| evolutionary persistence of the molybdopyranopterin-containing sulfite oxidase protein fold. | summary: the importance of molybdoenzymes is exemplified both by the debilitating and fatal human diseases caused by their deficiency and by their persistence throughout evolution. here, we show that the protein fold of the molybdopyranopterin-containing domain of sulfite oxidase (the suox fold) can be found in all three domains of life. analyses of sequence data and protein structure comparisons (secondary structure matching) show that the suox fold is found in enzymes that have quite distinct ... | 2008 | 18535145 |
| sulfite oxidizing enzymes. | sulfite oxidizing enzymes are essential mononuclear molybdenum (mo) proteins involved in sulfur metabolism of animals, plants and bacteria. there are three such enzymes presently known: (1) sulfite oxidase (so) in animals, (2) so in plants, and (3) sulfite dehydrogenase (sdh) in bacteria. x-ray crystal structures of enzymes from all three sources (chicken so, arabidopsis thaliana so, and starkeya novella sdh) show nearly identical square pyramidal coordination around the mo atom, even though the ... | 2007 | 17459792 |
| sulfur k-edge spectroscopic investigation of second coordination sphere effects in oxomolybdenum-thiolates: relationship to molybdenum-cysteine covalency and electron transfer in sulfite oxidase. | second-coordination sphere effects such as hydrogen bonding and steric constraints that provide for specific geometric configurations play a critical role in tuning the electronic structure of metalloenzyme active sites and thus have a significant effect on their catalytic efficiency. crystallographic characterization of vertebrate and plant sulfite oxidase (so) suggests that an average o(oxo)-mo-s(cys)-c dihedral angle of approximately 77 degrees exists at the active site of these enzymes. this ... | 2007 | 17291118 |
| starkeya koreensis sp. nov., isolated from rice straw. | a facultatively chemolithoautotrophic, gram-negative, aerobic, highly curved rod-shaped, non-motile, non-spore-forming bacterium, strain jip08(t), was isolated from rice straw in daejeon, south korea. strain jip08(t) produced colourless colonies (1.0-1.5 mm) on r2a medium after 3 days. on the basis of 16s rrna gene sequence similarity, strain jip08(t) was shown to belong to the alpha-2 subclass of the proteobacteria, and was most closely related to starkeya novella iam 12100(t) (98.6 %), angulom ... | 2006 | 17012571 |
| structure of the active site of sulfite dehydrogenase from starkeya novella. | in this paper, we report the results of molybdenum k-edge x-ray absorption studies performed on the oxidized and reduced active sites of the sulfite dehydrogenase from starkeya novella. our results provide the first direct structural information on the active site of the oxidized form of this enzyme and confirm the conclusions derived from protein crystallography that the molybdenum coordination is analogous to that of the sulfite oxidases. the molybdenum atom of the oxidized enzyme is bound by ... | 2006 | 16933953 |
| kinetic and structural evidence for the importance of tyr236 for the integrity of the mo active site in a bacterial sulfite dehydrogenase. | the sulfite dehydrogenase from starkeya novella is the only known sulfite-oxidizing enzyme that forms a permanent heterodimeric complex between a molybdenum and a heme c-containing subunit and can be crystallized in an electron transfer competent conformation. tyr236 is a highly conserved active site residue in sulfite oxidoreductases and has been shown to interact with a nearby arginine and a molybdenum-oxo ligand that is involved in catalysis. we have created a tyr236 to phe substitution in th ... | 2006 | 16893171 |
| structural study of two proteins sige and orf1 to predict their roles in the biochemical oxidation of sulfur anions via the global sulfur oxidation operon (sox). | microbial redox reactions involving inorganic sulfur compounds in the environment are one of the major reactions of the global sulfur cycle. these reactions are mediated by phylogenetically diverse prokaryotes containing the sulfur oxidizing gene cluster (sox). the sox gene cluster of alpha-proteobacteria comprises of at least 15 genes, which form two transcriptional units. recently two new orfs, which code for proteins named, sige and orf1, were identified in starkeya novella. sequence analyses ... | 2006 | 16720104 |
