Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

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Cell biology and molecular basis of denitrification.

Molybdenum is the only second-row transition metal required by most living organisms, and is nearly universally distributed in biology. Enzymes containing molybdenum in their active sites have long been recognized,1 and at present over 50 molybdenum-containing enzymes have been purified and biochemically characterized; a great many more gene products have been annotated as putative molybdenum-containing proteins on the basis of genomic and bioinformatic analysis.2 In certain cases, our understanding of the relationship between enzyme structure and function is such that we can speak with confidence as to the detailed nature of the reaction mechanism and, with the availability of high-resolution X-ray crystal structures, the specific means by which transition states are stabilized and reaction rate is accelerated within the friendly confines of the active site. At the same time, our understanding of the biosynthesis of the organic cofactor that accompanies molybdenum (variously called molybdopterin or pyranopterin), the manner in which molybdenum is incorporated into it, and then further modified as necessary prior to insertion into apoprotein has also (in at least some cases) become increasingly well understood.

It is now well-established that all molybdenum-containing enzymes other than nitrogenase (in which molybdenum is incorporated into a [MoFe7S9] cluster of the active site) fall into three large and mutually exclusive families, as exemplified by the enzymes xanthine oxidase, sulfite oxidase, and DMSO reductase; these enzymes represent the focus of the present account.3 The structures of the three canonical molybdenum centers in their oxidized Mo(VI) states are shown in Figure 1, along with that for the pyranopterin cofactor. The active sites of members of the xanthine oxidase family have an LMoVIOS-(OH) structure with a square-pyramidal coordination geometry. The apical ligand is a Mo=O ligand, and the equatorial plane has two sulfurs from the enedithiolate side chain of the pyranopterin cofactor, a catalytically labile Mo–OH group, and most frequently a Mo=S. Nonfunctional forms of these enzymes exist in which the equatorial Mo=S is replaced with a second Mo=O; in at least one member of the family the Mo=S is replaced by a Mo=Se, and in others it is replaced by a more complex –S–Cu–S–Cys to give a binuclear center. Members of the sulfite oxidase family have a related LMoVIO2(S–Cys) active site, again square-pyramidal with an apical Mo=O and a bidentate enedithiolate Ligand (L) in the equatorial plane but with a second equatorial Mo=O (rather than Mo–OH) and a cysteine ligand contributed by the protein (rather than a Mo=S) completing the molybdenum coordination sphere. The final family is the most diverse structurally, although all members possess two (rather than just one) equiv of the pyranopterin cofactor and have an L2MoVIY(X) trigonal prismatic coordination geometry. DMSO reductase itself has a catalytically labile Mo=O as Y and a serinate ligand as X completing the metal coordination sphere of oxidized enzyme. Other family members have cysteine (the bacterial Nap periplasmic nitrate reductases), selenocysteine (formate dehydrogenase H), –OH (arsenite oxidase), or aspartate (the NarGHI dissimilatory nitrate reductases) in place of the serine. Some enzymes have S or even Se in place of the Mo=O group. Members of the DMSO reductase family exhibit a general structural homology to members of the aldehyde:ferredoxin oxidoreductase family of tungsten-containing enzymes;4 indeed, the first pyranopterin-containing enzyme to be crystallographically characterized was the tungsten-containing aldehyde:ferredoxin oxidoreductase from Pyrococcus furiosus,5 a fact accounting for why many workers in the field prefer “pyranopterin” (or, perhaps waggishly, “tungstopterin”) to “molybdopterin”. The term pyranopterin will generally be used in the present account.




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Figure 1


Active site structures for the three families of mononuclear molybdenum enzymes. The structures shown are, from left to right, for xanthine oxidase, sulfite oxidase, and DMSO reductase. The structure of the pyranopterin cofactor common to all of these enzymes (as well as the tungsten-containing enzymes) is given at the bottom.

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The Mononuclear Molybdenum Enzymes

The pterin molybdenum cofactors.

Nitrate respiration in relation to facultative metabolism in enterobacteria.

Publisher Summary This chapter focuses on the immunological basis and clinical experiences with neopterin as an indicator for activation of the cell-mediated immune system. Neopterin was isolated from larvae of bee, worker bees, and royal jelly. Comprehensive information on the chemistry of pteridines is provided. Synthetic methods for some natural pteridines are reviewed, and the reactivity of pteridines is examined. The chapter discusses some reactions that are important for measurement of neopterin in biological specimens. The low-weight metabolite neopterin is biosynthetically derived from guanosine triphosphate via 7, 8-dihydroneopterin triphosphate. In vitro, human monocytes/macrophages produce neopterin when stimulated by interferon-γ released from activated T cells. High neopterin levels were observed in clinical settings recognized to involve activation of cell-mediated immunity in acute allograft rejections, viral infections, infections by intracellular parasites and bacteria, autoimmune diseases, and certain malignancies. Studies of neopterin levels in groups at high risk for AIDS and in patients infected with HIV have demonstrated that activation of T lymphocytes and macrophages represents a crucial event for HIV production. In malignant diseases, the degree of neopterin elevation is a measure of the clinical activity and in some tumor types, serves as a measure of the extent of disease. In ovarian cancer, cancer of the uterine cervix, prostatic tumor, and carcinoma of the lung, neopterin is of predictive value.

Neopterin as marker for activation of cellular immunity: immunologic basis and clinical application.

Characterization of the molybdenum cofactor of sulfite oxidase, xanthine, oxidase, and nitrate reductase. Identification of a pteridine as a structural component.

The pterin component of the molybdenum cofactor. Structural characterization of two fluorescent derivatives.

The molybdenum cofactor common to a variety of molybdoenzymes has been shown to contain a novel pterin. The pterin has been isolated from sulfite oxidase from several sources, xanthine-oxidizing enzymes from milk and chicken liver, and nitrate reductase of Chlorella vulgaris after denaturation of the proteins in the presence of I2. Investigation of the anionic nature of the isolated pterin has revealed that it is a monophosphate ester susceptible to cleavage by alkaline phosphatase. Quantitative analyses have shown that one molecule of the pterin phosphate is associated with each molybdenum atom in sulfite oxidase. Studies to date have shown that the pterin is present in a reduced form in sulfite oxidase and xanthine dehydrogenase, and that in situ oxidation of the pterin leads to inactivation of sulfite oxidase.

The pterin of the molybdenum cofactor.

The molybdenum cofactor has been isolated in an oxidized inactive form from purified molybdoenzymes. The isolated material is shown to be a novel pterin. The active cofactor is presumably composed of molybdenum and a reduced form of the pterin.

Bryan E. Hainline

Papers

Characterization of the molybdenum cofactor of sulfite oxidase, xanthine, oxidase, and nitrate reductase. Identification of a pteridine as a structural component.

The pterin component of the molybdenum cofactor. Structural characterization of two fluorescent derivatives.

The pterin of the molybdenum cofactor.

Characterization of the Molybdenum Cofactor of Sulfite Oxidase, Xanthine Oxidase, and Nitrate Reductase

The Pterin Component of the Molybdenum Cofactor (Molybdopterin): Relationship to Urothione