Publications

TitleAbstractYear(sorted descending)
Filter
PMID
Filter
[directed evolution of thermophilic esterase from the archaeon aeropyrum pemix k1].thermophilic esterase (ape1547) from aeropyrum pernix k1 was subjected to error-prone pcr (eppcr) to enhance activity. for the screening of mutants, an efficient and reliable assay suitable for high throughput screening was developed based on the enzyme thermostability. two successive rounds of random mutagenesis by eppcr resulted in a four amino acid substitution variant m020 with significantly increased activity (six-fold under the screening condition. further assay for the purified enzymes sh ...200616736588
characterization of a whole set of trna molecules in an aerobic hyper-thermophilic crenarchaeon, aeropyrum pernix k1.the trna molecule has an important role in translation, the function of which is to carry amino acids to the ribosomes. it is known that trna is transcribed from trna genes, some of which, in eukarya and archaea, contain introns. a computational analysis of the complete genome of aeropyrum pernix k1 predicted the presence of 14 intron-containing trna genes. to elucidate whether these introns are actually processed in living cells and what mechanism detects the intron regions, cdnas for premature ...200616769697
archaeal pre-mrna splicing: a connection to hetero-oligomeric splicing endonuclease.eukaryotic cbf5 is a protein subunit of the small nucleolar rna-protein complex. previously, we identified, in archaeal homologs of cbf5 of the crenarchaea, aeropyrum pernix, sulfolobus solfataricus, and sulfolobus tokodaii, the first examples of introns of archaeal protein-coding genes. here, we report the immunological detection of cbf5 protein of s. tokodaii, the product of the spliced cbf5 mrna. the hetero-oligomeric splicing endonuclease activity from recombinant s. tokodaii subunits cleave ...200616781672
hierarchical modularity of nested bow-ties in metabolic networks.the exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. topological analysis of graph models has often been applied to study the structural characteristics of complex metabolic networks.200616916470
a novel member of the protein disulfide oxidoreductase family from aeropyrum pernix k1: structure, function and electrostatics.the formation of disulfide bonds between cysteine residues is a rate-limiting step in protein folding. to control this oxidative process, different organisms have developed different systems. in bacteria, disulfide bond formation is assisted by the dsb protein family; in eukarya, disulfide bond formation and rearrangement are catalyzed by pdi. in thermophilic organisms, a potential key role in disulfide bond formation has recently been ascribed to a new cytosolic protein disulphide oxidoreductas ...200616934838
biochemical analysis of a dna replication origin in the archaeon aeropyrum pernix.we have characterised the interaction of the aeropyrum pernix origin recognition complex proteins (orc1 and orc2) with dna using dnase i footprinting. each protein binds upstream of its respective gene. however, orc1 protein alone interacts more tightly with an additional region containing multiple origin recognition box (orb) sites that we show to be a replication origin. at this origin, there are four orb elements disposed either side of an a+t-rich region. an orc1 protein dimer binds at each ...200616978641
compact archaeal variant of heme a synthase.the n- and c-terminal halves of the heme a synthase polypeptide of bacillus subtilis, and many other organisms, are homologous. this indicates that these enzyme proteins originate from a tandem duplication and fusion event of a gene encoding a protein half as large. the ape1694 gene of the hyperthermophilic archaeon aeropyrum pernix encodes a protein that is similar to the hypothetical small primordial protein. we demonstrate that this a. pernix protein is a heat-stable membrane bound heme a syn ...200616989823
optimization of growth for the hyperthermophilic archaeon aeropyrum pernix on a small-batch scale.growth of aeropyrum pernix, the first reported aerobic neutrophilic hyperthermophilic archaeon, was investigated under different cultivation parameters. different sources of seawater, ph, and the cultivation methods were tested with the aim to improve the biomass production. a 1-l glass flask fitted with a condenser and air diffuser was used as a bioreactor. the optimum conditions for maximizing a. pernix biomass were obtained when na2s2o3.5h2o (1 g/l) with added marine broth 2216 at ph 7.0 (20 ...200516391661
isocitrate dehydrogenase from the hyperthermophile aeropyrum pernix: x-ray structure analysis of a ternary enzyme-substrate complex and thermal stability.isocitrate dehydrogenase from aeropyrum pernix (apidh) is a homodimeric enzyme that belongs to the beta-decarboxylating dehydrogenase family and is the most thermostable idh identified. it catalyzes the nadp+ and metal-dependent oxidative decarboxylation of isocitrate to alpha-ketoglutarate. we have solved the crystal structures of a native apidh at 2.2 a, a pseudo-native apidh at 2.1 a, and of apidh in complex with nadp+, ca2+ and d-isocitrate at 2.3 a. the pseudo-native apidh is in complex wit ...200515581899
structure of an xpf endonuclease with and without dna suggests a model for substrate recognition.the xpf/mus81 structure-specific endonucleases cleave double-stranded dna (dsdna) within asymmetric branched dna substrates and play an essential role in nucleotide excision repair, recombination and genome integrity. we report the structure of an archaeal xpf homodimer alone and bound to dsdna. superposition of these structures reveals a large domain movement upon binding dna, indicating how the (hhh)(2) domain and the nuclease domain are coupled to allow the recognition of double-stranded/sing ...200515719018
log p effect of organic solvents on a thermophilic alcohol dehydrogenase.an alcohol dehydrogenase from the hyperthermophilic archaeon aeropyrum pernix was activated by water-miscible organic solvents. this activation was influenced by the kind and the concentration of the added organic solvents. the k(cat) was increased by a factor of over ten when the mole fraction of acetonitrile was 0.1. this effect was large when organic solvents with large log p values were added. in fact, the k(cat) showed a strong positive correlation with the log p value of the mixed solvent ...200515752697
crystal structure of the rna 2'-phosphotransferase from aeropyrum pernix k1.in the final step of trna splicing, the 2'-phosphotransferase catalyzes the transfer of the extra 2'-phosphate from the precursor-ligated trna to nad. we have determined the crystal structure of the 2'-phosphotransferase protein from aeropyrum pernix k1 at 2.8 angstroms resolution. the structure of the 2'-phosphotransferase contains two globular domains (n and c-domains), which form a cleft in the center. the n-domain has the winged helix motif, a subfamily of the helix-turn-helix family, which ...200515811369
gene expression and characterization of two 2-oxoacid:ferredoxin oxidoreductases from aeropyrum pernix k1.a hyperthermophilic and aerobic crenarchaeon, aeropyrum pernix k1, has two sets of genes possibly encoding 2-oxoacid:ferredoxin oxidoreductases. one is encoded in open reading frames (orfs) ape2126 and ape2128, and the other in orfs ape1473 and ape1472. the two sets of genes were expressed. the product enzymes, ape2126/2128 and ape1473/1472, showed optimal temperatures of 105 and over 110 degrees c, and optimal phs of 8.5 and 9.0, respectively, using pyruvate as a substrate. pyruvate, 2-oxobutyr ...200515848165
