Publications

divergent anticodon recognition in contrasting glutamyl-trna synthetases.	the pathogenic bacterium helicobacter pylori utilizes two essential glutamyl-trna synthetases (glurs1 and glurs2). these two enzymes are closely related in evolution and yet they aminoacylate contrasting trnas. glurs1 is a canonical discriminating glurs (d-glurs) that biosynthesizes glu-trna(glu) and cannot make glu-trna(gln). in contrast, glurs2 is non-canonical as it is only essential for the production of misacylated glu-trna(gln). the co-existence and evident divergence of these two enzymes ...	2004	15561136
cloning of cvipii nicking and modification system from chlorella virus nys-1 and application of nt.cvipii in random dna amplification.	the cloning and expression of the cvipii dna nicking and modification system encoded by chlorella virus nys-1 is described. the system consists of a co-linear mtase encoding gene (cvipiim) and a nicking endonuclease encoding gene (cvipiint) separated by 12 nt. m.cvipii possesses eight conserved amino acid motifs (i to viii) typical of c5 mtases, but, like another chlorella virus mtase m.cviji, lacks conserved motifs ix and x. in addition to modification of the first cytosine in ccd (d = a, g or ...	2004	15570069
mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization.	in fluorescent in situ hybridization (fish), the efficiency of hybridization between the dna probe and the rrna has been related to the accessibility of the rrna when ribosome content and cell permeability are not limiting. published rrna accessibility maps show that probe brightness is sensitive to the organism being hybridized and the exact location of the target site and, hence, it is highly unpredictable based on accessibility only. in this study, a model of fish based on the thermodynamics ...	2004	15574909
characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library.	it has been estimated that less than 1% of the microorganisms in nature can be cultivated by conventional techniques. thus, the classical approach of isolating enzymes from pure cultures allows the analysis of only a subset of the total naturally occurring microbiota in environmental samples enriched in microorganisms. to isolate useful microbial enzymes from uncultured soil microorganisms, a metagenome was isolated from soil samples, and a metagenomic library was constructed by using the puc19 ...	2004	15574921
in vivo 31p nuclear magnetic resonance investigation of tellurite toxicity in escherichia coli.	here we compare the physiological state of escherichia coli exposed to tellurite or selenite by using the noninvasive technique of phosphorus-31 nuclear magnetic resonance (nmr) spectroscopy. we studied glucose-fed escherichia coli hb101 cells containing either a normal puc8 plasmid with no tellurite resistance determinants present or the ptwt100 plasmid which contains the resistance determinants tehab. no differences could be observed in intracellular atp levels, the presence or absence of a tr ...	2004	15574934
thermoadaptation trait revealed by the genome sequence of thermophilic geobacillus kaustophilus.	we present herein the first complete genome sequence of a thermophilic bacillus-related species, geobacillus kaustophilus hta426, which is composed of a 3.54 mb chromosome and a 47.9 kb plasmid, along with a comparative analysis with five other mesophilic bacillar genomes. upon orthologous grouping of the six bacillar sequenced genomes, it was found that 1257 common orthologous groups composed of 1308 genes (37%) are shared by all the bacilli, whereas 839 genes (24%) in the g.kaustophilus genome ...	2004	15576355
paradoxical homozygous expression from heterozygotes and heterozygous expression from homozygotes as a consequence of transcriptional infidelity through a polyadenine tract in the ap3b1 gene responsible for canine cyclic neutropenia.	canine cyclic neutropenia is an autosomal recessive disease in which the number of neutrophils, the primary blood phagocyte, oscillates between almost zero and normal values with two week frequency. we previously found that the causative mutation is an insertion of an extra adenine residue within a tract of nine a's in exon 21 of the 27 exon canine ap3b1 gene. in the course of identifying the mutation, however, we observed an unusual phenomenon: heterozygous carrier dogs, who have one normal all ...	2004	15576359