| diverse bacteria associated with root nodules of spontaneous legumes in tunisia and first report for nifh-like gene within the genera microbacterium and starkeya. | we characterized 34 endophytic bacterial isolates associated to root nodules collected from spontaneous legumes in the arid zone of tunisia by 16s rdna polymerase chain reaction (pcr)-restriction fragment length polymorphism, whole cell protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page), 16s rdna and 16s-23s rdna internal transcribed spacer sequencing. phylogenetically, these isolates belong to the branches containing the genera inquilinus, bosea, rhodopseudomonas, para ... | 2006 | 16598639 |
| the hierarchical system of the 'alphaproteobacteria': description of hyphomonadaceae fam. nov., xanthobacteraceae fam. nov. and erythrobacteraceae fam. nov. | phylogenetic analysis of the class 'alphaproteobacteria', including physiologically diverse species, was conducted by using small-subunit rrna gene sequences. the 16s rrna gene sequences of 261 species in the class 'alphaproteobacteria' were obtained from genbank/embl/ddbj for constructing a phylogenetic tree by using maximum-likelihood analysis. in the resulting tree, members of the class 'alphaproteobacteria' were subdivided into five major clusters, which were compared with the taxonomic outl ... | 2005 | 16166687 |
| molecular basis of intramolecular electron transfer in sulfite-oxidizing enzymes is revealed by high resolution structure of a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit. | sulfite-oxidizing molybdoenzymes convert the highly reactive and therefore toxic sulfite to sulfate and have been identified in insects, animals, plants, and bacteria. although the well studied enzymes from higher animals serve to detoxify sulfite that arises from the catabolism of sulfur-containing amino acids, the bacterial enzymes have a central role in converting sulfite formed during dissimilatory oxidation of reduced sulfur compounds. here we describe the structure of the starkeya novella ... | 2005 | 15863498 |
| a recombinant diheme soxax cytochrome - implications for the relationship between epr signals and modified heme-ligands. | the multiheme soxax proteins are notable for their unusual heme ligation (his/cys-persulfide in the soxa subunit) and the complexity of their epr spectra. the diheme soxax protein from starkeya novella has been expressed using rhodobacter capsulatus as a host expression system. rsoxax was correctly formed in the periplasm of the host and contained heme c in similar amounts as the native soxax. esi-ms showed that the full length rsoxa, in spite of never having undergone catalytic turnover, existe ... | 2005 | 15848194 |
| polysaccharide-producing bacteria isolated from paper machine slime deposits. | development of novel enzymatic methods for slime deposit control in paper mills requires knowledge of polysaccharide-producing organisms and the polysaccharide structures present in deposits. in this work, 27 polysaccharide-producing bacteria were isolated from slime samples collected from different parts of a paper machine. most of the isolates produced polysaccharides in liquid culture and nine of them were selected for production of polysaccharides for characterisation. the selected isolates ... | 2005 | 15750806 |
| a sulphite respiration system in the chemoheterotrophic human pathogen campylobacter jejuni. | the ability to use sulphite as a respiratory electron donor is usually associated with free-living chemolithotrophic sulphur-oxidizing bacteria. however, this paper shows that the chemoheterotrophic human pathogen campylobacter jejuni has the ability to respire sulphite, with oxygen uptake rates of 23 +/- 8 and 28 +/- 15 nmol o(2) min(-1) (mg cell protein)(-1) after the addition of 0.5 mm sodium sulphite or metabisulphite, respectively, to intact cells. the c. jejuni nctc 11168 cj0004c and cj000 ... | 2005 | 15632441 |
| crystallization and preliminary x-ray analysis of sulfite dehydrogenase from starkeya novella. | crystals of purified heterodimeric sulfite dehydrogenase from starkeya novella have been grown using vapour diffusion. x-ray diffraction data have been collected from crystals of the native protein at lambda = 1.0 a and close to the iron absorption edge at lambda = 1.737 a. the crystals belong to space group p2(1)2(1)2, with unit-cell parameters a = 97.5, b = 92.5, c = 55.9 a. native data have been recorded to 1.8 a resolution and fe-edge data to 2.5 a. | 2004 | 15502330 |
| cytochrome c551 from starkeya novella: characterization, spectroscopic properties, and phylogeny of a diheme protein of the soxax family. | cytochromes from the soxax family have a major role in thiosulfate oxidation via the thiosulfate-oxidizing multi-enzyme system (tomes). previously characterized soxax proteins from rhodovulum sulfidophilum and paracoccus pantotrophus contain three heme c groups, two of which are located on the soxa subunit. in contrast, the soxax protein purified from starkeya novella was found to contain only two heme groups. mass spectrometry showed that a disulfide bond replaced the second heme group found in ... | 2004 | 14645228 |