active site of zn(2+)-dependent sn-glycerol-1-phosphate dehydrogenase from aeropyrum pernix k1.the enzyme sn-glycerol-1-phosphate dehydrogenase (gro1pdh, ec 1.1.1.261) is key to the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids. this enzyme catalyzes the reversible conversion between dihydroxyacetone phosphate and glycerol-1-phosphate. to date, no information about the active site and catalytic mechanism of this enzyme has been reported. using the sequence and structural information for glycerol dehydrogenas ...200515876564
identification of replication origins in archaeal genomes based on the z-curve method.the z-curve is a three-dimensional curve that constitutes a unique representation of a dna sequence, i.e., both the z-curve and the given dna sequence can be uniquely reconstructed from the other. we employed z-curve analysis to identify one replication origin in the methanocaldococcus jannaschii genome, two replication origins in the halobacterium species nrc-1 genome and one replication origin in the methanosarcina mazei genome. one of the predicted replication origins of halobacterium species ...200515876567
three-dimensional structure of a new enzyme, o-phosphoserine sulfhydrylase, involved in l-cysteine biosynthesis by a hyperthermophilic archaeon, aeropyrum pernix k1, at 2.0a resolution.o-phosphoserine sulfhydrylase is a new enzyme found in a hyperthermophilic archaeon, aeropyrum pernix k1. this enzyme catalyzes a novel cysteine synthetic reaction from o-phospho-l-serine and sulfide. the crystal structure of the enzyme was determined at 2.0a resolution using the method of multi-wavelength anomalous dispersion. a monomer consists of three domains, including an n-terminal domain with a new alpha/beta fold. the topology folds of the middle and c-terminal domains were similar to th ...200516005886
i-apeki [corrected]: a novel intron-encoded laglidadg homing endonuclease from the archaeon, aeropyrum pernix k1.over 50 introns have been reported in archaeal rrna genes (rdnas), a subset of which nests putative homing endonuclease (hease) genes. here, we report the identification and characterization of a novel archaeal laglidadg-type hease, i-apeki [corrected], encoded by the apek1.s908 intron within the 16s rdna of aeropyrum pernix k1. i-apeki [corrected] consists of 222 amino acids and harbors two laglidadg-like sequences. it recognizes the 20 bp non-palindromic sequence 5'-gcaaggctgaaac downward arro ...200516049020
bending and cutting forks and flaps. 200516084380
expression, purification and crystal structure of a truncated acylpeptide hydrolase from aeropyrum pernix k1.acylpeptide hydrolase (aph) catalyzes the n-terminal hydrolysis of nalpha-acylpeptides to release nalpha-acylated amino acids. the crystal structure of recombinant aph from the thermophilic archaeon aeropyrum pernix k1 (apaph) was reported recently to be at a resolution of 2.1 angstrom; using x-ray diffraction. a truncated mutant of apaph that lacks the first short alpha-helix at the n-terminal, apaph-delta(1-21), was cloned, expressed, characterized and crystallized. data from biochemical exper ...200516143816
characterization of a thermophilic atp-dependent dna ligase from the euryarchaeon pyrococcus horikoshii.archaea encode a dna ligase composed of a c-terminal catalytic domain typical of atp-dependent ligases plus an n-terminal domain similar to that found in eukaryotic cellular and poxvirus dna ligases. all archaeal dna ligases characterized to date have atp-dependent adenylyltransferase and nick-joining activities. however, recent reports of dual-specificity atp/nad+ ligases in two thermococcus species and pyrococcus abyssi and an atp/adp ligase in aeropyrum pernix raise the prospect that certain ...200516199559
crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon aeropyrum pernix k1.peroxiredoxins (prxs) are thiol-dependent peroxidases that catalyze the detoxification of various peroxide substrates such as h2o2, peroxinitrite, and hydroperoxides, and control some signal transduction in eukaryotic cells. prxs are found in all cellular organisms and represent an enormous superfamily. recent genome sequencing projects and biochemical studies have identified a novel subfamily, the archaeal prxs. their primary sequences are similar to those of the 1-cys prxs, which use only one ...200516214169
structure of a putative trans-editing enzyme for prolyl-trna synthetase from aeropyrum pernix k1 at 1.7 a resolution.the crystal structure of ape2540, the putative trans-editing enzyme prox from aeropyrum pernix k1, was determined in a high-throughput manner. the crystal belongs to the monoclinic space group p2(1), with unit-cell parameters a = 47.4, b = 58.9, c = 53.6 a, beta = 106.8 degrees. the structure was solved by the multiwavelength anomalous dispersion method at 1.7 a and refined to an r factor of 16.8% (rfree = 20.5%). the crystal structure includes two protein molecules in the asymmetric unit. each ...200516508081
crystallization and preliminary x-ray diffraction analysis of thioredoxin peroxidase from the aerobic hyperthermophilic archaeon aeropyrum pernix k1.thioredoxin peroxidase is a member of the peroxiredoxin family and plays a dominant role in a hydrogen peroxide metabolism. a recombinant form of the hyperthermostable thioredoxin peroxidase from the aerobic hyperthermophilic archaeon aeropyrum pernix k1, a polypeptide consisting of 250 amino acids, was purified. the c207s mutant protein was crystallized by the hanging-drop vapour-diffusion method using potassium sodium tartrate as the precipitant at 298 k. diffraction data were collected and pr ...200516511031
crystallization and preliminary x-ray diffraction studies of a protein disulfide oxidoreductase from aeropyrum pernix k1.a protein disulfide oxidoreductase from the archaeon aeropyrum pernix k1 has been overexpressed in escherichia coli and crystallized at 298 k using the hanging-drop vapour-diffusion method. crystals belong to the space group i222 or i2(1)2(1)2(1), with unit-cell parameters a = 90.59, b = 102.43, c = 128.96 a. a complete data set has been collected at the elettra synchrotron source in trieste to 1.93 a resolution using a single frozen crystal.200516511034
overexpression, purification and crystallization of tyrosyl-trna synthetase from the hyperthermophilic archaeon aeropyrum pernix k1.hyperthermophilic archaeal tyrosyl-trna synthetase from aeropyrum pernix k1 was cloned and overexpressed in escherichia coli. the expressed protein was purified by cibacron blue affinity chromatography following heat treatment at 363 k. crystals suitable for x-ray diffraction studies were obtained under optimized crystallization conditions in the presence of 1.5 m ammonium sulfate using the hanging-drop vapour-diffusion method. the crystals belonged to the tetragonal space group p4(3)2(1)2, with ...200516511219
recognition sites of glycine trna for glycyl-trna synthetase from hyperthermophilic archaeon, aeropyrum pernix k1.to elucidate the trna recognition sites of glycine trna from an extreme thermophilic and aerobic archaeon, aeropyrum pernix k1, we examined glycylation activities using in vitro mutant glycine trna transcripts and recombinant a. pernix glycyl-trna synthetase. the recognition nucleotides were determined to be c35 and c36 of anticodon, c2-g71 and g3-c70 base-pairs of acceptor stem. however, discriminator base a73 was not recognized by glycyl-trna synthetase.200517150752
