicer Martinez
  • Fonction : Auteur
Carlos Echavarri-Erasun
  • Fonction : Auteur
Xavier Vernède
  • Fonction : Auteur
Luis Rubio
  • Fonction : Auteur
Yvain Nicolet

Résumé

Nitrogenase is a key player in the global nitrogen cycle as it catalyzes the reduction of dinitrogen into ammonia. The active site of the nitrogenase MoFe protein corresponds to a [MoFe7S9C-(R)-homocitrate] species designated FeMo-cofactor, whose biosynthesis and insertion requires the action of over a dozen maturation proteins provided by the NIF (for NItrogen Fixation) assembly machinery. Among them, the radical SAM protein NifB plays an essential role, concomitantly inserting a carbide ion and coupling two [Fe4S4] clusters to form a [Fe8S9C] precursor called NifB-co. Here we report on the X-ray structure of NifB from Methanotrix thermoacetophila at 1.95 Å resolution in a state pending the binding of one [Fe4S4] cluster substrate. The overall NifB architecture indicates that this enzyme has a single SAM binding site, which at this stage is occupied by cysteine residue 62. The structure reveals a unique ligand binding mode for the K1 cluster involving cysteine residues 29 and 128 in addition to histidine 42 and glutamate 65. The latter, together with cysteine 62, belongs to a loop inserted in the active site, likely protecting the already present [Fe4S4] clusters. These two residues regulate the sequence of events, controlling SAM dual reactivity and preventing unwanted radical-based chemistry before the K2 [Fe4S4] cluster substrate is loaded into the protein. The location of K1 cluster, too far away from the SAM binding site, supports a mechanism in which the K2 cluster is the site of methylation.
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Dates et versions

hal-02775951 , version 1 (04-06-2020)

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Citer

Ana Sosa Fajardo, Pierre Legrand, Lucía Payá-Tormo, Lydie Martin, Maria Teresa Pellicer Martinez, et al.. Structural insights into the mechanism of the radical SAM carbide synthase NifB, a key nitrogenase cofactor maturating enzyme. Journal of the American Chemical Society, 2020, ⟨10.1021/jacs.0c02243⟩. ⟨hal-02775951⟩
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