control of rrna synthesis in escherichia coli: a systems biology approach.	the first part of this review contains an overview of the various contributions and models relating to the control of rrna synthesis reported over the last 45 years. the second part describes a systems biology approach to identify the factors and effectors that control the interactions between rna polymerase and rrna (rrn) promoters of escherichia coli bacteria during exponential growth in different media. this analysis is based on measurements of absolute rrn promoter activities as transcripts ...	2004	15590778
pa-agog, the founding member of a new family of archaeal 8-oxoguanine dna-glycosylases.	oxidative damage represents a major threat to genomic stability, as the major product of dna oxidation, 8-oxoguanine (go), frequently mispairs with adenine during replication. in order to prevent these mutagenic events, organisms have evolved go-dna glycosylases that remove this oxidized base from dna. we were interested to find out how go is processed in the hyperthermophilic archaeon pyrobaculum aerophilum, which lives at temperatures around 100 degrees c. to this end, we searched its genome f ...	2004	15604455
ddbj in the stream of various biological data.	in the past year we at ddbj (http://www.ddbj.nig. ac.jp) have made a steady increase in the number of data submissions with a 50.6% increment in the number of bases or 46.5% increment in the number of entries. among them the genome data of man, ascidian and rice hold the top three. our activity has extended to providing a tool that enables sequence retrieval using regular expressions, and to launching our soap server and web services to facilitate the acquisition of proper data and tools from a ...	2004	14681352
genetic evidence against the 16s ribosomal rna helix 27 conformational switch model.	a mechanistic understanding of ribosome function demands knowledge of the conformational changes that occur during protein synthesis. one current model proposes a conformational switch in helix 27 (h27) of 16s rrna involved in the decoding of mrna. this model was based on the behavior of mutations in the 912 region of h27 of escherichia coli 16s rrna, which were predicted to stabilize the helix in either of two alternative conformations. this interpretation was supported by evidence from both ge ...	2004	14681582
purine bases at position 37 of trna stabilize codon-anticodon interaction in the ribosomal a site by stacking and mg2+-dependent interactions.	the anticodon loop of trna contains a number of conserved or semiconserved nucleotides. in most trnas, a highly modified purine is found at position 37 immediately 3' to the anticodon. here, we examined the role of the base at position 37 for trna(phe) binding to the a site of escherichia coli ribosomes. affinities and rate constants of a-site binding of native yeast peptidyl-trna(phe) with hypermodified g (wybutine), or of unmodified peptidyl-trna(phe) transcripts with g, a, c, or u, at positio ...	2004	14681588
crystal structure of a central stalk subunit c and reversible association/dissociation of vacuole-type atpase.	the vacuole-type atpases (v-atpases) exist in various intracellular compartments of eukaryotic cells to regulate physiological processes by controlling the acidic environment. the crystal structure of the subunit c of thermus thermophilus v-atpase, homologous to eukaryotic subunit d of v-atpases, has been determined at 1.95-a resolution and located into the holoenzyme complex structure obtained by single particle analysis as suggested by the results of subunit cross-linking experiments. the resu ...	2004	14684831
thermostability of multidomain proteins: elongation factors ef-tu from escherichia coli and bacillus stearothermophilus and their chimeric forms.	recombinant mesophilic escherichia coli (ec) and thermophilic bacillus stearothermophilus (bst) elongation factors ef-tus, their isolated g-domains, and six chimeric ef-tus composed of domains of either ef-tu were prepared, and their gdp/gtp binding activities and thermostability were characterized. bstef-tu and bstg-domain bound gdp and gtp with affinities in nanomolar and submicromolar ranges, respectively, fully comparable with those of ecef-tu. in contrast, the ecg-domain bound the nucleotid ...	2004	14691225