molecular recognition of histidine trna by histidyl-trna synthetase from hyperthermophilic archaeon, aeropyrum pernix k1.to investigate the recognition sites of histidine trna for histidyl-trna synthetase from an extreme hyperthermophilic archaeon, aeropyrum pernix k1, we examined histidylation activities by using overexpressed histidyl-trna synthetase and various histidine trna transcripts that were prepared by in vitro transcription system. results indicated that anticodon was not recognized by the histidyl-trna synthetase similar to that of escherichia coli histidine trna recognition system. discriminator base ...200517150756
[the wonders of hell]. 200516296645
determination of tryptophan trna recognition sites for tryptophanyl-trna synthetase from hyperthermophilic archaeon, aeropyrum pernix k1.to investigate the recognition mechanism of tryptophan trna by tryptophanyl-trna synthetase from extreme hyperthermophilic and aerobic archaeon, aeropyrum pernix k1, tryptophanylation activities were examined by using mutant tryptophan trna transcripts prepared by in vitro transcription system. their transcripts were aminoacylated with tryptophan by overexpressed a. pernix tryptophanyl-trna synthetase. the results indicated that anticodon nucleotides c34, c35 and a36, discriminator base a73, g1- ...200417150540
gene recognition based on nucleotide distribution of orfs in a hyper-thermophilic crenarchaeon, aeropyrum pernix k1.the 2694 orfs originally annotated as potential genes in the genome of aeropyrum pernix can be categorized into three clusters (a, b, c), according to their nucleotide composition at three codon positions. coding potential was found to be responsible for the phenomenon of three clusters in a 9-dimensional space derived from the nucleotide composition of orfs: orfs assigned to cluster a are coding ones, while those assigned to clusters b and c are non-coding orfs. a "codingness" index called the ...200415871459
properties of an alcohol dehydrogenase from the hyperthermophilic archaeon aeropyrum pernix k1.a nad+-dependent medium-chain alcohol dehydrogenase from the hyperthermophilic archaeon aeropyrum pernix k1 was expressed in escherichia coli and purified. the recombinant enzyme was a homotetramer of molecular mass 1.6 x 10(2) kda. the optimum ph for the oxidative reaction was around 10.5 and that for the reductive reaction was around 8.0. the enzyme had a broad substrate specificity including aliphatic and aromatic alcohols, aliphatic and aromatic ketones, and benzylaldehyde. this enzyme produ ...200416233615
bifunctional phosphoglucose/phosphomannose isomerases from the archaea aeropyrum pernix and thermoplasma acidophilum constitute a novel enzyme family within the phosphoglucose isomerase superfamily.the hyperthermophilic crenarchaeon aeropyrum pernix contains phosphoglucose isomerase (pgi) activity. however, obvious homologs with significant identity to known pgis could not be identified in the sequenced genome of this organism. the pgi activity from a. pernix was purified and characterized. kinetic analysis revealed that, unlike all known pgis, the enzyme catalyzed reversible isomerization not only of glucose 6-phosphate but also of epimeric mannose 6-phosphate at similar catalytic efficie ...200414551194
a proton pore in a potassium channel voltage sensor reveals a focused electric field.voltage-dependent potassium channels are essential for the generation of nerve impulses. voltage sensitivity is conferred by charged residues located mainly in the fourth transmembrane segment (s4) of each of the four identical subunits that make up the channel. these charged segments relocate when the potential difference across the membrane changes, controlling the ability of the pore to conduct ions. in the crystal structure of the aeropyrum pernix potassium channel kvap, the s4 and part of t ...200414765197
molybdenum-containing arsenite oxidase of the chemolithoautotrophic arsenite oxidizer nt-26.the chemolithoautotroph nt-26 oxidizes arsenite to arsenate by using a periplasmic arsenite oxidase. purification and preliminary characterization of the enzyme revealed that it (i) contains two heterologous subunits, aroa (98 kda) and arob (14 kda); (ii) has a native molecular mass of 219 kda, suggesting an alpha2beta2 configuration; and (iii) contains two molybdenum and 9 or 10 iron atoms per alpha2beta2 unit. the genes that encode the enzyme have been cloned and sequenced. sequence analyses r ...200414996791
archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the methanopyrus kandleri paradox.phylogenetic analysis of the archaea has been mainly established by 16s rrna sequence comparison. with the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. we analyzed archaeal phylogeny using two concatenated datasets consisting of 14 proteins involved in transcription and 53 ribosomal proteins (3,275 and 6,377 positions, respectively).200415003120
aeropyrum camini sp. nov., a strictly aerobic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney.a novel hyperthermophilic archaeon, designated strain sy1(t), was isolated from a deep-sea hydrothermal vent chimney sample collected from the suiyo seamount in the izu-bonin arc, japan, at a depth of 1385 m. the cells were irregular cocci (1.2 to 2.1 micro m in diameter), occurring singly or in pairs, and stained gram-negative. growth was observed between 70 and 97 degrees c (optimum, 85 degrees c; 220 min doubling time), ph 6.5 and 8.8 (optimum, ph 8.0), and salinity of 2.2 and 5.3 % (optimum, ...200415023940
hyperthermophilic dehydrogenase enzymes.archaeal dehydrogenases are often found to be of a specific class of dehydrogenase which has low sequence identity to the equivalent bacterial and eukaryotic counterparts. this paper focuses on two different types of hyperthermophilic dehydrogenase enzyme that have been cloned and over-expressed in escherichia coli. the crystallographic structures of the apo form of gapdh (glyceraldehyde-3-phosphate dehydrogenase) from sulfolobus solfataricus and the related holo form of gapdh from methanothermu ...200415046583
structure, function and evolution of the archaeal class i fructose-1,6-bisphosphate aldolase.fbpa (fructose-1,6-bisphosphate aldolase) catalyses the reversible aldol condensation of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate to form fructose 1,6-bisphosphate. two classes of fbpa, which rely on different reaction mechanisms, have so far been discovered, class i mainly found in eucarya and class ii mainly in bacteria. only recently were genes encoding proteins with fbpa activity identified in archaea. archaeal fbpas do not share any significant overall sequence identity wit ...200415046584
ancestral hemoglobins in archaea.hemoglobins are ubiquitous in eukarya and bacteria but, until now, have not been found in archaea. a phylogenetic analysis of the recently revealed microbial family of globin-coupled heme-based sensors suggests that these sensors descended from an ancient globin-only progenitor, or a protoglobin (pgb). here, we report the discovery and characterization of two pgbs from the archaea: appgb from the obligately aerobic hyperthermophile aeropyrum pernix, and mapgb from the strictly anaerobic methanog ...200415096613
