6Y1X

X-ray structure of the radical SAM protein NifB, a key nitrogenase maturating enzyme

Summary for 6Y1X

• Entry DOI: 10.2210/pdb6y1x/pdb
• Descriptor: Radical SAM domain protein, IRON/SULFUR CLUSTER, SULFATE ION, ... (5 entities in total)
• Functional Keywords: carbide synthase femo-co nifb-co fes cluster assembly machinery metalloprotein, metal binding protein
• Biological source: Methanothrix thermoacetophila (strain DSM 6194 / JCM 14653 / NBRC 101360 / PT)
• Total number of polymer chains: 2
• Total formula weight: 72547.55

Authors

Sosa-Fajardo, A.,Legrand, P.,Paya-Tormo, L.,Martin, L.,Pellicer-Martinez, M.T.,Echavarri-Erasun, C.,Vernede, X.,Rubio, L.M.,Nicolet, Y. (deposition date: 2020-02-14, release date: 2020-06-17, Last modification date: 2024-05-15)

Primary citation

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.
Structural Insights into the Mechanism of the Radical SAM Carbide Synthase NifB, a Key Nitrogenase Cofactor Maturating Enzyme.
J.Am.Chem.Soc., 142:11006-11012, 2020

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 [MoFeSC-()-homocitrate] species designated FeMo-cofactor, whose biosynthesis and insertion requires the action of over a dozen maturation proteins provided by the NIF (for trogen ixation) assembly machinery. Among them, the radical SAM protein NifB plays an essential role, concomitantly inserting a carbide ion and coupling two [FeS] clusters to form a [FeSC] precursor called NifB-co. Here we report on the X-ray structure of NifB from at 1.95 Å resolution in a state pending the binding of one [FeS] 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 [FeS] clusters. These two residues regulate the sequence of events, controlling SAM dual reactivity and preventing unwanted radical-based chemistry before the K2 [FeS] 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.

PubMed: 32476412
DOI: 10.1021/jacs.0c02243

Experimental method

X-RAY DIFFRACTION (1.95 Å)