Publications

aeropyrum pernix gen. nov., sp. nov., a novel aerobic hyperthermophilic archaeon growing at temperatures up to 100 degrees c.	a novel aerobic hyperthermophilic archaeon was isolated from a coastal solfataric vent at kodakara-jima island, japan. the new isolate, strain k1, is the first strictly aerobic organism growing at temperatures up to 100 degrees c. it grows optimally at 90 to 95 degrees c, ph 7.0, and a salinity of 3.5%. the cells are spherical shaped and 0.8 to 1.2 microns in diameter. various proteinaceous complex compounds served as substrates during aerobic growth. thiosulfate stimulates growth without produc ...	1996	8863437
an extremely heat-stable extracellular proteinase (aeropyrolysin) from the hyperthermophilic archaeon aeropyrum pernix k1.	an extracellular metalloproteinase, which we had designated aeropyrolysin, from the aerobic marine hyperthermophilic archaeon aeropyrum pernix k1 (jcm 9820), was purified by ammonium sulfate precipitation, anionic exchange chromatography, and gel filtration chromatography. the purified enzyme was composed of a single polypeptide chain with a molecular mass of 52 kda as determined by sds-page. the proteinase had a broad ph optimum (ph 5-9) with a maximal activity at ph 6-8 for azocasein hydrolysi ...	1997	9357994
molecular characterization and postsplicing fate of three introns within the single rrna operon of the hyperthermophilic archaeon aeropyrum pernix k1.	the single rrna operon (arns-arnl) of the hyperthermophilic archaeon aeropyrum pernix k1 was sequenced. the dna sequence data and detailed rna analyses disclosed an unusual feature: the presence of three introns at hitherto undescribed insertion positions within the rrna genes. the 699-nucleotide (nt) intron ialpha was located at position 908 (escherichia coli numbering [h. f. noller, annu. rev. biochem. 53:119-162, 1984]) of the 16s rrna, while the 202-nt intron ibeta and 575-nt intron igamma w ...	1998	9658008
a novel phosphoglycolipid archaetidyl(glucosyl)inositol with two sesterterpanyl chains from the aerobic hyperthermophilic archaeon aeropyrum pernix k1.	the structures of two novel polar lipids (agi and ai) of an aerobic hyperthermophilic archaeon, aeropyrum pernix, were elucidated. agi and ai were the only two major lipids and accounted for 91 mol% and 9 mol%, respectively, of total polar lipids of this organism. the core lipid of a. pernix total lipids consisted solely of 2,3-di-o-sesterterpanyl-sn-glycerol (c25,25-archaeol). the molecular weights of the free acid forms of agi and ai were shown by fab-mass spectrometry to be 1196 and 1034, res ...	1999	9989273
purification and characterization of an intracellular heat-stable proteinase (pernilase) from the marine hyperthermophilic archaeon aeropyrum pernix k1.	a novel intracellular serine proteinase from the marine aerobic hyperthermophilic archaeon aeropyrum pernix k1 (jcm 9820) that we designated pernilase was purified by ammonium sulfate precipitation, anionic-exchange chromatography, affinity chromatography, and gel filtration chromatography. the purified enzyme was composed of a single polypeptide chain with a molecular mass of 50 kda as determined by sds-page. the proteinase had a broad ph profile (ph 5-10) with an optimum ph of 9.0 for peptide ...	1999	10086839
complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, aeropyrum pernix k1.	the complete sequence of the genome of an aerobic hyper-thermophilic crenarchaeon, aeropyrum pernix k1, which optimally grows at 95 degrees c, has been determined by the whole genome shotgun method with some modifications. the entire length of the genome was 1,669,695 bp. the authenticity of the entire sequence was supported by restriction analysis of long pcr products, which were directly amplified from the genomic dna. as the potential protein-coding regions, a total of 2,694 open reading fram ...	1999	10382966
a cambialistic sod in a strictly aerobic hyperthermophilic archaeon, aeropyrum pernix.	the superoxide dismutase (sod) gene of aeropyrum pernix, a strictly aerobic hyperthermophilic archaeon, was cloned and expressed in escherichia coli, and its gene product was characterized. the molecular mass of the protein, based on the deduced amino acid sequence, was 24.6 kda. the sequence showed overall similarity to the sequences of known mn- and fe-sods. the metal binding residues conserved in mn- and fe-sods were also found in a. pernix sod. when the sod gene was expressed in e. coli cell ...	1999	10393342
two family b dna polymerases from aeropyrum pernix, an aerobic hyperthermophilic crenarchaeote.	dna polymerase activities in fractionated cell extract of aeropyrum pernix, a hyperthermophilic crenarchaeote, were investigated. aphidicolin-sensitive (fraction i) and aphidicolin-resistant (fraction ii) activities were detected. the activity in fraction i was more heat stable than that in fraction ii. two different genes (pola and polb) encoding family b dna polymerases were cloned from the organism by pcr using degenerated primers based on the two conserved motifs (motif a and b). the deduced ...	1999	10498710
lessons from the aeropyrum pernix genome.	aeropyrum pernix is the first crenarchaeote and first aerobic member of the archaea for which the complete genome sequence has been determined. the sequence confirms the distinct nature of crenarchaeotes and provides new insight into the relationships between the three domains: bacteria, archaea and eukaryotes.	1999	10607556
novel prenyltransferase gene encoding farnesylgeranyl diphosphate synthase from a hyperthermophilic archaeon, aeropyrum pernix. molecularevolution with alteration in product specificity.	prenyltransferases catalyse sequential condensations of isopentenyl diphosphate with allylic diphosphates. previously, we reported the presence of farnesylgeranyl diphosphate (fgpp) synthase activity synthesizing c25 isoprenyl diphosphate in natronobacterium pharaonis which is a haloalkaliphilic archaeon having c20-c25 diether lipids in addition to c20-c20 diether lipids commonly occurring in archaea [tachibana, a. (1994) febs lett. 341, 291-294]. recently, it was found that a newly isolated aer ...	2000	10632701