a novel phospholipase a2/esterase from hyperthermophilic archaeon aeropyrum pernix k1.an open reading frame of the hyperthermophilic archaeon aeropyrum pernix k1 ape2325, which composed of 474 bases, was cloned and expressed in escherichia coli bl21 (de3) codon plus-ril. the recombinant protein was purified by ni-chelation affinity chromatography. it showed a single band with a molecular mass of 18kda in sds-page. the purified enzyme exhibited both phospholipase a(2) and esterase activities with the optimal catalytic temperature at 90 degrees c. the enzyme activity was ca(2+)-ind ...200415135393
crystal structure of isocitrate dehydrogenase from aeropyrum pernix. 200415146507
quantifying intrachromosomal gc heterogeneity in prokaryotic genomes.the sequencing of prokaryotic genomes covering a wide taxonomic range has sparked renewed interest in intrachromosomal compositional (gc) heterogeneity, largely in view of lateral transfers. we present here a brief overview of some methods for visualizing and quantifying gc variation in prokaryotes. we used these methods to examine heterogeneity levels in sequenced prokaryotes, for a range of scales or stringencies. some species are consistently homogeneous, whereas others are markedly heterogen ...200415177687
anticodon and wobble evolution.the location of the root of life within the archaea domain close to methanopyrus kandleri and aeropyrum pernix on the basis of trna sequence clustering has allowed the tracing of evolutionary change in anticodon usages and the wobble rules governing them among different living lineages. analysis suggests that the primitive archaea employed simple modes of wobble of anticodon-codon pairing that enable the reading of standard one-amino acid and two-amino acid odon boxes with the uniform use of gnn ...200415177692
an evolutionarily conserved network of amino acids mediates gating in voltage-dependent potassium channels.a novel sequence-analysis technique for detecting correlated amino acid positions in intermediate-size protein families (50-100 sequences) was developed, and applied to study voltage-dependent gating of potassium channels. most contemporary methods for detecting amino acid correlations within proteins use very large sets of data, typically comprising hundreds or thousands of evolutionarily related sequences, to overcome the relatively low signal-to-noise ratio in the analysis of co-variations be ...200415201054
localization of the voltage-sensor toxin receptor on kvap.a variety of venomous animals produce small protein toxins that impair the function of voltage-dependent cation channels by affecting the motions of the voltage-sensor domains and altering the energetics of the opening of the channel. in this study, we investigate the location of the receptor for tarantula venom voltage-sensor toxins on the voltage-dependent k+ channel from aeropyrum pernix (kvap), an archeabacterial channel that is functionally inhibited by members of this toxin family. we show ...200415287735
crystal structure of an acylpeptide hydrolase/esterase from aeropyrum pernix k1.acylpeptide hydrolases (aph; also known as acylamino acid releasing enzyme) catalyze the removal of an n-acylated amino acid from blocked peptides. the crystal structure of an aph from the thermophilic archaeon aeropyrum pernix k1 to 2.1 a resolution confirms it to be a member of the prolyl oligopeptidase family of serine proteases. the structure of apaph is a symmetric homodimer with each subunit comprised of two domains. the n-terminal domain is a regular seven-bladed beta-propeller, while the ...200415296741
electron microscopic analysis of kvap voltage-dependent k+ channels in an open conformation.voltage-dependent ion channels serve as field-effect transistors by opening a gate in response to membrane voltage changes. the gate's response to voltage is mediated by voltage sensors, which are arginine-containing structures that must move with respect to the membrane electric field. we have analysed by electron microscopy a voltage-dependent k(+) channel from aeropyrum pernix (kvap). fab fragments were attached to 'voltage sensor paddles' and identified in the electron microscopy map at 10.5 ...200415306816
crystallization of the xeroderma pigmentosum group f endonuclease from aeropyrum pernix.the xeroderma pigmentosa group f protein (xpf) is a founding member of a family of 3'-flap endonucleases that play an essential role in nucleotide-excision repair, dna replication and recombination. the xpf gene has been cloned from aeropyrum pernix, encoding a 254-residue protein (apxpf). recombinant protein was produced in escherichia coli and purified by three chromatographic steps. three different crystal forms of apxpf were grown in trigonal, monoclinic and triclinic systems. the trigonal c ...200415333947
a preliminary solubility screen used to improve crystallization trials: crystallization and preliminary x-ray structure determination of aeropyrum pernix flap endonuclease-1.crystallization of protein and protein complexes is a multi-parametric problem that involves the investigation of a vast number of physical and chemical conditions. the buffers, salts and additives used to prepare the protein will be present in every crystallization condition. it is imperative that these conditions be defined prior to crystal screening since they will have a ubiquitous involvement in the crystal-growth experiments. this study involves the crystallization and preliminary analysis ...200415333952
structure of aldolase from thermus thermophilus hb8 showing the contribution of oligomeric state to thermostability.2-deoxyribose-5-phosphate aldolase catalyzes a reversible aldol condensation of two aldehydes via formation of a covalent schiff-base intermediate at the active lysine residue. the crystal structure of 2-deoxyribose-5-phosphate aldolase from thermus thermophilus hb8 has been determined with and without the substrate at atomic resolution. this enzyme, which has a unique homotetramer structure, has been compared with the previously reported crystal structures of two orthologues from escherichia co ...200415388928
conformational changes induced by nucleotide binding in cdc6/orc from aeropyrum pernix.archaea contain one or more proteins with homology to eukaryotic orc/cdc6 proteins. sequence analysis suggests the existence of at least two subfamilies of these proteins, for which we propose the nomenclature orc1 and orc2. we have determined crystal structures of the orc2 protein from the archaeon aeropyrum pernix in complexes with adp or a non-hydrolysable atp analogue, adpnp. between two crystal forms, there are three crystallographically independent views of the adp complex and two of the a ...200415465044
characterization of sac10a, a hyperthermophile dna-binding protein from sulfolobus acidocaldarius.sac10a is a member of a group of basic dna-binding proteins thought to be important in chromatin structure and regulation in the archaeon sulfolobus. we describe here the isolation, gene identification, and biophysical characterization of native sac10a. the protein exists as a 23.8 kda homodimer at ph 7 and unfolds with a t degrees of 122 degrees c. dissociation of the dimer into folded globular subunits is promoted by decreased ph and salt concentration. thermal unfolding of the monomeric subun ...200415476396
alteration of product specificity of aeropyrum pernix farnesylgeranyl diphosphate synthase (fgs) by directed evolution.directed evolution of the c25 farnesylgeranyl diphosphate synthase of aeropyrum pernix (fgs) was carried out by error-prone pcr with an in vivo color complementation screen utilizing carotenoid biosynthetic pathway enzymes. screening yielded 12 evolved clones with c20 geranylgeranyl diphosphate synthase activity which were isolated and characterized in order to understand better the chain elongation mechanism of this enzyme. analysis of these mutants revealed three different mechanisms of produc ...200415548566
