nitrogenase and molybdenum-cofactor

X-ray absorption (XAS) and X-ray emission spectroscopy (XES) provide element specific probes of the geometric and electronic structures of metalloprotein active sites. As such, these methods have played an integral role in nitrogenase research beginning with the first EXAFS studies on nitrogenase in the late 1970s. Herein, we briefly explain the information that can be extracted from XAS and XES. We then highlight the recent applications of these methods in nitrogenase research. The influence of X-ray spectroscopy on our current understanding of the atomic structure and electronic structure of iron molybdenum cofactor (FeMoco) is emphasized. Contributions of X-ray spectroscopy to understanding substrate interactions and cluster biosynthesis are also discussed. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.

Topics: Coenzymes; Iron; Metalloproteins; Models, Molecular; Molecular Structure; Molybdenum Cofactors; Nitrogenase; Protein Conformation; Pteridines; Spectrometry, X-Ray Emission; X-Ray Absorption Spectroscopy

The transition element molybdenum (Mo) is of primordial importance for biological systems, because it is required by enzymes catalyzing key reactions in the global carbon, sulfur, and nitrogen metabolism. To gain biological activity, Mo has to be complexed by a special cofactor. With the exception of bacterial nitrogenase, all Mo-dependent enzymes contain a unique pyranopterin-based cofactor coordinating a Mo atom at their catalytic site. Various types of reactions are catalyzed by Mo-enzymes in prokaryotes including oxygen atom transfer, sulfur or proton transfer, hydroxylation, or even nonredox reactions. Mo-enzymes are widespread in prokaryotes and many of them were likely present in the Last Universal Common Ancestor. To date, more than 50--mostly bacterial--Mo-enzymes are described in nature. In a few eubacteria and in many archaea, Mo is replaced by tungsten bound to the same unique pyranopterin. How Mo-cofactor is synthesized in bacteria is reviewed as well as the way until its insertion into apo-Mo-enzymes.

Topics: Archaea; Bacteria; Biocatalysis; Coenzymes; Enzymes; Escherichia coli; Metalloproteins; Molybdenum; Molybdenum Cofactors; Nitrogenase; Pteridines; Pterins; Sulfur; Tungsten

Topics: Biological Transport; Chlorates; Coenzymes; Drug Resistance, Microbial; Escherichia coli; Genes, Bacterial; Iron; Metalloproteins; Models, Biological; Molecular Structure; Molybdenum; Molybdenum Cofactors; Mutation; Nitrogenase; Pteridines; Pterins

Topics: Azotobacter; Coenzymes; Genes, Bacterial; Klebsiella pneumoniae; Metalloproteins; Molybdenum; Molybdenum Cofactors; Molybdoferredoxin; Nitrogen Fixation; Nitrogenase; Pteridines; Tungsten

Mo nitrogenase is the primary source of biologically fixed nitrogen, making this system highly interesting for developing new, energy efficient ways of ammonia production. Although heavily investigated, studies of the active site of this enzyme have generally been limited to spectroscopic methods that are compatible with the presence of water and relatively low protein concentrations. One method of overcoming this limitation is through lyophilization, which allows for measurements to be performed on solvent free, high concentration samples. This method also has the potential for allowing efficient protein storage and solvent exchange. To investigate the viability of this preparatory method with Mo nitrogenase, we employ a combination of electron paramagnetic resonance, Mo and Fe K-edge X-ray absorption spectroscopy, and acetylene reduction assays. Our results show that while some small distortions in the metallocofactors occur, oxidation and spin states are maintained through the lyophilization process and that reconstitution of either lyophilized protein component into buffer restores acetylene reducing activity.