cloning and characterization of a family b dna polymerase from the hyperthermophilic crenarchaeon pyrobaculum islandicum.	in order to extend the limited knowledge about crenarchaeal dna polymerases, we cloned a gene encoding a family b dna polymerase from the hyperthermophilic crenarchaeon pyrobaculum islandicum. the enzyme shared highest sequence identities with a group of phylogenetically related dna polymerases, designated b3 dna polymerases, from members of the kingdom crenarchaeota, pyrodictium occultum and aeropyrum pernix, and several members of the kingdom euryarchaeota. six highly conserved regions as well ...	2000	10633098
characterization of a thermostable dna glycosylase specific for u/g and t/g mismatches from the hyperthermophilic archaeon pyrobaculum aerophilum.	u/g and t/g mismatches commonly occur due to spontaneous deamination of cytosine and 5-methylcytosine in double-stranded dna. this mutagenic effect is particularly strong for extreme thermophiles, since the spontaneous deamination reaction is much enhanced at high temperature. previously, a u/g and t/g mismatch-specific glycosylase (mth-mig) was found on a cryptic plasmid of the archaeon methanobacterium thermoautotrophicum, a thermophile with an optimal growth temperature of 65 degrees c. we re ...	2000	10671447
recombinant superoxide dismutase from a hyperthermophilic archaeon, pyrobaculum aerophilium.	superoxide dismutase (sod) from the hyperthermophilic archaeon pyrobaculum aerophilum (a facultative aerobe) has been cloned and expressed in a mesophilic host (escherichia coli) as a soluble tetrameric apoprotein. the purified apoprotein can be reconstituted with either mn or fe by heating the protein with the appropriate metal salt at an elevated temperature (95 degrees c). both mn- and fe-reconstituted p. aerophilum sod exhibit superoxide dismutase activity, with the mn-containing enzyme havi ...	2000	10907751
sequence analysis of three family b dna polymerases from the thermoacidophilic crenarchaeon sulfurisphaera ohwakuensis.	three family b dna polymerase genes, designated b1, b2, and b3, were cloned from the thermoacidophilic crenarchaeon sulfurisphaera ohwakuensis, and sequenced. deduced amino acid sequences of b1 and b3 dna polymerases have all exonuclease and polymerase motifs which include critical residues for catalytic activities. furthermore, a yxgg/a motif, which is located between 3'-5' exonuclease and polymerization domains of family b dna polymerases, was also found in each of the b1 and b3 sequences. the ...	2000	10997874
status of genome projects for nonpathogenic bacteria and archaea.	since the first microbial genome was sequenced in 1995, 30 others have been completed and an additional 99 are known to be in progress. although the early emphasis of microbial genomics was on human pathogens for obvious reasons, a significant number of sequencing projects have focused on nonpathogenic organisms, beginning with the release of the complete genome sequence of the archaeon methanococcus jannaschii in 1996. the past 18 months have seen the completion of the genomes of several unusua ...	2000	11017041
links from genome proteins to known 3-d structures.	we describe a genome annotation service provided by the entrez browser, http://www.ncbi.nlm.nih.gov/entrez. all protein products identified in fully sequenced microbial genomes have been compared with proteins with known 3-d structure by use of the blast sequence comparison algorithm. for the approximately 20% of genome proteins in which unambiguous sequence similarity is detected, entrez provides a link from the gene product to its predicted structure. the service uses the cn3d molecular graphi ...	2000	11042161
glutamate dehydrogenase from the aerobic hyperthermophilic archaeon aeropyrum pernix k1: enzymatic characterization, identification of the encoding gene, and phylogenetic implications.	nadp-dependent glutamate dehydrogenase (l-glutamate: nadp oxidoreductase, deaminating, ec 1.4.1.4) from the aerobic hyperthermophilic archaeon aeropyrum pernix k1 (jcm 9820) was purified to homogeneity for characterization. the enzyme retained its full activity on heating at 95 degrees c for 30 min, and the maximum activity in l-glutamate deamination was obtained around 100 degrees c. the enzyme showed a strict specificity for l-glutamate and nadp on oxidative deamination and for 2-oxoglutarate ...	2000	11139075
phylogenetic analysis of archaeal pcna homologues.	proliferating cell nuclear antigen (pcna) is an essential component of the dna replication and repair machinery in the domain eucarya. eukaryotes and euryarchaeotes, which belong to one subdomain of archaea, possess a single pcna homologue, whereas two distinct pcna homologues have been identified from sulfolobus solfataricus, which belongs to the other archaeal subdomain, crenarchaeota. we have cloned and sequenced two genes of pcna homologues from the thermoacidophilic crenarchaeon sulfurispha ...	2000	11139078
towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (cogs).	standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. we used the database of clusters of orthologous groups of proteins (cogs) to reannotate the genomes of two archaea, aeropyrum pernix, the first member of the crenarchaea to be sequenced, and pyrococcus abyssi.	2000	11178258
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 ...	2001	11443357
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 ...	2001	11506912
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 ...	2001	11533060
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 ...	2001	11549007
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 ...	2001	11778837
recognition of trna by aminoacyl-trna synthetase from hyperthermophilic archaea, aeropyrum pernix k1.	to study the recognition sites of trna for archaeal aminoacyl-trna synthetase, several aminoacyl-trna synthetase genes from hyperthermophilic archaeon, aeropyrum pernix k1 were cloned and expressed. all the expressed enzymes showed extreme thermostability. expressed threonyl-trna synthetase threonylated not only archaeal (a. pernix and haloferax volcanii) threonine trnas but also escherichia coli threonine trna. however, threonyl-trna synthetase from h. volcanii did not threonylate e. coli threo ...	2001	12836292