expression and biochemical characterization of two small heat shock proteins from the thermoacidophilic crenarchaeon sulfolobus tokodaii strain 7.	we expressed and characterized two shsps, sthsp19.7 and sthsp14.0, from a thermoacidophilic crenarchaeon, sulfolobus tokodaii strain 7. sthsp19.7 forms a filamentous structure consisting of spherical particles and lacks molecular chaperone activity. fractionation of sulfolobus extracts by size exclusion chromatography with immunoblotting indicates that sthsp19.7 exists as a filamentous structure in vivo. on the other hand, sthsp14.0 exists as a spherical oligomer like other shsps. it showed mole ...	2004	14691229
crystal structure of the hyperthermophilic inorganic pyrophosphatase from the archaeon pyrococcus horikoshii.	a homolog to the eubacteria inorganic pyrophosphatase (ppase, ec 3.6.1.1) was found in the genome of the hyperthermophilic archaeon pyrococcus horikoshii. this inorganic pyrophosphatase (pho-ppase) grows optimally at 88 degrees c. to understand the structural basis for the thermostability of pho-ppase, we have determined the crystal structure to 2.66 a resolution. the crystallographic asymmetric unit contains three monomers related by approximate threefold symmetry, and a hexamer is built up by ...	2004	14695284
dihydropteridine reductase as an alternative to dihydrofolate reductase for synthesis of tetrahydrofolate in thermus thermophilus.	a strategy devised to isolate a gene coding for a dihydrofolate reductase from thermus thermophilus dna delivered only clones harboring instead a gene (the t. thermophilus dehydrogenase [dh(tt)] gene) coding for a dihydropteridine reductase which displays considerable dihydrofolate reductase activity (about 20% of the activity detected with 6,7-dimethyl-7,8-dihydropterine in the quinonoid form as a substrate). dh(tt) appears to account for the synthesis of tetrahydrofolate in this bacterium, sin ...	2004	14702303
interactions between the 2.4 and 4.2 regions of sigmas, the stress-specific sigma factor of escherichia coli, and the -10 and -35 promoter elements.	the sigmas subunit of escherichia coli rna polymerase holoenzyme (esigmas) is a key factor of gene expression upon entry into stationary phase and in stressful conditions. the selectivity of promoter recognition by esigmas and the housekeeping esigma70 is as yet not clearly understood. we used a genetic approach to investigate the interaction of sigmas with its target promoters. starting with down-promoter variants of a sigmas promoter target, osmep, altered in the -10 or -35 elements, we isolat ...	2004	14704342
adaptation to extreme environments: macromolecular dynamics in bacteria compared in vivo by neutron scattering.	mean macromolecular dynamics was quantified in vivo by neutron scattering in psychrophile, mesophile, thermophile and hyperthermophile bacteria. root mean square atomic fluctuation amplitudes determining macromolecular flexibility were found to be similar for each organism at its physiological temperature ( approximately 1 a in the 0.1 ns timescale). effective force constants determining the mean macromolecular resilience were found to increase with physiological temperature from 0.2 n/m for the ...	2004	14710189
adaptation to extreme environments: macromolecular dynamics in bacteria compared in vivo by neutron scattering.	mean macromolecular dynamics was quantified in vivo by neutron scattering in psychrophile, mesophile, thermophile and hyperthermophile bacteria. root mean square atomic fluctuation amplitudes determining macromolecular flexibility were found to be similar for each organism at its physiological temperature ( approximately 1 a in the 0.1 ns timescale). effective force constants determining the mean macromolecular resilience were found to increase with physiological temperature from 0.2 n/m for the ...	2004	14710189
rapid and specific detection of salmonella spp. in animal feed samples by pcr after culture enrichment.	a pcr procedure has been developed for routine analysis of viable salmonella spp. in feed samples. the objective was to develop a simple pcr-compatible enrichment procedure to enable dna amplification without any sample pretreatment such as dna extraction or cell lysis. pcr inhibition by 14 different feed samples and natural background flora was circumvented by the use of the dna polymerase tth. this dna polymerase was found to exhibit a high level of resistance to pcr inhibitors present in thes ...	2004	14711627