Topics: Acetylene; Biocatalysis; Coenzymes; Electron Spin Resonance Spectroscopy; Enzyme Assays; Freeze Drying; Iron; Metalloproteins; Molybdenum; Molybdenum Cofactors; Nitrogenase; Pteridines; X-Ray Absorption Spectroscopy

Mo and Fe K-edge EXAFS analysis of NifQ shows the presence of a [MoFe

Topics: 2,2'-Dipyridyl; Azotobacter vinelandii; Bacterial Proteins; Coenzymes; Copper; Iron; Metalloproteins; Molybdenum Cofactors; Nitrogenase; Pteridines; Transcription Factors; X-Ray Absorption Spectroscopy

The molybdenum nitrogenase, present in a diverse group of bacteria and archea, is the major contributor to biological nitrogen fixation. The nitrogenase active site contains an iron-molybdenum cofactor (FeMo-co) composed of 7Fe, 9S, 1Mo, one unidentified light atom, and homocitrate. The nifQ gene was known to be involved in the incorporation of molybdenum into nitrogenase. Here we show direct biochemical evidence for the role of NifQ in FeMo-co biosynthesis. As-isolated NifQ was found to carry a molybdenum-iron-sulfur cluster that serves as a specific molybdenum donor for FeMo-co biosynthesis. Purified NifQ supported in vitro FeMo-co synthesis in the absence of an additional molybdenum source. The mobilization of molybdenum from NifQ required the simultaneous participation of NifH and NifEN in the in vitro FeMo-co synthesis assay, suggesting that NifQ would be the physiological molybdenum donor to a hypothetical NifEN/NifH complex.

Topics: Azotobacter vinelandii; Bacterial Proteins; Biological Transport; Coenzymes; Iron; Iron-Sulfur Proteins; Metalloproteins; Molybdenum; Molybdenum Cofactors; Nitrogen Fixation; Nitrogenase; Protein Binding; Pteridines; Transcription Factors

The structures of the P cluster and cofactor cluster of nitrogenase are well-defined crystallographically. They have been obtained only by biosynthesis; their chemical synthesis remains a challenge. Synthetic routes are sought to the P cluster in the P(N) state in which two cuboidal Fe(3)S(3) units are connected by a mu(6)-S atom and two Fe-(mu(2)-S(Cys))-Fe bridges. A reaction scheme affording a Mo(2)Fe(6)S(9) cluster in molecular form having the topology of the P(N) cluster has been devised. Reaction of the single cubane [(Tp)MoFe(3)S(4)Cl(3)](1)(-) with PEt(3) gives [(Tp)MoFe(3)S(4)(PEt(3))(3)](1+) (2), which upon reduction with BH(4)(-) affords the edge-bridged all-ferrous double cubane [(Tp)(2)Mo(2)Fe(6)S(8)(PEt(3))(4)] (4) (Tp = tris(pyrazolylhydroborate(1-)). Treatment of 4 with 3 equiv of HS(-) produces [(Tp)(2)Mo(2)Fe(6)S(9)(SH)(2)](3)(-) (7) as the Et(4)N(+) salt in 86% yield. The structure of 7 is built of two (Tp)MoFe(3)(mu(3)-S)(3) cuboidal fragments bridged by two mu(2)-S atoms and one mu(6)-S atom in an arrangement of idealized C(2) symmetry. The cluster undergoes three one-electron oxidation reactions and is oxidatively cleaved by p-tolylthiol to [(Tp)MoFe(3)S(4)(S-p-tol)(3)](2)(-) and by weak acids to [(Tp)MoFe(3)S(4)(SH)(3)](2-). The cluster core of 7 has the bridging pattern [Mo(2)Fe(6)(mu(2)-S)(2)(mu(3)-S)(6)(mu(6)-S)](1+) with the probable charge distribution [Mo(3+)(2)Fe(2+)(5)Fe(3+)S(9)](1+). Cluster 7 is a topological analogue of the P(N) cluster but differs in having two heteroatoms and two Fe-(mu(2)-S)-Fe instead of two Fe-(mu(2)-S(Cys))-Fe bridges. A best-fit superposition of the two cluster cores affords a weighted rms deviation in atom positions of 0.38 A. Cluster 7 is the first molecular topological analogue of the P(N) cluster. This structure had been prepared previously only as a fragment of complex high-nuclearity Mo-Fe-S clusters.

