Spectroscopic Characterization of an Eight‐Iron Nitrogenase Cofactor Precursor that Lacks the “9 th Sulfur”

X-Ray Crystallographic Analysis of NifB with a Full Complement of Clusters: Structural Insights into the Radical SAM-Dependent Carbide Insertion During Nitrogenase Cofactor Assembly

NifB is an essential radical SAM enzyme required for the assembly of an 8Fe core of the nitrogenase cofactor. Herein, we report the X-ray crystal structures of Methanobacterium thermoautotrophicum NifB without (apo MtNifB) and with (holo MtNifB) a full complement of three [Fe₄ S₄ ] clusters. Both apo and holo MtNifB contain a partial TIM barrel core, but unlike apo MtNifB, holo MtNifB is fully assembled and competent in cofactor biosynthesis. The radical SAM (RS)-cluster is coordinated by three Cys, and the adjacent K1- and K2-clusters, representing the precursor to an 8Fe cofactor core, are each coordinated by one His and two Cys. Prediction of substrate channels, combined with in silico docking of SAM in holo MtNifB, suggests the binding of SAM between the RS- and K2-clusters and putative paths for entry of SAM and exit of products of SAM cleavage, thereby providing important mechanistic insights into the radical SAM-dependent carbide insertion concomitant with cofactor core formation.

Reactions of [Fe6C(CO)14(S)]2-: Cluster Growth, Redox, Sulfiding

Redox reactions, substitutions, and metalations are reported for the iron carbido sulfide [Fe6C(CO)14(S)]2- ([1]2-). Dianion [1]2- oxidized to [Fe6C(CO)16(S)]0 ([2]0) upon treatment with of [Fe(C5H5)2]BF4 or HBF4 (H2 formation) under an atmosphere of CO. Reaction of [2]0 with tBuNC gave [Fe6C(S)(CO)13(tBuNC)5], consisting of Fe5C(CO)13 and [Fe(tBuNC)5]2+ subunits linked by a μ3-S2-. The Fe7CS cluster [Fe7C(CO)17(S)]2- formed upon treatment of (Ph4P)2[1] with Fe(benzylideneacetone)(CO)3. The Fe7 species is an edge-fused cluster with [Fe6C(CO)10(μ-CO)4] and Fe(CO)3 subunits joined by μ3-S and two Fe-Fe bonds. The analogous reaction using Mo(CO)4(norbornadiene) gave [MoFe6C(CO)18(S)]2-. In this cluster, the Mo center is located in the octahedral subunit. Treatment of [1]2- with SO2 afforded [Fe6C(S)(SO2)(CO)13]2-. This cluster features an Fe6C core decorated with μ3-S and μ2-SO2 ligands. These experiments were undertaken in an effort to connect organometallic clusters to FeMoco.

Electron Paramagnetic Resonance and Magnetic Circular Dichroism Spectra of the Nitrogenase M Cluster Precursor Suggest Sulfur Migration upon Oxidation: A Proposal for Substrate and Inhibitor Binding

The active site of the nitrogen-fixing enzyme Mo-nitrogenase is the M cluster ([MoFe7 S9 C⋅R-homocitrate]), also known as the FeMo cofactor or FeMoco. The biosynthesis of this highly complex metallocluster involves a series of proteins. Among them, NifB, a radical-SAM enzyme, is instrumental in the assembly of the L cluster ([Fe8 S9 C]), a precursor and all-iron core of the M cluster. In the absence of sulfite, NifB assembles a precursor form of the L cluster called the L* cluster ([Fe8 S8 C]), which lacks the final ninth sulfur. EPR and MCD spectroscopies are used to probe the electronic structures of the paramagnetic, oxidized forms of both the L and L* clusters, labeled LOx and [L*]Ox . This study shows that both LOx and [L*]Ox have nearly identical EPR and MCD spectra, thus suggesting that the two clusters have identical structures upon oxidation; in other words, a sulfur migrates away from LOx following oxidation, thereby rendering the cluster identical to [L*]Ox . It is proposed that a similar migration could occur to the M cluster upon oxidation, and that this is an instrumental part of both M cluster formation and nitrogenase substrate/inhibitor binding.

Heterologous Expression and Engineering of the Nitrogenase Cofactor Biosynthesis Scaffold NifEN

NifEN plays a crucial role in the biosynthesis of nitrogenase, catalyzing the final step of cofactor maturation prior to delivering the cofactor to NifDK, the catalytic component of nitrogenase. The difficulty in expressing NifEN, a complex, heteromultimeric metalloprotein sharing structural/functional homology with NifDK, is a major challenge in the heterologous expression of nitrogenase. Herein, we report the expression and engineering of Azotobacter vinelandii NifEN in Escherichia coli. Biochemical and spectroscopic analyses demonstrate the integrity of the heterologously expressed NifEN in composition and functionality and, additionally, the ability of an engineered NifEN variant to mimic NifDK in retaining the matured cofactor at an analogous cofactor-binding site. This is an important step toward piecing together a viable pathway for the heterologous expression of nitrogenase and identifying variants for the mechanistic investigation of this enzyme.