the single-stranded dna-binding protein of deinococcus radiodurans.	deinococcus radiodurans r1 is one of the most radiation-resistant organisms known and is able to repair an unusually large amount of dna damage without induced mutation. single-stranded dna-binding (ssb) protein is an essential protein in all organisms and is involved in dna replication, recombination and repair. the published genomic sequence from deinococcus radiodurans includes a putative single-stranded dna-binding protein gene (ssb; dr0100) requiring a translational frameshift for synthesis ...	2004	14718065
direct glutaminyl-trna biosynthesis and indirect asparaginyl-trna biosynthesis in pseudomonas aeruginosa pao1.	the genomic sequence of pseudomonas aeruginosa pao1 was searched for the presence of open reading frames (orfs) encoding enzymes potentially involved in the formation of gln-trna and of asn-trna. we found orfs similar to known glutamyl-trna synthetases (glurs), glutaminyl-trna synthetases (glnrs), aspartyl-trna synthetases (asprs), and trimeric trna-dependent amidotransferases (adt) but none similar to known asparaginyl-trna synthetases (asnrs). the absence of asnrs was confirmed by biochemical ...	2004	14729703
crystal structure of the catalytic domain of rlud, the only rrna pseudouridine synthase required for normal growth of escherichia coli.	escherichia coli pseudouridine synthase rlud makes pseudouridines 1911, 1915, and 1917 in the loop of helix 69 in 23s rna. these are the most highly conserved ribosomal pseudouridines known. of 11 pseudouridine synthases in e. coli, only cells lacking rlud have severe growth defects and abnormal ribosomes. we have determined the 2.0 a structure of the catalytic domain of rlud (residues 77-326), the first structure of an rlua family member. the catalytic domain folds into a mainly antiparallel be ...	2004	14730022
a primordial rna modification enzyme: the case of trna (m1a) methyltransferase.	the modified nucleoside 1-methyladenosine (m(1)a) is found in the t-loop of many trnas from organisms belonging to the three domains of life (eukaryota, bacteria, archaea). in the t-loop of eukaryotic and bacterial trnas, m(1)a is present at position 58, whereas in archaeal trnas it is present at position(s) 58 and/or 57, m(1)a57 being the obligatory intermediate in the biosynthesis of 1-methylinosine (m(1)i57). in yeast, the formation of m(1)a58 is catalysed by the essential trna (m(1)a58) meth ...	2004	14739239
in vitro selection and characterization of resistance to macrolides and related antibiotics in mycoplasma pneumoniae.	macrolide-resistant mutants of mycoplasma pneumoniae were selected in vitro from the susceptible reference strain m129, by 23 to 50 serial passages in subinhibitory concentrations of macrolides and related antibiotics, erythromycin a, azithromycin, josamycin, clindamycin, quinupristin, quinupristin-dalfopristin, pristinamycin, and telithromycin. mutants for which the mics are increased could be selected with all antibiotics except the streptogramin b quinupristin. portions of genes encoding 23s ...	2004	14742195
the clamp-loader-helicase interaction in bacillus. atomic force microscopy reveals the structural organisation of the dnab-tau complex in bacillus.	the clamp-loader-helicase interaction is an important feature of the replisome. although significant biochemical and structural work has been carried out on the clamp-loader-clamp-dna polymerase alpha interactions in escherichia coli, the clamp-loader-helicase interaction is poorly understood by comparison. the tau subunit of the clamp-loader mediates the interaction with dnab. we have recently characterised this interaction in the bacillus system and established a tau(5)-dnab(6) stoichiometry. ...	2004	14757052
pre-steady-state kinetics shows differences in processing of various dna lesions by escherichia coli formamidopyrimidine-dna glycosylase.	formamidopyrimidine-dna-glycosylase (fpg protein, mutm) catalyses excision of 8-oxoguanine (8-oxog) and other oxidatively damaged purines from dna in a glycosylase/apurinic/apyrimidinic-lyase reaction. we report pre-steady-state kinetic analysis of fpg action on oligonucleotide duplexes containing 8-oxo-2'-deoxyguanosine, natural abasic site or tetrahydrofuran (an uncleavable abasic site analogue). monitoring fpg intrinsic tryptophan fluorescence in stopped-flow experiments reveals multiple conf ...	2004	14769949