Topics: Biomimetic Materials; Coenzymes; Crystallography, X-Ray; Iron; Magnetic Resonance Spectroscopy; Metalloproteins; Models, Molecular; Molecular Structure; Molybdenum; Molybdenum Cofactors; Nitrogenase; Organometallic Compounds; Pteridines; Selenium Compounds; Sulfur

The nifNE gene products of Klebsiella pneumoniae are required for the in vivo and in vitro synthesis of the iron-molybdenum cofactor (FeMo-co) of nitrogenase. Derepression of nifNE mutants for nitrogenase resulted in the accumulation of a small molecule, factor F395. Factor F395 is protein associated in vivo. We report here initial spectral characterization of this factor.

Topics: Biological Factors; Coenzymes; Enzyme Repression; Genes, Bacterial; Klebsiella pneumoniae; Metalloproteins; Molybdenum Cofactors; Mutation; Nitrogen Fixation; Nitrogenase; Pteridines; Species Specificity

All molybdenum enzymes except nitrogenase contain a common molybdenum cofactor, whose organic moiety is a novel pterin called molybdopterin (MPT). To assist in elucidating the biosynthetic pathway of MPT, two MPT-deficient mutants of Escherichia coli K-12 were isolated. They lacked activities of the molybdenum enzymes nitrate reductase and formate dehydrogenase, did not reconstitute apo nitrate reductase from a Neurospora crassa nit-1 strain, and did not yield form A, a derivative of MPT. By P1 mapping, these two mutations mapped to chlA and chlE, loci previously postulated but never definitely shown to be involved in MPT biosynthesis. The two new mutations are in different genetic complementation groups from previously isolated chlA and chlE mutations and have been designated as chlM and chlN (closely linked to chlA and chlE, respectively). The reported presence of Mo cofactor activity in the chlA1 strain is shown to be due to in vitro synthesis of MPT through complementation between a trypsin-sensitive macromolecule from the chlA1 strain and a low-molecular-weight compound from the nit-l strain.

Topics: Chromatography, High Pressure Liquid; Coenzymes; Escherichia coli; Formate Dehydrogenases; Genes, Bacterial; Genetic Complementation Test; Metalloproteins; Molybdenum; Molybdenum Cofactors; Mutation; Neurospora crassa; Nitrate Reductase; Nitrate Reductases; Nitrogenase; Pteridines; Spectrometry, Fluorescence

Aerial oxidation of the iron-molybdenum cofactor (FeMoco) of Azotobacter vinelandii nitrogenase has been shown to yield either the tetrathiomolybdate ion ([MoS4]2-) or the oxotrithiomolybdate ion ([MoOS3]2-), depending on the reaction conditions. Thus, when N-methylformamide (NMF) solutions of FeMoco either were titrated with measured aliquots of air or were diluted with air-saturated NMF, [MoOS3]2- was found to be the predominant product while dilution of NMF solutions of FeMoco with air-saturated methanol produced [MoS4]2- almost exclusively. Similar aerial oxidation of solutions of chemically synthesized Fe-Mo-S clusters showed that significant information about the molybdenum environment in these species could be deduced from the nature of the elicited thiomolybdates. The differences in decomposition products as a function of solvent are postulated to be due to the loss through precipitation of the reducing agent sodium dithionite on addition of methanol but not NMF. These overall decomposition results are discussed in the context of recent X-ray absorption spectroscopic data which suggest the presence of an 'MoS3' core in FeMoco. A possible mechanism whereby [MoS4]2- might be rapidly formed from this core is presented.

