Nitrogenase and homologs

Abstract

Nitrogenase catalyzes biological nitrogen fixation, a key step in the global nitrogen cycle. Three homologous nitrogenases have been identified to date, along with several structural and/or functional homologs of this enzyme that are involved in nitrogenase assembly, bacteriochlorophyll biosynthesis and methanogenic process, respectively. In this article, we provide an overview of the structures and functions of nitrogenase and its homologs, which highlights the similarity and disparity of this uniquely versatile group of enzymes.

Fig. 1

(A) Surface presentation (transparent) of the structure of the MgADP•AlF₄⁻-stabilized Fe protein/MoFe protein complex. MgADP•AlF₄⁻, [Fe₄S₄] cluster, P-cluster and M-cluster are shown as space-filling models. The two subunits of the Fe protein (labeled as H) are colored gray and light wheat, respectively, and the α- and β-subunits of the MoFe protein are colored red (labeled as D) and light blue (labeled as K), respectively. (B) Components involved in electron transfer during catalysis. All clusters are shown as ball-and-stick models. Atoms are colored as follows: Fe, orange; S, yellow; Mo, cyan; O, red; C, gray; N, blue; Mg, dark green; Al, light green; F, light blue. PYMOL was used to create this figure (PDB IDs: 1N2C, 3U7Q).

Fig. 2

(A) Schematic presentation (transparent) of the hypothetical structural layout of the MgADP•AlF₄⁻-stabilized Fe protein/VFe protein complex. MgADP•AlF₄⁻, [Fe₄S₄] cluster, P*-cluster and V-cluster are shown as space-filling models. The two subunits of the Fe protein (labeled as H) are colored gray and light wheat, respectively, and the α-, β- and δ-subunits of the MoFe protein are colored red (labeled as D), light blue (labeled as K) and dark gray (labeled as G), respectively. (B) Components involved in electron transfer during catalysis. All clusters are shown as ball-and-stick models. The structures of the clusters are derived from the available XAS/EXAFS and XES data. Atoms are colored as follows: Fe, orange; S, yellow; V, dark gray; O, red; C, gray; N, blue; Mg, dark green; Al, light green; F, light blue. HCs, hydrocarbons.

Fig. 3

(A) Surface presentation (transparent) of the hypothetical structural layout of the MgADP•AlF₄⁻-stabilized Fe protein/NifEN complex. MgADP•AlF₄⁻, [Fe₄S₄] clusters and L-cluster are shown as space-filling models. The two subunits of the Fe protein (labeled as H) are colored gray and light wheat, respectively, and the α- and β-subunits of the NifEN are colored red (labeled as E) and light blue (labeled as N), respectively. (B) Components involved in electron transfer during catalysis. All clusters are shown as ball-and-stick models. (C) Schematic presentation of the conversion of L- to M-cluster (C, top) on NifEN upon the replacement of a terminal Fe atom by Mo and homocitrate (HC). The Fe protein (C, bottom) serves as an ATP-dependent Mo/HC insertase in this process. Atoms are colored as follows: Fe, orange; S, yellow; O, red; C, gray; N, blue; Mg, dark green; Al, light green; F, light blue. PYMOL was used to create this figure (PDB IDs: 1N2C, 3PDI).

Fig. 4

(A) Surface presentation (transparent) of the structure of the MgADP•AlF₄⁻-stabilized ChlL/ChlNB complex. MgADP•AlF₄⁻, [Fe₄S₄] clusters and Pchlide are shown as space-filling models. The two subunits of ChlL (labeled as L) are colored gray and light wheat, respectively, and the α- and β-subunits of ChlNB are colored red (labeled as N) and light blue (labeled as B), respectively. (B) Components involved in electron transfer during catalysis. All clusters and Pchlide are shown as ball-and-stick models. Atoms are colored as follows: Fe, orange; S, yellow; O, red; C, gray; N, blue; Mg, dark green; Al, light green; F, light blue. PYMOL was used to create this figure (PDB ID: 2YNM). (C) DPOR catalyzes the formation of Chlide through ATP-dependent, stereospecific reduction of the C17–C18 double bond of Pchlide, while COR catalyzes the formation of Bchlide through ATP-dependent, stereospecific reduction of the C7–C8 double bond of Chlide,

Fig. 5

(A) Schematic presentation (transparent) of the hypothetical structural layout of the MgADP•AlF₄⁻-stabilized NflH/NflD complex. MgADP•AlF₄⁻, [Fe₄S₄] clusters and cofactor F430 are shown as space-filling models. The two subunits of NflH (labeled as H) are colored gray and light wheat, respectively, and the two subunits of NflD (labeled as D) are colored red and light blue, respectively. (B) Components involved in the proposed electron transfer during catalysis. All clusters and cofactor F430 are shown as ball-and-stick models. Atoms are colored as follows: Fe, orange; S, yellow; V, dark gray; O, red; C, gray; N, blue; Mg, dark green; Al, light green; F, light blue.