interactions among cii protein, rna polymerase and the lambda pre promoter: contacts between rna polymerase and the -35 region of pre are identical in the presence and absence of cii protein.	the dna recognition sequence for the transcriptional activator, cii protein, which is critical for lysogenization by bacteriophage lambda, overlaps the -35 region of the p(re) promoter. data presented here show that activation by cii does not change the pattern of cleavage of the -35 region of p(re) by iron (s)-1-(p-bromoacetamidobenzyl)-edta (fe-babe) conjugated to the sigma subunit of rna polymerase (rnap). thus, the overall interaction between sigma and the -35 region of p(re) is not signific ...	2004	14872063
atypical archaeal trna pyrrolysine transcript behaves towards ef-tu as a typical elongator trna.	the newly discovered trna(pyl) is involved in specific incorporation of pyrrolysine in the active site of methylamine methyltransferases in the archaeon methanosarcina barkeri. in solution probing experiments, a transcript derived from trna(pyl) displays a secondary fold slightly different from the canonical cloverleaf and interestingly similar to that of bovine mitochondrial trna(ser)(uga). aminoacylation of trna(pyl) transcript by a typical class ii synthetase, lysrs from yeast, was possible w ...	2004	14872064
mycobacterium tuberculosis rv2118c codes for a single-component homotetrameric m1a58 trna methyltransferase.	modified nucleosides in trnas play important roles in trna structure, biosynthesis and function, and serve as crucial determinants of bacterial growth and virulence. in the yeast saccharomyces cerevisiae, mutants defective in n1-methylation of a highly conserved adenosine (a58) in the tpsic loop of initiator trna are non-viable. the yeast m1a58 methyltransferase is a heterotetramer consisting of two different polypeptide chains, gcd14p and gcd10p. interestingly, while m1a58 is not found in most ...	2004	14960715
functional group recognition at the aminoacylation and editing sites of e. coli valyl-trna synthetase.	to correct misactivation and misacylation errors, escherichia coli valyl-trna synthetase (valrs) catalyzes a trna(val)-dependent editing reaction at a site distinct from its aminoacylation site. here we examined the effects of replacing the conserved 3'-adenosine of trna(val) with nucleoside analogs, to identify structural elements of the 3'-terminal nucleoside necessary for trna function at the aminoacylation and editing sites of valrs. the results show that the exocyclic amino group (n6) is no ...	2004	14970394
domain movements of elongation factor eef2 and the eukaryotic 80s ribosome facilitate trna translocation.	an 11.7-a-resolution cryo-em map of the yeast 80s.eef2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eef2 and the 80s ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. sordarin positions domain iii of eef2 so that it can interact with the sarcin-ricin loop of 25s rrna and protein rps23 (s12p). this particular conformation explains the inhibitory action of sordari ...	2004	14976550
dominant gain-of-function mutations in hsp104p reveal crucial roles for the middle region.	heat-shock protein 104 (hsp104p) is a protein-remodeling factor that promotes survival after extreme stress by disassembling aggregated proteins and can either promote or prevent the propagation of prions (protein-based genetic elements). hsp104p can be greatly overexpressed without slowing growth, suggesting tight control of its powerful protein-remodeling activities. we isolated point mutations in hsp104p that interfere with this control and block cell growth. each mutant contained alterations ...	2004	14978213
differential recruitment of nuclear receptor coactivators may determine alternative rna splice site choice in target genes.	the biological consequences of steroid hormone-mediated transcriptional activation of target genes might be difficult to predict because alternative splicing of a single neosynthesized precursor rna can result in production of different protein isoforms with opposite biological activities. therefore, an important question to address is the manner in which steroid hormones affect the splicing of their target gene transcripts. in this report, we demonstrate that individual steroid hormones had dif ...	2004	14982999
x-ray crystallography study on ribosome recycling: the mechanism of binding and action of rrf on the 50s ribosomal subunit.	this study presents the crystal structure of domain i of the escherichia coli ribosome recycling factor (rrf) bound to the deinococcus radiodurans 50s subunit. the orientation of rrf is consistent with the position determined on a 70s-rrf complex by cryoelectron microscopy (cryo-em). alignment, however, requires a rotation of 7 degrees and a shift of the cryo-em rrf by a complete turn of an alpha-helix, redefining the contacts established with ribosomal components. at 3.3 a resolution, rrf is se ...	2004	15616575