crystallization and preliminary x-ray diffraction studies of a novel alcohol dehydrogenase from the hyperthermophilic archaeon aeropyrum pernix.a novel alcohol dehydrogenase enzyme has been cloned from the hyperthermophilic archaeon aeropyrum pernix and overexpressed in escherichia coli. this zinc-containing enzyme has been crystallized by the sitting-drop vapour-diffusion method using peg 600 as precipitant. the crystals diffract to 1.5 a resolution and belong to the orthorhombic space group p2(1)2(1)2, with unit-cell parameters a = 100.7, b = 103.2, c = 67.5 a. the asymmetric unit contains two enzyme monomers. two synchrotron data set ...200312499562
the first crystal structure of archaeal aldolase. unique tetrameric structure of 2-deoxy-d-ribose-5-phosphate aldolase from the hyperthermophilic archaea aeropyrum pernix.a gene encoding a 2-deoxy-d-ribose-5-phosphate aldolase (dera) homolog was identified in the hyperthermophilic archaea aeropyrum pernix. the gene was overexpressed in escherichia coli, and the produced enzyme was purified and characterized. the enzyme is an extremely thermostable dera; its activity was not lost after incubation at 100 degrees c for 10 min. the enzyme has a molecular mass of approximately 93 kda and consists of four subunits with an identical molecular mass of 24 kda. this is the ...200312529358
crystallization and preliminary x-ray diffraction analysis of o-acetylserine sulfhydrylase from aeropyrum pernix k1.crystals of o-acetylserine sulfhydrylase from aeropyrum pernix k1 were obtained by the hanging-drop vapour-diffusion method at 298 k. an x-ray diffraction data set was collected to 2.25 a resolution at 100 k. the crystal belonged to space group p42(1)2, p4(1)2(1)2, p4(2)2(1)2 or p4(3)2(1)2. the unit-cell parameters were a = b = 74.5, c = 276.0 a. the presence of two subunits of the enzyme per asymmetric unit gives a crystal volume per protein mass (v(m)) of 2.28 a(3) da(-1) and a solvent content ...200312554945
the hexokinase of the hyperthermophile thermoproteus tenax. atp-dependent hexokinases and adp-dependent glucokinases, teo alternatives for glucose phosphorylation in archaea.the phosphorylation of glucose by different sugar kinases plays an essential role in archaea because of the absence of a phosphoenolpyruvate-dependent transferase system characteristic for bacteria. in the genome of the hyperthermophilic archaeon thermoproteus tenax a gene was identified with sequence similarity to glucokinases of the so-called rok family (repressor protein, open reading frame, sugar kinase). the t. tenax enzyme, like the recently described atp-dependent "glucokinase" from aerop ...200312626506
a novel complexity measure for comparative analysis of protein sequences from complete genomes.analysis of sequence complexities of proteins is an important step in the characterization and classification of new genomes. a new measure has been proposed to compute sequence complexity in protein sequences based on linguistic complexity. the algorithm requires a single parameter, is computationally simple and provides a framework for comparative genomic analysis. protein sequences were classified into groups of high or low complexity based on a quantitative measure termed f(c), which is prop ...200312643768
characterization of a novel thermostable o-acetylserine sulfhydrylase from aeropyrum pernix k1.an o-acetylserine sulfhydrylase (oass) from the hyperthermophilic archaeon aeropyrum pernix k1, which shares the pyridoxal 5'-phosphate binding motif with both oass and cystathionine beta-synthase (cbs), was cloned and expressed by using escherichia coli rosetta(de3). the purified protein was a dimer and contained pyridoxal 5'-phosphate. it was shown to be an enzyme with cbs activity as well as oass activity in vitro. the enzyme retained 90% of its activity after a 6-h incubation at 100 degrees ...200312644499
comparative analysis of pyruvate kinases from the hyperthermophilic archaea archaeoglobus fulgidus, aeropyrum pernix, and pyrobaculum aerophilum and the hyperthermophilic bacterium thermotoga maritima: unusual regulatory properties in hyperthermophilic archaea.pyruvate kinases (pk, ec 2.7.1.40) from three hyperthermophilic archaea (archaeoglobus fulgidus strain 7324, aeropyrum pernix, and pyrobaculum aerophilum) and from the hyperthermophilic bacterium thermotoga maritima were compared with respect to their thermophilic, kinetic, and regulatory properties. pks from the archaea are 200-kda homotetramers composed of 50-kda subunits. the enzymes required divalent cations, mg2+ and mn2+ being most effective, but were independent of k+. temperature optima ...200312654928
characterization of novel hexadecameric thioredoxin peroxidase from aeropyrum pernix k1.a gene (ape2278) encoding the peroxiredoxin (prx) homologous protein of yeast and human was identified in the genome data base of the aerobic hyperthermophilic archaeon aeropyrum pernix. we cloned the gene and produced the encoded protein in escherichia coli cells. the isolated recombinant protein showed peroxidase activity in vitro and used the thioredoxin system of a. pernix as an electron donor. these results indicate that the recombinant protein is in fact thioredoxin peroxidase (aptpx) of a ...200312707274
x-ray structure of a voltage-dependent k+ channel.voltage-dependent k+ channels are members of the family of voltage-dependent cation (k+, na+ and ca2+) channels that open and allow ion conduction in response to changes in cell membrane voltage. this form of gating underlies the generation of nerve and muscle action potentials, among other processes. here we present the structure of kvap, a voltage-dependent k+ channel from aeropyrum pernix. we have determined a crystal structure of the full-length channel at a resolution of 3.2 a, and of the i ...200312721618
cloning, expression, and characterization of the first archaeal atp-dependent glucokinase from aerobic hyperthermophilic archaeon aeropyrum pernix.the gene encoding the atp-dependent glucokinase of hyperthermophilic archaeon aeropyrum pernix was identified, cloned, and functionally expressed in escherichia coli. the deduced amino acid sequence showed 40% identity to that of the putative glucokinase from hyperthermophilic archaeon pyrobacurum aerophilum. the purified recombinant enzyme was a monomer with a molecular mass of 35 kda. the enzyme retained its full activity on heating at 70 degrees c for 10 min and retained 65% of the activity a ...200312761185
transfer rna paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life.a search has been performed on 2878 trna sequences from 60 different genomes in order to detect the existence of closely related 'alloacceptor' trnas accepting dissimilar amino acids that could be paralogs generated by gene duplications. this has led to the identification of extremely conserved trna(phe)-trna(tyr) pairs displaying as high as 94% identity between them, and also other potentially paralogous trna pairs in archaeal species. these paralogous pairs are enriched for amino acid pairs be ...200312801633
