molybdenum-cofactor and tungsten-cofactor

The oxidoreductase YdhV in Escherichia coli has been predicted to belong to the family of molybdenum/tungsten cofactor (Moco/Wco)-containing enzymes. In this study, we characterized the YdhV protein in detail, which shares amino acid sequence homology with a tungsten-containing benzoyl-CoA reductase binding the bis-W-MPT (for metal-binding pterin) cofactor. The cofactor was identified to be of a bis-Mo-MPT type with no guanine nucleotides present, which represents a form of Moco that has not been found previously in any molybdoenzyme. Our studies showed that YdhV has a preference for bis-Mo-MPT over bis-W-MPT to be inserted into the enzyme. In-depth characterization of YdhV by X-ray absorption and electron paramagnetic resonance spectroscopies revealed that the bis-Mo-MPT cofactor in YdhV is redox active. The bis-Mo-MPT and bis-W-MPT cofactors include metal centers that bind the four sulfurs from the two dithiolene groups in addition to a cysteine and likely a sulfido ligand. The unexpected presence of a bis-Mo-MPT cofactor opens an additional route for cofactor biosynthesis in E. coli and expands the canon of the structurally highly versatile molybdenum and tungsten cofactors.

Topics: Coenzymes; Electron Spin Resonance Spectroscopy; Escherichia coli; Escherichia coli Proteins; Ferredoxins; Guanine Nucleotides; Metalloproteins; Molecular Structure; Molybdenum; Molybdenum Cofactors; Organometallic Compounds; Oxidation-Reduction; Oxidoreductases; Pteridines; Pterins

A density functional theory study of the influence of the various functional groups of the molybdopterin ligand on electronic and geometric properties of active-site models for the molybdenum and tungsten cofactors has been undertaken. We used analogous molybdenum and tungsten complexes with increasingly accurate representation of the molybdopterin ligands and compared bond lengths, angles, charge distribution, composition of the binding orbitals, as well as the redox potentials in relation to each other. On the basis of our findings, we suggest using ligand systems including the pyrane and the pyrazine rings, besides the dithiolene function, to obtain sufficiently reliable computational, but also synthetic, models for the molybdenum and tungsten cofactors, whereas the second ring of the pterin might be neglected for efficiency reasons.

Topics: Catalysis; Catalytic Domain; Coenzymes; Computational Biology; Ligands; Metalloproteins; Models, Molecular; Molecular Structure; Molybdenum; Molybdenum Cofactors; Organometallic Compounds; Pteridines; Pterins; Tungsten

Molybdenum (Mo) and tungsten (W) enzymes catalyze important redox reactions in the global carbon, nitrogen, and sulfur cycles. Except in nitrogenases both metals are exclusively associated with a unique metal-binding pterin (MPT) that is synthesized by a conserved multistep biosynthetic pathway, which ends with the insertion and thereby biological activation of the respective element. Although the biosynthesis of Mo cofactors has been intensively studied in various systems, the biogenesis of W-containing enzymes, mostly found in archaea, is poorly understood. Here, we describe the function of the Pyrococcus furiosus MoaB protein that is homologous to bacterial (such as MogA) and eukaryotic proteins (such as Cnx1) involved in the final steps of Mo cofactor synthesis. MoaB reconstituted the function of the homologous Escherichia coli MogA protein and catalyzes the adenylylation of MPT in a Mg2+ and ATP-dependent way. At room temperature reaction velocity was similar to that of the previously described plant Cnx1G domain, but it was increased up to 20-fold at 80 degrees C. Metal and nucleotide specificity for MPT adenylylation is well conserved between W and Mo cofactor synthesis. Thermostability of MoaB is believed to rely on its hexameric structure, whereas homologous mesophilic MogA-related proteins form trimers. Comparison of P. furiosus MoaB to E. coli MoaB and MogA revealed that only MogA is able to catalyze MPT adenylylation, whereas E. coli MoaB is inactive. In summary, MogA, Cnx1G, and MoaB proteins exhibit the same adenylyl transfer activity essential for metal insertion in W or Mo cofactor maturation.