| intramolecular electron transfer in a bacterial sulfite dehydrogenase. | sulfite dehydrogenase (sdh) from starkeya novella, a sulfite-oxidizing molybdenum-containing enzyme, has a novel tightly bound alphabeta-heterodimeric structure in which the mo cofactor and the c-type heme are located on different subunits. flash photolysis studies of intramolecular electron transfer (iet) in sdh show that the process is first-order, independent of solution viscosity, and not inhibited by sulfate, which strongly indicates that iet in sdh proceeds directly through the protein med ... | 2003 | 14640631 |
| direct electrochemistry of a bacterial sulfite dehydrogenase. | sulfite dehydrogenase from starkeya novella is an alphabeta heterodimer comprising a 40.6 kda subunit (containing the mo cofactor) and a smaller 8.8 kda heme c subunit. the enzyme catalyses the oxidation of sulfite to sulfate with the natural electron acceptor being cytochrome c550. its catalytic mechanism is thought to resemble that found in eukaryotic sulfite oxidases. using protein film voltammetry and redox potentiometry, we have identified both mo- and heme-centered redox responses from the ... | 2003 | 12517167 |
| a system for the heterologous expression of complex redox proteins in rhodobacter capsulatus: characterisation of recombinant sulphite:cytochrome c oxidoreductase from starkeya novella. | the phototrophic purple non-sulfur bacterium rhodobacter capsulatus expresses a wide variety of complex redox proteins in response to changing environmental conditions. here we report the construction and evaluation of an expression system for recombinant proteins in that organism which makes use of the dor promoter from the same organism. a generic expression vector, pdorex, was constructed and used to express sulphite:cytochrome c oxidoreductase from starkeya novella, a heterodimeric protein c ... | 2002 | 12372602 |
| phylogeny and distribution of the soxb gene among thiosulfate-oxidizing bacteria. | a pcr protocol for the detection of sulfur-oxidizing bacteria based on soxb genes that are essential for thiosulfate oxidation by sulfur-oxidizing bacteria of various phylogenetic groups which use the 'paracoccus sulfur oxidation' pathway was developed. five degenerate primers were used to specifically amplify fragments of soxb genes from different sulfur-oxidizing bacteria previously shown to oxidize thiosulfate. the pcr yielded a soxb fragment of approximately 1000 bp from most of the bacteria ... | 2001 | 11313131 |
| evidence for two pathways of thiosulfate oxidation in starkeya novella (formerly thiobacillus novellus). | the pathway of thiosulfate oxidation in the facultatively chemolithotrophic, sulfur-oxidizing bacterium starkeya novella (formerly thiobacillus novellus) has not been established beyond doubt. recently, isolation of the sorab genes, which encode a soluble sulfite:cytochrome c oxidoreductase, has been reported, indicating that a thiosulfate-oxidizing pathway not involving a multienzyme complex may exist in this organism. here we report the cloning and sequencing of the soxbcd genes from s. novell ... | 2001 | 11285738 |
| proposal for the reclassification of thiobacillus novellus as starkeya novella gen. nov., comb. nov., in the alpha-subclass of the proteobacteria. | thiobacillus novellus is a facultatively chemolithoautotrophic and methylotrophic, gram-negative, rod-shaped sulfur bacterium, shown by 16s rrna gene sequence analysis to be a member of the alpha-2 subclass of the proteobacteria. as such, it must be excluded from the genus thiobacillus, whose species are members of the beta-proteobacteria. it closest phylogenetic neighbour appears to be ancylobacter, from which it is distinct morphologically and in some physiological characteristics. it is disti ... | 2000 | 11034489 |
| pulsed epr investigations of the mo(v) centers of the r55q and r55m variants of sulfite dehydrogenase from starkeya novella. | continuous-wave and pulsed electron paramagnetic resonance (epr) spectroscopy have been used to characterize two variants of bacterial sulfite dehydrogenase (sdh) from starkeya novella in which the conserved active-site arginine residue (r55) is replaced by a neutral amino acid residue. substitution by the hydrophobic methionine residue (sdh(r55m)) has essentially no effect on the ph dependence of the epr properties of the mo(v) center, even though the x-ray structure of this variant shows that ... | 2010 | 20084533 |