inhibitory effect of maillard reaction products on growth of the aerobic marine hyperthermophilic archaeon aeropyrum pernix.it was found that the growth of aeropyrum pernix was severely inhibited in a medium containing reducing sugars and tryptone due to the formation of maillard reaction products. the rate of the maillard browning reaction was markedly enhanced under aerobic conditions, and the addition of maillard reaction products to the culture medium caused fatal growth inhibition.200312839824
a novel extracellular subtilisin-like protease from the hyperthermophile aeropyrum pernix k1: biochemical properties, cloning, and expression.a novel extracellular serine protease designated pernisine was purified to homogeneity and characterized from the archaeon aeropyrum pernix k1. the molecular mass, estimated by sds-page analysis and by gel filtration chromatography, was about 34 kda suggesting that the enzyme is monomeric. pernisine was active in a broad range of ph (5.0-12.0) and temperature (60-120 degrees c) with maximal activity at 90 degrees c and between ph 8.0 and 9.0. in the presence of 1 mm cacl(2) the activity, as a fu ...200312908102
the structure of an alcohol dehydrogenase from the hyperthermophilic archaeon aeropyrum pernix.the structure of the recombinant medium chain alcohol dehydrogenase (adh) from the hyperthermophilic archaeon aeropyrum pernix has been solved by the multiple anomalous dispersion technique using the signal from the naturally occurring zinc ions. the enzyme is a tetramer with 222 point group symmetry. the adh monomer is formed from a catalytic and a cofactor-binding domain, with the overall fold similar to previously solved adh structures. the 1.62 a resolution a.pernix adh structure is that of ...200312927540
a novel adp-dependent dna ligase from aeropyrum pernix k1.a gene encoding a putative atp-dependent dna ligase from the aerobic hyperthermophilic archaeon aeropyrum pernix k1 was cloned and the biochemical characteristics of the resulting recombinant protein were examined. the gene (accession no. ape1094) from a. pernix encoding a 69-kda protein showed a 39-61% identity with other atp-dependent dna ligases from the archaea. normally dna ligase is activated by nad(+) or atp. there has been no report about the other activators for dna ligase. the recombin ...200312935888
a novel o-phospho-l-serine sulfhydrylation reaction catalyzed by o-acetylserine sulfhydrylase from aeropyrum pernix k1.o-acetylserine sulfhydrylase (oass), a pyridoxal 5'-phosphate (plp)-dependent enzyme, catalyzes the synthesis of l-cysteine from o-acetyl-l-serine and sulfide. o-acetyl-l-serine is labile at high temperatures at which hyperthermophilic archaea live. herein, a study of the substrate specificity of oass from aeropyrum pernix k1 with respect to o-acetyl-l-serine in l-cysteine synthesis is described. l-azaserine, 3-chloro-l-alanine, and o-phospho-l-serine reacted with a. pernix oass in a plp-depende ...200312965218
comparison of sequence masking algorithms and the detection of biased protein sequence regions.motivation: separation of protein sequence regions according to their local information complexity and subsequent masking of low complexity regions has greatly enhanced the reliability of function prediction by sequence similarity. comparisons with alternative methods that focus on compositional sequence bias rather than information complexity measures have shown that removal of compositional bias yields at least as sensitive and much more specific results. besides the application of sequence ma ...200312967964
molecular recognition of proline trna by prolyl-trna synthetase from hyperthermophilic archaeon, aeropyrum pernix k1.to investigate the recognition mechanism of trna(pro) by prolyl-trna synthetase from hyperthermophilic archaeon, aeropyrum pernix k1, various trna(pro) transcripts were prepared by in vitro transcription system. these transcripts were aminoacylated with proline by overexpressed a. pernix prolyl-trna synthetase. from prolylation experiments, recognition elements of a. pernix trna(pro) were determined to be g35 and g36 of anticodon, discriminator base a73, and g1-c72 base pair at acceptor stem end ...200314510473
growth of the hyperthermophilic marine archaeon aeropyrum pernix in a defined medium.the nutritional requirements of aeropyrum pernix were studied to investigate the growth of a hyperthermophilic marine archaeon in a defined medium. various nutrients including sugars, amino acids, and nucleoside bases were tested to determine their effects on cell growth. it was found that adenine and six amino acids (arg, ile, len, lys, met, val) are essential for the growth of a. pernix. an artificial seawater-based medium, containing 11 amino acids, adenine, vitamins, kh2po4, na2s2o3 and trac ...200316233467
molecular recognition of threonine trna by threonyl-trna synthetase from an extreme thermophilic archaeon, aeropyrum pernix k1.to investigate the recognition sites of trna(thr) for threonyl-trna synthetase (thrrs) from an extreme thermophilic and aerobic archaeon, aeropyrum pernix k1, threonylation experiments using various in vitro mutant transcripts of trna(thr) were examined. the results indicated that a. pernix thrrs did recognize the first three base pairs of acceptor stem in addition to the second and the third letters of anticodon of trna(thr), in spite of its n-terminal truncated unique structure. discriminator ...200212903115
differences in tyrosine trna identity between escherichia coli and archaeon, aeropyrum pernix k1.recognition sites of tyrosine trna for tyrosyl-trna synthetase from escherichia coli and extreme thermophilic archaeon, aeropyrum pernix k1 were examined using various in vitro transcripts. with respect to the long variable arm in e. coli tyrosine trna, some base pairs in length was required for tyrosylation. none of the recognition sites were found in the acceptor stem, except the discriminator base a73 in e. coli tyrosine trna. in case of a. pernix tyrosine trna, c1-g72 base pair and discrimin ...200212903187
introns in protein-coding genes in archaea.introns in protein-coding genes are ubiquitous in eukaryotic cells, but pre-mrna splicing has yet to be reported in archaeal and its viral genomes. we present evidence of introns in genes encoding a homolog of eukaryotic cbf5p (centromere-binding factor 5; a subunit of a small nucleolar ribonucleoprotein) in three archaea; aeropyrum pernix, sulfolobus solfataricus and sulfolobus tokodaii. splicing of pre-mrnas in vivo was demonstrated by reverse transcriptase-mediated polymerase chain reaction. ...200211755525
propionate coa-transferase from clostridium propionicum. cloning of gene and identification of glutamate 324 at the active site.propionate coa-transferase from clostridium propionicum has been purified and the gene encoding the enzyme has been cloned and sequenced. the enzyme was rapidly and irreversibly inactivated by sodium borohydride or hydroxylamine in the presence of propionyl-coa. the reduction of the thiol ester between a catalytic site glutamate and coa with borohydride and the cleavage by hydroxylamine were used to introduce a site-specific label, which was followed by maldi-tof-ms. this allowed the identificat ...200211784332
three proliferating cell nuclear antigen-like proteins found in the hyperthermophilic archaeon aeropyrum pernix: interactions with the two dna polymerases.proliferating cell nuclear antigen (pcna) is an essential component in the eukaryotic dna replication machinery, in which it works for tethering dna polymerases on the dna template to accomplish processive dna synthesis. the pcna also interacts with many other proteins in important cellular processes, including cell cycle control, dna repair, and an apoptotic pathway in the domain eucarya: we identified three genes encoding pcna-like sequences in the genome of aeropyrum pernix, a crenarchaeal ar ...200211790738
