Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:1.7.1.2 (nitrate reductase)
3,861 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Anaerobic metabolism of the simplest, best understood enteric bacteria such as Escherichia coli is unexpectedly complex. Recent studies of the biochemistry and genetics of nitrate reduction via nitrite to ammonia by enteric bacteria have provided insights into the reasons for this complexity. An NADH-dependent nitrite reductase in the cytoplasm works in partnership with the respiratory nitrate reductase on the cytoplasmic side of the membrane when nitrate is abundant. There is also an electrogenic, formate-dependent nitrite reductase ready to work in partnership with a periplasmic nitrate reductase when nitrite is available but nitrate is scarce. A third E. coli nitrate reductase, NarZYWV, and the poorly expressed formate dehydrogenase O possibly facilitate rapid adaptation to oxygen starvation pending the synthesis of the major respiratory formate-nitrate oxidoreductase. Although most anaerobically expressed genes are subject to transcription control, none of them are totally switched off. This enables the bacteria to be ready for a change in fortune: when growing anaerobically with nitrate, they can respond equally rapidly whether times get better with the arrival of oxygen, or get worse when the nitrate is depleted. Far from being redundant, the complexity is essential for survival in a changing environment.
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PMID:Nitrate reduction to ammonia by enteric bacteria: redundancy, or a strategy for survival during oxygen starvation? 891 48

The secondary metabolite hydrogen cyanide (HCN) is produced by Pseudomonas fluorescens from glycine, essentially under microaerophilic conditions. The genetic basis of HCN synthesis in P. fluorescens CHA0 was investigated. The contiguous structural genes hcnABC encoding HCN synthase were expressed from the T7 promoter in Escherichia coli, resulting in HCN production in this bacterium. Analysis of the nucleotide sequence of the hcnABC genes showed that each HCN synthase subunit was similar to known enzymes involved in hydrogen transfer, i.e., to formate dehydrogenase (for HcnA) or amino acid oxidases (for HcnB and HcnC). These similarities and the presence of flavin adenine dinucleotide- or NAD(P)-binding motifs in HcnB and HcnC suggest that HCN synthase may act as a dehydrogenase in the reaction leading from glycine to HCN and CO2. The hcnA promoter was mapped by primer extension; the -40 sequence (TTGGC ... ATCAA) resembled the consensus FNR (fumarate and nitrate reductase regulator) binding sequence (TTGAT ... ATCAA). The gene encoding the FNR-like protein ANR (anaerobic regulator) was cloned from P. fluorescens CHA0 and sequenced. ANR of strain CHA0 was most similar to ANR of P. aeruginosa and CydR of Azotobacter vinelandii. An anr mutant of P. fluorescens (CHA21) produced little HCN and was unable to express an hcnA-lacZ translational fusion, whereas in wild-type strain CHA0, microaerophilic conditions strongly favored the expression of the hcnA-lacZ fusion. Mutant CHA21 as well as an hcn deletion mutant were impaired in their capacity to suppress black root rot of tobacco, a disease caused by Thielaviopsis basicola, under gnotobiotic conditions. This effect was most pronounced in water-saturated artificial soil, where the anr mutant had lost about 30% of disease suppression ability, compared with wild-type strain CHA0. These results show that the anaerobic regulator ANR is required for cyanide synthesis in the strictly aerobic strain CHA0 and suggest that ANR-mediated cyanogenesis contributes to the suppression of black root rot.
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PMID:Characterization of the hcnABC gene cluster encoding hydrogen cyanide synthase and anaerobic regulation by ANR in the strictly aerobic biocontrol agent Pseudomonas fluorescens CHA0. 962 Sep 70

