Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites

NifEN-B complex of Azotobacter vinelandii is fully functional in nitrogenase FeMo cofactor assembly

Assembly of nitrogenase FeMoco is one of the key processes in bioinorganic chemistry. NifB and NifEN are two essential elements immediately adjacent to each other along the biosynthetic pathway of FeMoco. Previously, an 8Fe-precursor of FeMoco was identified on NifEN; however, the identity of the biosynthetic intermediate on NifB has remained elusive to date. Here, we present a combined biochemical and spectroscopic investigation of a His-tagged NifEN-B fusion protein of Azotobacter vinelandii. Our data from the EPR and activity analyses confirm the presence of the 8Fe-precursor in the NifEN entity of NifEN-B; whereas those from the metal, EPR, and UV/Vis experiments reveal the presence of additional [Fe(4)S(4)]-type cluster species in the NifB entity of NifEN-B. EPR-, UV/Vis- and metal-based quantitative analyses suggest that the newly identified cluster species in NifEN-B consist of both SAM-motif (CXXXCXXC)- and non-SAM-motif-bound [Fe(4)S(4)]-type clusters. Moreover, EPR and activity experiments indicate that the non-SAM-motif [Fe(4)S(4)] cluster is a NifB-bound intermediate of FeMoco assembly, which could be converted to the 8Fe-precursor in a SAM-dependent mechanism. Combined outcome of this work provides the initial insights into the biosynthetic events of FeMoco on NifB. More importantly, the full capacity of NifEN-B in FeMoco biosynthesis demonstrates the potential of this fusion protein as an excellent platform for further investigations of the role of NifB and its interaction with NifEN during the process of FeMoco assembly.

Biosynthesis of Nitrogenase FeMoco

Biosynthesis of nitrogenase FeMoco is a highly complex process that requires, minimally, the participation of nifS, nifU, nifB, nifE, nifN, nifV, nifH, nifD and nifK gene products. Previous genetic analyses have identified the essential factors for the assembly of FeMoco; however, the exact functions of these factors and the precise sequence of events during the assembly process had remained unclear until recently, when a number of the biosynthetic intermediates of FeMoco were identified and characterized by combined biochemical, spectroscopic and structural analyses. This review gives a brief account of the recent progress toward understanding the assembly process of FeMoco, which has identified some important missing pieces of this biosynthetic puzzle.

Dimerization of pentanuclear clusters [Fe3Q(AsMe)(CO)9] (Q = Se, Te) as a conversion pathway to novel cubane-like aggregates

The first examples of carbonyl heterocubane-type clusters, [Fe(4)(μ(3)-Q)(2)(μ(3)-AsMe)(2)(CO)(12)] (2, Q = Se (a), Te (b)), which simultaneously contain elements of group 15 and 16, were obtained by thermolysis of [Fe(3)(μ(3)-Q)(μ(3)-AsMe)(CO)(9)] (1) in acetonitrile. The clusters 2 possess a cubic Fe(4)Q(2)As(2) core with alternating Fe and Q/As atoms. The coordination environment of the Fe atoms is close to octahedral, and those of Q or As atoms are tetrahedral, which determines the distorted cubic cluster core geometry. The second main products of thermolysis are the clusters [Fe(6)(μ(3)-Q)(μ(4)-Q)(μ(4)-AsMe)(2)(CO)(12)] (3a,b), whose core contains double the elemental composition of the initial cluster 1. In the case of the Se-containing cluster two other minor products [Fe(4)(μ(4)-Se)(μ(4)-SeAsMe)(CO)(12)] (4) and [Fe(3)(μ(3)-AsMe)(2)(CO)(9)] (5) are formed. Based on the structures and properties of the products, a reaction route for the conversion of 1 into 2 is proposed, which includes the associative formation of the clusters 3 as intermediates, unlike the dissociative pathways previously known for the transformations of similar clusters of the type [Fe(3)Q(2)(CO)(9)].

From thioxo cluster to dithio cluster: exploring the chemistry of polynuclear zirconium complexes with S,O and S,S ligands

Three different zirconium thio and oxothio clusters, characterized by different coordination modes of dithioacetate and/or monothioacetate ligands, were obtained by the reaction of monothioacetic acid with zirconium n-butoxide, Zr(O(n)Bu)4, in different experimental conditions. In particular, we isolated the three polynuclear Zr3(μ3-SSSCCH3)2(SSCCH3)6·2(n)BuOH (Zr3), Zr4(μ3-O)2(μ-η(1)-SOCCH3)2(SOCCH3)8(O(n)Bu)2 (Zr4), and Zr6(μ3-O)5(μ-SOCCH3)2(μ-OOCCH3)(SOCCH3)11((n)BuOH) (Zr6) derivatives, presenting some peculiar characteristics. Zr6 has an unusual star-shaped structure. Only sulfur-based ligands, viz., chelating dithioacetate monoanions and an unusual ethane-1,1,1-trithiolate group μ3 coordinating the Zr ions, were observed in the case of Zr3. 1D and 2D NMR analyses confirmed the presence of differently coordinated ligands. Raman spectroscopy was further used to characterize the new polynuclear complexes. Time-resolved extended X-ray absorption fine structure measurements, devoted to unraveling the cluster formation mechanisms, evidenced a fast coordination of sulfur ligands and subsequent relatively rapid rearrangements.