kinetic study of sn-glycerol-1-phosphate dehydrogenase from the aerobic hyperthermophilic archaeon, aeropyrum pernix k1.a gene having high sequence homology (45-49%) with the glycerol-1-phosphate dehydrogenase gene from methanobacterium thermoautotrophicum was cloned from the aerobic hyperthermophilic archaeon aeropyrum pernix k1 (jcm 9820). this gene expressed in escherichia coli with the pet vector system consists of 1113 nucleotides with an atg initiation codon and a tag termination codon. the molecular mass of the purified enzyme was estimated to be 38 kda by sds/page and 72.4 kda by gel column chromatography ...200211846799
gene duplication and gene conversion shape the evolution of archaeal chaperonins.chaperonins are multi-subunit double-ring complexes that mediate the folding of nascent or denatured proteins. gene duplication has been a potent force in the evolution of chaperonins in archaea. here we show that gene conversion has also been an important factor. we utilized a novel maximum likehood-based phylogenetic method for scanning dna sequence alignments for regions of anomalous phylogenetic signal, such as those affected by gene conversion. our results suggest that in crenarchaeotes, wh ...200211884142
using homolog groups to create a whole-genomic tree of free-living organisms: an update.genomic trees have been constructed based on the presence and absence of families of protein-encoding genes observed in 27 complete genomes, including genomes of 15 free-living organisms. this method does not rely on the identification of suspected orthologs in each genome, nor the specific alignment used to compare gene sequences because the protein-encoding gene families are formed by grouping any protein with a pairwise similarity score greater than a preset value. because of this all inclusi ...200211956692
unique presence of a manganese catalase in a hyperthermophilic archaeon, pyrobaculum calidifontis va1.we had previously isolated a facultatively anaerobic hyperthermophilic archaeon, pyrobaculum calidifontis strain va1. here, we found that strain va1, when grown under aerobic conditions, harbors high catalase activity. the catalase was purified 91-fold from crude extracts and displayed a specific activity of 23,500 u/mg at 70 degrees c. the enzyme exhibited a k(m) value of 170 mm toward h(2)o(2) and a k(cat) value of 2.9 x 10(4) s(-1).subunit(-1) at 25 degrees c. gel filtration chromatography in ...200212029047
temperature dependence of kinetic parameters for hyperthermophilic glutamate dehydrogenase from aeropyrum pernix k1.the temperature dependence of the steady-state kinetic parameters for a glutamate dehydrogenase from aeropyrum pernix k1 was investigated. the enzyme showed a biphasic kinetic characteristic for l-glutamate and a monophasic one for nadp at 50-90 degrees c. at low concentrations of l-glutamate the km decreased from 2.02 to 0.56 mm and the catalytic efficiency (vmax/km) markedly increased (4-150 micromol x mg(-1) x mm(-1)) along with the increase of temperature from 50 to 90 degrees c. at high con ...200212036066
crystallization and preliminary crystallographic analysis of acylamino-acid releasing enzyme from the hyperthermophilic archaeon aeropyrum pernix.crystals of acylamino-acid releasing enzyme from the hyperthermophilic archaeon aeropyrum pernix strain k1 have been grown at 291 k using ammonium phosphate as a precipitant. the diffraction pattern of the crystal extends to 2.4 a resolution at 100 k using cu kalpha radiation. the crystal belongs to space group p1, with unit-cell parameters a = 107.5, b = 109.9, c = 119.4 a, alpha = 108.1, beta = 109.8, gamma = 91.9 degrees. the presence of eight molecules per asymmetric unit gives a crystal vol ...200212037315
genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds.disulfide bonds have only rarely been found in intracellular proteins. that pattern is consistent with the chemically reducing environment inside the cells of well-studied organisms. however, recent experiments and new calculations based on genomic data of archaea provide striking contradictions to this pattern. our results indicate that the intracellular proteins of certain hyperthermophilic archaea, especially the crenarchaea pyrobaculum aerophilum and aeropyrum pernix, are rich in disulfide b ...200212107280
updating carbamoylphosphate synthase (cps) phylogenies: occurrence and phylogenetic identity of archaeal cps genes.among bacteria the cara and carb genes encoding the small (cara) and large (carb) subunits of carbamoylphosphate synthase (cps) have been lost in certain symbionts (haemophylus influenzae) and in most obligate intracellular parasites (chlamydiae, spirochaetes, mycoplasmatales, rickettsiae) having genome sizes in the 0.7- to 1.1-mb range. compared to bacteria, archaea exhibit a more varied pattern of cps gene losses and an unusual propensity to incorporate cps genes derived from both bacteria and ...200212107592
crystallization and preliminary x-ray diffraction analysis of glutamate dehydrogenase from an aerobic hyperthermophilic archaeon, aeropyrum pernix k1.glutamate dehydrogenase from an aerobic hyperthermophilic archaeon, aeropyrum pernix k1, was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol (peg) 400 as the precipitant. the crystals belong to the hexagonal space group p6(3), with unit-cell parameters a = b = 98.9, c = 394.8 a, alpha = beta = 90, gamma = 120 degrees. the asymmetric unit contained one hexamer of the enzyme, giving a crystal volume per enzyme mass (v(m)) of 1.98 a(3) da(-1) and a solvent content ...200212136148
expression of two kinds of recombinant glutamate dehydrogenase from aeropyrum pernix with different n-terminal sequence length in escherichia coli.two recombinant aeropyrum pernix glutamate dehydrogenase (gdh) enzymes with different length n-termini were cloned and expressed in escherichia coli: sgdh begins with the amino acid sequence of the extracted native enzyme (m-q-p-t-d-p-l-e-e), whereas lgdh begins with the sequence of the predicted orf (m-e-v-l-a-l-q-p-t-d) and is longer than sgdh by five amino acids (m-e-v-l-a). purified recombinant lgdh was more stable than sgdh, indicating that the n-terminal extension, containing mostly hydrop ...200212172610
heterogeneous yet similar introns reside in identical positions of the rrna genes in natural isolates of the archaeon aeropyrum pernix.some archaeal ribosomal dna (rdna) introns carry homing endonuclease-like genes and are therefore assumed to propagate by "intron homing". a previous study demonstrated that three introns are located within the rrna operon (arnsl) of aeropyrum pernix strain k1, two of which, ialpha and igamma, harbor open reading frames (orfs) encoding putative laglidadg-type endonucleases. in an effort to understand further the rdna intron distribution in natural a. pernix populations, 11 a. pernix strains were ...200212242010