The X-ray absorption spectra at the molybdenum and selenium K-edges and the tungsten L2,3-edges are acquired for a set of 14 Mo(IV) and W(IV,VI) bis(dithiolene) complexes related to the active sites of molybdo- and tungstoenzymes. The set includes square pyramidal [MoIVL(S2C2Me2)2]- (L = O2-, R3SiO-, RO-, RS-, RSe-) and [WIV(OR)(S2C2Me2)2]-, distorted trigonal prismatic [MoIV(CO)(SeR)(S2C2Me2)2]- and [WIV(CO)L(S2C2Me2)2]- (L = RS-, RSe-), and distorted octahedral [WVIO(OR)(S2C2Me2)2]-. The dithiolene simulates the pterin-dithiolene cofactor ligand, and L represents a protein ligand. Bond lengths are determined by EXAFS analysis using the GNXAS protocol. Normalized edge spectra, non-phase-shift-corrected Fourier transforms, and EXAFS data and fits are presented. Bond lengths determined by EXAFS and X-ray crystallography agree to < or = 0.02 A as do the M-Se distances determined by both metal and selenium EXAFS. The complexes [MoIV(QR)(S2C2Me2)2]- simulate protein ligation by the DMSO reductase family of enzymes, including DMSO reductase itself (Q = O), dissimilatory nitrate reductase (Q = S), and formate dehydrogenase (Q = Se). Edge shifts of these complexes correlate with the ligand electronegativities. Terminal ligand binding is clearly distinguished in the presence of four Mo-S(dithiolene) interactions. Similarly, five-coordinate [ML(S2C2Me2)2]- and six-coordinate [M(CO)L(S2C2Me2)2]- are distinguishable by edge and EXAFS spectra. This study expands a previous XAS investigation of bis(dithiolene)metal(IV,V,VI) complexes (Musgrave, K. B.; Donahue, J. P.; Lorber, C.; Holm, R. H.; Hedman, B.; Hodgson, K. O. J. Am. Chem. Soc. 1999, 121, 10297) by including a larger inventory of molecules with variant physiologically relevant terminal ligation. The previous and present XAS results should prove useful in characterizing and refining metric features and structures of enzyme sites.
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PMID:X-ray spectroscopy of enzyme active site analogues and related molecules: bis(dithiolene)molybdenum(IV) and -tungsten(IV,VI) complexes with variant terminal ligands. 1115 82

The tungsten-containing formate dehydrogenase (W-FDH) isolated from Desulfovibrio gigas has been crystallized in space group P2(1), with cell parameters a = 73.8 A, b = 111.3 A, c = 156.6 A and beta = 93.7 degrees. These crystals diffract to beyond 2.0 A on a synchrotron radiation source. W-FDH is a heterodimer (92 kDa and 29 kDa subunits) and two W-FDH molecules are present in the asymmetric unit. Although a molecular replacement solution was found using the periplasmic nitrate reductase as a search model, additional phasing information was needed. A multiple-wavelength anomalous dispersion (MAD) dataset was collected at the W- and Fe-edges, at four different wavelengths. Anomalous and dispersive difference data allowed us to unambiguously identify the metal atoms bound to W-FDH as one W atom with a Se-cysteine ligand as well as one [4Fe-4S] cluster in the 92 kDa subunit, and three additional [4Fe-4S] centers in the smaller 29 kDa subunit. The D. gigas W-FDH was previously characterized based on metal analysis and spectroscopic data. One W atom was predicted to be bound to two molybdopterin guanine dinucleotide (MGD) pterin cofactors and two [4Fe-4S] centers were proposed to be present. The crystallographic data now reported reveal a selenium atom (as a Se-cysteine) coordinating to the W site, as well as two extra [4Fe-4S] clusters not anticipated before. The EPR data were re-evaluated in the light of these new results.
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PMID:Tungsten-containing formate dehydrogenase from Desulfovibrio gigas: metal identification and preliminary structural data by multi-wavelength crystallography. 1137 98