Topics: Azotobacter; Coenzymes; Metalloproteins; Molybdenum; Molybdenum Cofactors; Nitrogenase; Oxidation-Reduction; Oxidoreductases; Pteridines; Spectrophotometry; Sulfur

Cells of Clostridium pasteurianum whose N source is switched from NH3 to N2 accumulate large amounts of molybdenum beginning 1.5 h before the detection of nitrogenase activity. Anaerobic multiphasic gel electrophoresis and anion-exchange chromatography were used to identify the molybdoproteins and molybdenum-containing components present in N2-fixing cells. In addition to molybdate, six distinct 99Mo-labeled species were detected, i.e., a membrane fragment, the MoFe protein of nitrogenase, formate dehydrogenase, a Mo "binding-storage" protein, a 30-kilodalton molybdoprotein, and a low-molecular-weight molybdenum species. Of these, the MoFe protein, formate dehydrogenase, and the Mo binding-storage protein were present in more than one zone because of complex formation with other proteins, partial denaturation, and variation in the amount of Mo bound to the protein, respectively. In addition to the six proteins, a soluble "free" Mo cofactor in the cytosol was detected by showing that it reconstituted nitrate reductase activity in crude extracts of the Neurospora crassa mutant nit-1.

Topics: Anaerobiosis; Bacterial Proteins; Clostridium; Coenzymes; Formate Dehydrogenases; Metalloproteins; Molecular Weight; Molybdenum; Molybdenum Cofactors; Nitrogenase; Pteridines; Sulfates

A single mutation, nifC1005 (Jin et al. Sci. Sin. 23:108-118, 1980), located between nifH and nifJ in the nif cluster of Klebsiella pneumoniae, genetically complemented mutations in each of the 17 known nif genes. This suggested that the mutation is located in a new nif gene. We showed by complementation analyses that only 3 of 12 nifJ mutations tested were complemented by nifC1005. Nitrogenase activity in cell extracts of the mutant with nifC1005 as well as NifJ- mutants was stimulated by the addition of the iron-molybdenum cofactor or nitrogenase component I. The molecular weight of the native NifJ protein is approximately 257,000--a dimer of identical subunits. Some nifC-/nifJ- or nifJ-/nifJ- merodiploids produced active but unstable nifJ proteins. Fine-structure mapping placed the nifC1005 allele within the nifJ gene bounded on both sides by well-characterized nifJ mutations. This indicates that the nifC1005 does not define a separate gene from nifJ. The data are consistent with the occurrence of intragenic complementation between two defective nifJ polypeptides. This explains the isolated examples of genetic complementation between the nifC1005 mutation and certain nifJ mutations.

Topics: Bacterial Proteins; Chromosome Mapping; Chromosomes, Bacterial; Coenzymes; Genes, Bacterial; Genetic Complementation Test; Hot Temperature; Iron; Klebsiella pneumoniae; Metalloproteins; Molecular Weight; Molybdenum; Molybdenum Cofactors; Mutation; Nitrogen Fixation; Nitrogenase; Pteridines

Reductive EPR and optical titrations of oxidized MoFe protein using reduced methyl viologen as reductant were used to quantitate the stoichiometry of the various spectroscopically and electrochemically distinct redox centers in the oxidized MoFe protein. Three centers were found to correlate with the EPR signal development (MoFe cofactor centers), and three centers were found to be independent of the EPR signal (P clusters) but to demonstrate distinct optical and kinetic properties. Oxidative EPR and optical titrations of reduced MoFe protein are reported which support the presence of three P-cluster centers. The optical titrations show a distinct change in kinetic behavior between the MoFe cofactor and P-cluster centers. Controlled potential coulometry demonstrates that incremental oxidation of reduced protein by methylene blue, thionine, or indigodisulfonate occurs specifically at three P-cluster sites. Subsequent oxidation by methylene blue and thionine (but not indigodisulfonate) causes the EPR signal to disappear. Three P-cluster sites, two EPR sites, and one presently uncharacterized site are suggested by the results of this study.

Topics: Anaerobiosis; Azotobacter; Coenzymes; Electron Spin Resonance Spectroscopy; Ferredoxins; Kinetics; Metalloproteins; Methylene Blue; Molybdenum; Molybdenum Cofactors; Molybdoferredoxin; Nitrogenase; Oxidation-Reduction; Pteridines