Topics: Adenosine Triphosphate; Amino Acid Sequence; Amino Acid Substitution; Coenzymes; Escherichia coli; Escherichia coli Proteins; Kinetics; Metalloproteins; Models, Chemical; Molecular Sequence Data; Molybdenum Cofactors; Nitrate Reductase; Organometallic Compounds; Protein Binding; Pteridines; Pterins; Pyrococcus furiosus; Recombinant Proteins; Sequence Homology, Amino Acid; Substrate Specificity; Sulfurtransferases; Temperature; Transfection

We have identified a highly conserved RNA motif located upstream of genes encoding molybdate transporters, molybdenum cofactor (Moco) biosynthesis enzymes, and proteins that utilize Moco as a coenzyme. Bioinformatics searches have identified 176 representatives in gamma-Proteobacteria, delta-Proteobacteria, Clostridia, Actinobacteria, Deinococcus-Thermus species and DNAs from environmental samples. Using genetic assays, we demonstrate that a Moco RNA in Escherichia coli associated with the Moco biosynthetic operon controls gene expression in response to Moco production. In addition, we provide evidence indicating that this conserved RNA discriminates against closely related analogues of Moco. These results, together with extensive phylogenetic conservation and typical gene control structures near some examples, indicate that representatives of this structured RNA represent a novel class of riboswitches that sense Moco. Furthermore, we identify variants of this RNA that are likely to be triggered by the related tungsten cofactor (Tuco), which carries tungsten in place of molybdenum as the metal constituent.

Topics: 5' Untranslated Regions; Base Sequence; Coenzymes; Computational Biology; Conserved Sequence; Escherichia coli; Gene Expression Regulation, Bacterial; Ligands; Metalloproteins; Molecular Sequence Data; Molybdenum; Molybdenum Cofactors; Mutation; Operon; Organometallic Compounds; Phylogeny; Pteridines; Pterins; RNA, Bacterial

The crystal structure of the tungsten-containing aldehyde ferredoxin oxidoreductase (AOR) from Pyrococcus furiosus, a hyperthermophilic archaeon (formerly archaebacterium) that grows optimally at 100 degrees C, has been determined at 2.3 angstrom resolution by means of multiple isomorphous replacement and multiple crystal form averaging. AOR consists of two identical subunits, each containing an Fe4S4 cluster and a molybdopterin-based tungsten cofactor that is analogous to the molybdenum cofactor found in a large class of oxotransferases. Whereas the general features of the tungsten coordination in this cofactor were consistent with a previously proposed structure, each AOR subunit unexpectedly contained two molybdopterin molecules that coordinate a tungsten by a total of four sulfur ligands, and the pterin system was modified by an intramolecular cyclization that generated a three-ringed structure. In comparison to other proteins, the hyperthermophilic enzyme AOR has a relatively small solvent-exposed surface area, and a relatively large number of both ion pairs and buried atoms. These properties may contribute to the extreme thermostability of this enzyme.

Topics: Aldehyde Oxidoreductases; Amino Acid Sequence; Archaea; Binding Sites; Coenzymes; Computer Graphics; Crystallography, X-Ray; Enzyme Stability; Ferrous Compounds; Metalloproteins; Models, Molecular; Molecular Sequence Data; Molybdenum Cofactors; Organometallic Compounds; Oxidation-Reduction; Protein Conformation; Protein Structure, Secondary; Pteridines; Pterins; Surface Properties; Temperature; Tungsten

The hyperthermophilic Archaea represent some of the most ancient organisms on earth. A study of enzymatic cofactors in these organisms could provide basic information on the origins of related cofactors in man and other more recently evolved organisms. To this end, the nature of the tungsten cofactor in aldehyde ferredoxin oxidoreductases from Pyrococcus furiosus and ES-4 and in formaldehyde ferredoxin oxidoreductases from P. furiosus and Thermococcus litoralis has been investigated. All four proteins contain molybdopterin, previously characterized as the organic component of the molybdenum cofactor in a large number of molybdoenzymes. Molybdopterin was identified by conversion to the dicarboxamidomethyl derivative by alkylation of the vicinal sulfhydryl groups on the pterin side chain and by conversion to the oxidized fluorescent derivative, Form A. The pterin of the tungsten cofactor in the four enzymes was examined for the presence of appended GMP, CMP, AMP, or IMP previously observed in molybdenum cofactors of some molybdoenzymes. No evidence for the presence of a molybdopterin dinucleotide or other modified form of molybdopterin was obtained. These results further document the essential nature of molybdopterin for the function of molybdenum and tungsten enzymes in diverse life forms.

Topics: Aldehyde Oxidoreductases; Archaea; Chromatography, High Pressure Liquid; Coenzymes; Metalloproteins; Molecular Structure; Molybdenum Cofactors; Organometallic Compounds; Protein Conformation; Pteridines; Pterins; Spectrometry, Fluorescence; Spectrophotometry, Ultraviolet