Download MendeleyStructural Insights into the Mechanism of the Radical SAM Carbide Synthase NifB, a Key Nitrogenase Cofactor Maturating Enzyme.
Fajardo, A.S., Legrand, P., Paya-Tormo, L.A., Martin, L., Pellicer Marti Nez, M.T., Echavarri-Erasun, C., Vernede, X., Rubio, L.M., Nicolet, Y.(2020) J Am Chem Soc 142: 11006-11012
- PubMed: 32476412
- DOI: https://doi.org/10.1021/jacs.0c02243
- Primary Citation of Related Structures:
6Y1X - PubMed Abstract:
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 [MoFe 7 S 9 C-( R )-homocitrate] species designated FeMo-cofactor, whose biosynthesis and insertion requires the action of over a dozen maturation proteins provided by the NIF (for NI trogen F ixation) assembly machinery. Among them, the radical SAM protein NifB plays an essential role, concomitantly inserting a carbide ion and coupling two [Fe 4 S 4 ] clusters to form a [Fe 8 S 9 C] 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 [Fe 4 S 4 ] 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 [Fe 4 S 4 ] clusters. These two residues regulate the sequence of events, controlling SAM dual reactivity and preventing unwanted radical-based chemistry before the K2 [Fe 4 S 4 ] cluster substrate is loaded into the protein. The location of the K1-cluster, too far away from the SAM binding site, supports a mechanism in which the K2-cluster is the site of methylation.
Organizational Affiliation:
Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria, Pozuelo de Alarcón, 28223 Madrid, Spain.