the first archaeal atp-dependent glucokinase, from the hyperthermophilic crenarchaeon aeropyrum pernix, represents a monomeric, extremely thermophilic rok glucokinase with broad hexose specificity.an atp-dependent glucokinase of the hyperthermophilic aerobic crenarchaeon aeropyrum pernix was purified 230-fold to homogeneity. the enzyme is a monomeric protein with an apparent molecular mass of about 36 kda. the apparent k(m) values for atp and glucose (at 90 degrees c and ph 6.2) were 0.42 and 0.044 mm, respectively; the apparent v(max) was about 35 u/mg. the enzyme was specific for atp as a phosphoryl donor, but showed a broad spectrum for phosphoryl acceptors: in addition to glucose, whi ...200212374829
holliday junction-resolving enzymes from eight hyperthermophilic archaea differ in reactions with cruciform dna.holliday junction-resolving enzymes have been identified in a broad variety of organisms and tissues. in this study, six new holliday junction-cleaving enzymes (hjcs) were obtained from hyperthermophilic crenarchaeal and euryarchaeal species, including pyrococcus horikoshii, pyrococcus abyssi, methanococcus jannaschii, methanobacterium thermautotrophicum, archaeoglobus fulgidus, and aeropyrum pernix. the genes were cloned and overexpressed in escherichia coli, and the respective proteins were pu ...200212382111
identification and characterization of thioredoxin and thioredoxin reductase from aeropyrum pernix k1.we have identified and characterized a thermostable thioredoxin system in the aerobic hyperthermophilic archaeon aeropyrum pernix k1. the gene (accession no. ape0641) of a. pernix encoding a 37 kda protein contains a redox active site motif (cphc) but its n-terminal extension region (about 200 residues) shows no homology within the genome database. a second gene (accession no. ape1061) has high homology to thioredoxin reductase and encodes a 37 kda protein with the active site motif (csvc), and ...200212423340
crystallization and preliminary x-ray structure analysis of isocitrate dehydrogenase from two hyperthermophiles, aeropyrum pernix and thermotoga maritima.isocitrate dehydrogenase (idh) catalyses the dehydrogenation and decarboxylation of isocitrate to alpha-ketoglutarate and co(2) with nad or nadp as cofactor. idh from aeropyrum pernix is the most thermostable idh identified. crystals of a. pernix idh diffracted to 2.6 a with synchrotron radiation and belong to space group p4(3)2(1)2. idh from thermotoga maritima is the only idh that has been characterized as homotetrameric and might be an evolutionary link between two different idh subfamilies. ...200212454487
aeropyrum pernix k1, a strictly aerobic and hyperthermophilic archaeon, has two terminal oxidases, cytochrome ba3 and cytochrome aa3.aeropyrum pernix k1 is a strictly aerobic and hyperthermophilic archaeon that thrives even at 100 degrees c. the archaeon is quite interesting with respect to the evolution of aerobic electron transport systems and the thermal stability of the respiratory components. an isolated membrane fraction was found to oxidize bovine cytochrome c. the activity was solubilized in the presence of detergents and separated into two fractions by successive chromatography. two cytochrome oxidases, designated as ...200212471503
prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach.by comparing the gene order in the completely sequenced archaeal genomes complemented by sequence profile analysis, we predict the existence and protein composition of the archaeal counterpart of the eukaryotic exosome, a complex of rnases, rna-binding proteins, and helicases that mediates processing and 3'->5' degradation of a variety of rna species. the majority of the predicted archaeal exosome subunits are encoded in what appears to be a previously undetected superoperon. in methanobacterium ...200111157787
sequence, expression, and characterization of the first archaeal atp-dependent 6-phosphofructokinase, a non-allosteric enzyme related to the phosphofructokinase-b sugar kinase family, from the hyperthermophilic crenarchaeote aeropyrum pernix.the gene (orf apf0012) encoding the atp-dependent 6-phosphofructokinase (atp-pfk) of the hyperthermophilic archaeon aeropyrum pernix was identified, cloned, and functionally expressed in escherichia coli. the deduced amino acid sequence showed similarity (25-40%) to members of pfk-b sugar kinases. the purified recombinant enzyme is a heterotetramer of 115 kda, composed of 34-kda subunits. rate dependence (at 85 degrees c) on both fructose 6-phosphate (f-6-p) and atp followed michaelis-menten kin ...200111797046
the biochemical properties and phylogenies of phosphofructokinases from extremophiles.the enzyme phosphofructokinase (pfk) is a defining activity of the highly conserved glycolytic pathway, and is present in the domains bacteria, eukarya, and archaea. pfk subtypes are now known that utilize either atp, adp, or pyrophosphate as the primary phosphoryl donor and share the ability to catalyze the transfer of phosphate to the 1-position of fructose-6-phosphate. because of the crucial position in the glycolytic pathway of pfks, their biochemical characteristics and phylogenies may play ...200111778837
the closest blast hit is often not the nearest neighbor.it is well known that basing phylogenetic reconstructions on uncorrected genetic distances can lead to errors in their reconstruction. nevertheless, it is often common practice to report simply the most similar blast (altschul et al. 1997) hit in genomic reports that discuss many genes (ruepp et al. 2000; freiberg et al. 1997). this is because blast hits can provide a rapid, efficient, and concise analysis of many genes at once. these hits are often interpreted to imply that the gene is most clo ...200111443357
cloning, expression and characterisation of a family b atp-dependent phosphofructokinase activity from the hyperthermophilic crenarachaeon aeropyrum pernix.we have cloned a family b sugar kinase gene from the aerobic hyperthermophilic crenarchaeon aeropyrum pernix and have subsequently expressed the protein in escherichia coli. the enzyme was purified with its associated histidine-tag by affinity chromatography with a nickel-nitrilotriacetic acid column followed by cation exchange chromatography and possesses a high degree of thermostable atp-dependent phosphofructokinase activity. the enzyme has an estimated apparent k(m) for atp and fructose-6-ph ...200111506912
comparison of isocitrate dehydrogenase from three hyperthermophiles reveals differences in thermostability, cofactor specificity, oligomeric state, and phylogenetic affiliation.with the aim of gaining insight into the molecular and phylogenetic relationships of isocitrate dehydrogenase (idh) from hyperthermophiles, we carried out a comparative study of putative idhs identified in the genomes of the eubacterium thermotoga maritima and the archaea aeropyrum pernix and pyrococcus furiosus. an optimum for activity at 90 degrees c or above was found for each idh. pfidh and apidh were the most thermostable with a melting temperature of 103.7 and 109.9 degrees c, respectively ...200111533060
characterization of native glutamate dehydrogenase from an aerobic hyperthermophilic archaeon aeropyrum pernix k1.glutamate dehydrogenase (gdh) was purified and characterized from an aerobic hyperthermophilic archaeon aeropyrum pernix (a. pernix) k1. the enzyme has a hexameric structure with a native molecular mass of about 285 +/- 15 kda. it was specific for nadp and thermostable (74% activity was remained after 5 h incubation at 100 degrees c). the activity of the enzyme increased in the presence of polar water-miscible organic solvents such as acetonitrile, methanol, and ethanol. the n-terminal sequence ...200111549007
Refresh
firstprev
123
nextlast
Displaying items 101 - 200 of 221