| spectroscopic characterization of yedy: the role of sulfur coordination in a mo(v) sulfite oxidase family enzyme form. | electronic paramagnetic resonance (epr), electronic absorption, and magnetic circular dichroism spectroscopies have been performed on yedy, a suox fold protein with a mo domain that is remarkably similar to that found in chicken sulfite oxidase, arabidopsis thaliana plant sulfite oxidase, and the bacterial sulfite dehydrogenase from starkeya novella. low-energy dithiolene --> mo and cysteine thiolate --> mo charge-transfer bands have been assigned for the first time in a mo(v) form of a suox fol ... | 2009 | 19860477 |
| description of ancylobacter oerskovii sp. nov. and two additional strains of ancylobacter polymorphus. | a gram-negative, pleomorphic, rod-shaped, non-spore-forming bacterium, designated strain ns05t, was isolated from soil after enrichment with oxalate. on the basis of 16s rrna gene sequence similarity, strain ns05t was shown to be phylogenetically related to the genera ancylobacter, starkeya and angulomicrobium (96.3-98.1% sequence similarity), class alphaproteobacteria. strain ns05t was most closely related to ancylobacter rudongensis as 1.1761t (98.1% sequence similarity). the whole-cell fatty ... | 2008 | 18768594 |
| direct catalytic electrochemistry of sulfite dehydrogenase: mechanistic insights and contrasts with related mo enzymes. | under hydrodynamic electrochemical conditions with slow cyclic voltammetry sweep rates we have been able to probe catalytic events at the molybdenum active site of sulfite dehydrogenase (sdh) from starkeya novella adsorbed on an edge plane graphite electrode within a polylysine film. the electrochemically driven catalytic behaviour of sdh mirrors that seen in solution assays suggesting that the adsorbed enzyme retains its native activity. however, at high sulfite concentrations, the voltammetric ... | 2008 | 18601898 |
| soxax cytochromes, a new type of heme copper protein involved in bacterial energy generation from sulfur compounds. | soxax cytochromes are essential for the function of the only confirmed pathway for bacterial thiosulfate oxidation, the so-called "sox pathway," in which they catalyze the initial formation of a s-s bond between thiosulfate and the soxyz carrier protein. our work using the starkeya novella diheme soxax protein reveals for the first time that in addition to two active site heme groups, soxax contains a mononuclear cu(ii) center with a distorted tetragonal geometry and three to four nitrogen ligan ... | 2008 | 18552405 |
| highly sensitive and stable electrochemical sulfite biosensor incorporating a bacterial sulfite dehydrogenase. | this paper describes a highly sensitive electrochemical (voltammetric) determination of sulfite using a combination of starkeya novella sulfite dehydrogenase (sdh), horse heart cytochrome c (cyt c), and a self-assembled monolayer of 11-mercaptoundecanol (mu) cast on a gold electrode. the biosensor was optimized in terms of ph and the ratio of cyt c/sdh. the electrocatalytic oxidation current of sulfite increased linearly from 1 to 6 microm at the enzyme-modified electrode with a correlation coef ... | 2010 | 20698497 |
| short circuiting a sulfite oxidising enzyme with direct electrochemistry: active site substitutions and their effect on catalysis and electron transfer. | sulfite dehydrogenase (sdh) from starkeya novella is a heterodimeric enzyme comprising a mo active site and a heme c electron relay, which mediates electron transfer from the mo cofactor to cytochrome c following sulfite oxidation. studies on the wild type enzyme (sdh(wt)) and its variants have identified key amino acids at the active site, specifically arg-55 and his-57. we report the mo(vi/v), mo(v/iv) and fe(iii/ii) (heme) redox potentials of the variants sdh(r55k), sdh(r55m), sdh(r55q) and s ... | 2010 | 20863809 |
| self-organizing maps: a tool to ascertain taxonomic relatedness based on features derived from 16s rdna sequence. | exploitation of microbial wealth, of which almost 95% or more is still unexplored, is a growing need. the taxonomic placements of a new isolate based on phenotypic characteristics are now being supported by information preserved in the 16s rrna gene. however, the analysis of 16s rdna sequences retrieved from metagenome, by the available bioinformatics tools, is subject to limitations. in this study, the occurrences of nucleotide features in 16s rdna sequences have been used to ascertain the taxo ... | 2010 | 21289444 |