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 ...	2001	11157787
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 ...	2001	11797046
conserved 'hypothetical' proteins: new hints and new puzzles.	conserved hypothetical proteins, i.e. conserved proteins whose functions are still unknown, pose a challenge not just to functional genomics but also to general biology. for many conserved proteins, computational analysis provides only a general prediction of biochemical function; their exact biological functions have to be established through direct experimentation. in the few cases when this has been accomplished, the results were remarkable, revealing the deoxyxylulose pathway and a new essen ...	2001	18628897
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 ...	2002	11846799
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 ...	2002	11884142
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 ...	2002	11956692
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 ...	2002	12029047
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 ...	2002	12036066
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 ...	2002	12037315
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 ...	2002	12107280
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 ...	2002	12107592
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 ...	2002	12136148
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 ...	2002	12172610
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 ...	2002	12242010
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 ...	2002	12374829
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 ...	2002	12382111
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 ...	2002	12423340
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. ...	2002	12454487
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 ...	2002	12471503
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 ...	2002	12903115
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 ...	2002	12903187
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 ...	2002	11784332
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 ...	2002	11790738
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. ...	2002	11755525
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.	2003	12839824
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 ...	2003	16233467
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 ...	2003	12908102
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 ...	2003	12927540
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 ...	2003	12935888
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 ...	2003	12965218
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 ...	2003	12967964
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 ...	2003	14510473
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 ...	2003	12499562
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 ...	2003	12529358
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 ...	2003	12554945
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 ...	2003	12626506
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 ...	2003	12643768
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 ...	2003	12644499
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 ...	2003	12654928
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 ...	2003	12707274
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 ...	2003	12721618
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 ...	2003	12761185
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 ...	2003	12801633
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 ...	2004	14551194
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 ...	2004	14765197
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 ...	2004	14996791
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).	2004	15003120
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, ...	2004	15023940
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 ...	2004	15046583
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 ...	2004	15046584
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 ...	2004	15096613
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 ...	2004	15135393
crystal structure of isocitrate dehydrogenase from aeropyrum pernix.		2004	15146507
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 ...	2004	15177687
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 ...	2004	15177692
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 ...	2004	15201054
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 ...	2004	15287735
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 ...	2004	15296741
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 ...	2004	15306816
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 ...	2004	15333947
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 ...	2004	15333952
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 ...	2004	15388928
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 ...	2004	15465044
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 ...	2004	15476396
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 ...	2004	15548566
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 ...	2004	16233615
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- ...	2004	17150540
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 ...	2004	15871459
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 ...	2005	15876564
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 ...	2005	15876567
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 ...	2005	16005886
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 ...	2005	16049020
bending and cutting forks and flaps.		2005	16084380
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 ...	2005	16143816
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 ...	2005	16199559