A series of dithiolene complexes of the general type [Mo(IV)(QR')(S(2)C(2)Me(2))(2)](1)(-) has been prepared and structurally characterized as possible structural and reactivity analogues of reduced sites of the enzymes DMSOR and TMAOR (QR' = PhO(-), 2-AdO(-), Pr(i)()O(-)), dissimilatory nitrate reductase (QR' = 2-AdS(-)), and formate dehydrogenase (QR' = 2-AdSe(-)). The complexes are square pyramidal with the molybdenum atom positioned 0.74-0.80 A above the S(4) mean plane toward axial ligand QR'. In part on the basis of a recent clarification of the active site of oxidized Rhodobacter sphaeroides DMSOR (Li, H.-K.; Temple, C.; Rajagopalan, K. V.; Schindelin, H. J. Am. Chem. Soc. 2000, 122, 7673), we have adopted the minimal reaction paradigm Mo(IV) + XO right arrow over left arrow Mo(VI)O + X involving desoxo Mo(IV), monooxo Mo(VI), and substrate/product XO/X for direct oxygen atom transfer of DMSOR and TMAOR enzymes. The [Mo(OR')(S(2)C(2)Me(2))(2)](1)(-) species carry dithiolene and anionic oxygen ligands intended to simulate cofactor ligand and serinate binding in DMSOR and TMAOR catalytic sites. In systems with N-oxide and S-oxide substrates, the observed overall reaction sequence is [Mo(IV)(OR')(S(2)C(2)Me(2))(2)](1)(-) + XO --> [Mo(VI)O(OR')(S(2)C(2)Me(2))(2)](1)(-) --> [Mo(V)O(S(2)C(2)Me(2))(2)](1)(-). Direct oxo transfer in the first step has been proven by isotope labeling. The reactivity of [Mo(OPh)(S(2)C(2)Me(2))(2)](1)(-) (1) has been the most extensively studied. In second-order reactions, 1 reduces DMSO and (CH(2))(4)SO (k(2) approximately 10(-)(6), 10(-)(4) M(-)(1) s(-)(1); DeltaS(double dagger) = -36, -39 eu) and Me(3)NO (k(2) = 200 M(-)(1) s(-)(1); DeltaS(double dagger) = -21 eu) in acetonitrile at 298 K. Activation entropies indicate an associative transition state, which from relative rates and substrate properties is inferred to be concerted with X-O bond weakening and Mo-O bond making. The Mo(VI)O product in the first step, such as [Mo(VI)O(OR')(S(2)C(2)Me(2))(2)](1)(-), is an intermediate in the overall reaction sequence, inasmuch as it is too unstable to isolate and decays by an internal redox process to a Mo(V)O product, liberating an equimolar quantity of phenol. This research affords the first analogue reaction systems of biological N-oxide and S-oxide substrates that are based on desoxo Mo(IV) complexes with biologically relevant coordination. Oxo-transfer reactions in analogue systems are substantially slower than enzyme systems based on a k(cat)/K(M) criterion. An interpretation of this behavior requires more information on the rate-limiting step(s) in enzyme catalytic cycles. (2-Ad = 2-adamantyl, DMSOR = dimethyl sulfoxide reductase, TMAOR = trimethylamine N-oxide reductase)
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PMID:Bis(dithiolene)molybdenum analogues relevant to the DMSO reductase enzyme family: synthesis, structures, and oxygen atom transfer reactions and kinetics. 1145 13

In contrast to its parent strain, transposon Tn5-Mob insertion mutant HB6 of the facultative chemoautotroph Ralstonia eutropha was unable to grow organoautotrophically on formate and exhibited no activity of Mo-dependent, membrane-bound formate dehydrogenase (M-FDH) when cultivated mixotrophically on fructose plus formate. The activity of another molybdoenzyme, the soluble, NAD+-linked formate dehydrogenase which is the key enzyme of formate utilization in R. eutropha, was greatly diminished in the mutant. HB6 also lacked the W-dependent M-FDH activities that were newly discovered in organoautotrophically, lithoautotrophically, or mixotrophically grown wildtype cells. However, an additional W-dependent M-FDH activity, observed in heterotrophically grown stationary-phase cells, was present in the mutant although at a considerably reduced level. Sequence analyses of the complementing chromosomal wildtype and the corresponding mutant DNA fragment revealed the transposon insertion to be located in moeA, a gene involved in the biosynthesis of the molybdopterin cofactor (MoCo). Nevertheless, mutant HB6 was able to grow on xanthine as carbon and energy source and with nitrate as nitrogen source. The utilization of these substrates requires the function of the MoCo-containing enzymes xanthine dehydrogenase and assimilatory nitrate reductase, respectively, that were still active in the mutant. A moeA deletion mutant exhibited the same phenotype as that of HB6. The moeA gene belongs to an unusual mol operon consisting of four genes (moeA, moaD, moaE, and moaF) and being constitutively expressed at low level. Unlike MoeA, the large subunit of molybdopterin synthase encoded by moaE is essential for molybdopterin biosynthesis as was evident by the phenotype of a moaE deletion mutant. MoaF is a novel gene product which showed no similarity to proteins with known function but was indispensable for reconstituting organoautotrophic growth in HB6. The findings suggest that MoeA of R. eutropha is differentially involved in the biosynthesis or incorporation of pterin cofactors of/into the various molybdo- and tungstoenzymes.
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PMID:Involvement of an unusual mol operon in molybdopterin cofactor biosynthesis in Ralstonia eutropha. 1154 79