Historic overview of nitrogenase research

The history of nitrogenase research dates all the way back to the 1800s. This chapter provides a brief account of the advances in this particular research area over the past few hundred years, which include such events as the initial discovery of biological nitrogen fixation, the preparation of active cell-free extracts, the purification of nitrogenase enzyme, the proposal of the Thorneley-Lowe model, and the report of x-ray crystallographic structures of the component proteins of nitrogenase.

Reactions of the terminal Ni(II)-OH group in substitution and electrophilic reactions with carbon dioxide and other substrates: structural definition of binding modes in an intramolecular Ni(II)...Fe(II) bridged site

A singular feature of the catalytic C-cluster of carbon monoxide dehydrogenase is a sulfide-bridged Ni...Fe locus where substrate is bound and transformed in the reversible reaction CO + H(2)O right harpoon over left harpoon CO(2) + 2H(+) + 2e(-). A similar structure has been sought in this work. Mononuclear planar Ni(II) complexes [Ni(pyN(2)(Me2))L](1-) (pyN(2)(Me2) = bis(2,6-dimethylphenyl)-2,6-pyridinedicarboxamidate(2-)) derived from a NNN pincer ligand have been prepared including L = OH(-) (1) and CN(-) (7). Complex 1 reacts with ethyl formate and CO(2) to form unidentate L = HCO(2)(-) (5) and HCO(3)(-) (6) products. A binucleating macrocycle was prepared which specifically binds Ni(II) at a NNN pincer site and five-coordinate Fe(II) at a triamine site. The Ni(II) macrocyle forms hydroxo (14) and cyanide complexes (15) analogous to 1 and 7. Reaction of 14 with FeCl(2) alone and with ethyl formate and 15 with FeCl(2) affords molecules with the Ni(II)-L-Fe(II) bridge unit in which L = mu(2):eta(1)-OH(-) (17) and mu(2):eta(2)-HCO(2)(-) (18) and -CN(-) (19). All bridges are nonlinear (17, 140.0 degrees ; 18, M-O-C 135.9 degrees (Ni), 120.2 degrees (Fe); 19, Ni-C-N 170.3 degrees , Fe-N-C 141.8 degrees ) with Ni...Fe separations of 3.7-4.8 A. The Ni(II)Fe(II) complexes, lacking appropriate Ni-Fe-S cluster structures, are not site analogues, but their synthesis and reactivity provide the first demonstration that molecular Ni(II)...Fe(II) sites and bridges can be attained, a necessity in the biomimetic chemistry of C-clusters.

The useful properties of H2O as a ligand of a hydrogenase mimic

This paper investigates the required properties of Ru-coordinated ligands of a Ni-Ru based hydrogenase mimic. A series of ligands, including MeCN, pyridine, H(2)O and OH(-) were coordinated to Ru, with H(2)O being the only ligand to promote H(2)-activation. In addition, a tethered pyridyl moiety was synthesised and found to completely inhibit H(2)-activation. We conclude, therefore, that H(2)O is the ideal ligand for this mimic as a result of both its mild basicity and the availability of two lone pairs for simultaneous binding to Ru and H(2).

Concerto catalysis--harmonising [NiFe]hydrogenase and NiRu model catalysts

This communication reports the successful merging of the chemical properties of a natural [NiFe]hydrogenase (Desulfovibrio vulgaris Miyazaki F) and our previously reported [NiRu] hydrogenase-mimic. The catalytic activity of both the natural enzyme and the mimic is almost identical, with the exception of working pH ranges, and this allows us to use them simultaneously in the same reaction flask. In such a manner, isotope exchange between D(2) and H(2)O could be conducted over an extended pH range (about 2-10) in one pot under mild conditions at ambient temperature and pressure.

Molybdenum cofactors, enzymes and pathways

The trace element molybdenum is essential for nearly all organisms and forms the catalytic centre of a large variety of enzymes such as nitrogenase, nitrate reductases, sulphite oxidase and xanthine oxidoreductases. Nature has developed two scaffolds holding molybdenum in place, the iron-molybdenum cofactor and pterin-based molybdenum cofactors. Despite the different structures and functions of molybdenum-dependent enzymes, there are important similarities, which we highlight here. The biosynthetic pathways leading to both types of cofactor have common mechanistic aspects relating to scaffold formation, metal activation and cofactor insertion into apoenzymes, and have served as an evolutionary 'toolbox' to mediate additional cellular functions in eukaryotic metabolism.