Dissimilatory nitrate reductase (Nar) was solubilized and partially purified from the large particle (mitochondrial) fraction of the denitrifying fungus Fusarium oxysporum and characterized. Many lines of evidence showed that the membrane-bound Nar is distinct from the soluble, assimilatory nitrate reductase. Further, the spectral and other properties of the fungal Nar were similar to those of dissimilatory Nars of Escherichia coli and denitrifying bacteria, which are comprised of a molybdoprotein, a cytochrome b, and an iron-sulfur protein. Formate-nitrate oxidoreductase activity was also detected in the mitochondrial fraction, which was shown to arise from the coupling of formate dehydrogenase (Fdh), Nar, and a ubiquinone/ubiquinol pool. This is the first report of the occurrence in a eukaryote of Fdh that is associated with the respiratory chain. The coupling with Fdh showed that the fungal Nar system is more similar to that involved in the nitrate respiration by Escherichia coli than that in the bacterial denitrifying system. Analyses of the mutant species of F. oxysporum that were defective in Nar and/or assimilatory nitrate reductase conclusively showed that Nar is essential for the fungal denitrification.
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PMID:Nitrate reductase-formate dehydrogenase couple involved in the fungal denitrification by Fusarium oxysporum. 1192 96

Desulfovibrio gigas formate dehydrogenase is the first representative of a tungsten-containing enzyme from a mesophile that has been structurally characterized. It is a heterodimer of 110 and 24 kDa subunits. The large subunit, homologous to E. coli FDH-H and to D. desulfuricans nitrate reductase, harbors the W site and one [4Fe-4S] center. No small subunit ortholog containing three [4Fe-4S] clusters has been reported. The structural homology with E. coli FDH-H shows that the essential residues (SeCys158, His159, and Arg407) at the active site are conserved. The active site is accessible via a positively charged tunnel, while product release may be facilitated, for H(+) by buried waters and protonable amino acids and for CO(2) through a hydrophobic channel.
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PMID:Gene sequence and the 1.8 A crystal structure of the tungsten-containing formate dehydrogenase from Desulfovibrio gigas. 1222 Apr 97

Operons coding for the enzyme arsenite oxidase have been detected in the genomes from Archaea and Bacteria by Blast searches using the amino acid sequences of the respective enzyme characterized in two different beta-proteobacteria as templates. Sequence analyses show that in all these species, arsenite oxidase is transported over the cytoplasmic membrane via the tat system and most probably remains membrane attached by an N-terminal transmembrane helix of the Rieske subunit. The biochemical and biophysical data obtained for arsenite oxidase in the green filamentous bacterium Chloroflexus aurantiacus allow a structural model of the enzyme's membrane association to be proposed. Phylogenies for the two constituent subunits (i.e., the molybdopterin-containing and the Rieske subunit) of the heterodimeric enzyme and their respective homologs in DMSO-reductase, formate dehydrogenase, nitrate reductase, and the Rieske/cytb complexes were calculated from multiple sequence alignments. The obtained phylogenetic trees indicate an early origin of arsenite oxidase before the divergence of Archaea and Bacteria. Evolutionary implications of these phylogenies are discussed.
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PMID:Arsenite oxidase, an ancient bioenergetic enzyme. 1267 50

Molybdenum and tungsten are second- and third-row transition elements, respectively, which are found in a mononuclear form in the active site of a diverse group of enzymes that generally catalyze oxygen atom transfer reactions. Mononuclear Mo-containing enzymes have been classified into three families: xanthine oxidase, DMSO reductase, and sulfite oxidase. The proteins of the DMSO reductase family present the widest diversity of properties among its members and our knowledge about this family was greatly broadened by the study of the enzymes nitrate reductase and formate dehydrogenase, obtained from different sources. We discuss in this review the information of the better characterized examples of these two types of Mo enzymes and W enzymes closely related to the members of the DMSO reductase family. We briefly summarize, also, the few cases reported so far for enzymes that can function either with Mo or W at their active site.
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PMID:Mo and W bis-MGD enzymes: nitrate reductases and formate dehydrogenases. 1531 35


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