x-ray crystallography study on ribosome recycling: the mechanism of binding and action of rrf on the 50s ribosomal subunit.	this study presents the crystal structure of domain i of the escherichia coli ribosome recycling factor (rrf) bound to the deinococcus radiodurans 50s subunit. the orientation of rrf is consistent with the position determined on a 70s-rrf complex by cryoelectron microscopy (cryo-em). alignment, however, requires a rotation of 7 degrees and a shift of the cryo-em rrf by a complete turn of an alpha-helix, redefining the contacts established with ribosomal components. at 3.3 a resolution, rrf is se ...	2004	15616575
selenocysteine trna-specific elongation factor selb is a structural chimaera of elongation and initiation factors.	in all three kingdoms of life, selb is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a uga stop codon in the presence of a downstream mrna hairpin loop. here, we present the x-ray structures of selb from the archaeon methanococcus maripaludis in the apo-, gdp- and gppnhp-bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl-binding pocket. all three s ...	2004	15616587
selenocysteine trna-specific elongation factor selb is a structural chimaera of elongation and initiation factors.	in all three kingdoms of life, selb is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a uga stop codon in the presence of a downstream mrna hairpin loop. here, we present the x-ray structures of selb from the archaeon methanococcus maripaludis in the apo-, gdp- and gppnhp-bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl-binding pocket. all three s ...	2004	15616587
the structure of a rigorously conserved rna element within the sars virus genome.	we have solved the three-dimensional crystal structure of the stem-loop ii motif (s2m) rna element of the sars virus genome to 2.7-a resolution. sars and related coronaviruses and astroviruses all possess a motif at the 3' end of their rna genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable rna genome. we find that this extreme conservation is clearly explained by the requirement to form a highly structured rna ...	2004	15630477
the structure of a rigorously conserved rna element within the sars virus genome.	we have solved the three-dimensional crystal structure of the stem-loop ii motif (s2m) rna element of the sars virus genome to 2.7-a resolution. sars and related coronaviruses and astroviruses all possess a motif at the 3' end of their rna genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable rna genome. we find that this extreme conservation is clearly explained by the requirement to form a highly structured rna ...	2004	15630477
genomic and proteomic adaptations to growth at high temperature.	most positively selected mutations cause changes in metabolism, resulting in a better-adapted phenotype. but as well as acting on the information content of genes, natural selection may also act directly on nucleic acid and protein molecules. we review the evidence for direct temperature-dependent natural selection acting on genomes, transcriptomes and proteomes.	2004	15461805
sigi: score-based identification of genomic islands.	genomic islands can be observed in many microbial genomes. these stretches of dna have a conspicuous composition with regard to sequence or encoded functions. genomic islands are assumed to be frequently acquired via horizontal gene transfer. for the analysis of genome structure and the study of horizontal gene transfer, it is necessary to reliably identify and characterize these islands.	2004	15113412
prediction of rna-binding proteins from primary sequence by a support vector machine approach.	elucidation of the interaction of proteins with different molecules is of significance in the understanding of cellular processes. computational methods have been developed for the prediction of protein-protein interactions. but insufficient attention has been paid to the prediction of protein-rna interactions, which play central roles in regulating gene expression and certain rna-mediated enzymatic processes. this work explored the use of a machine learning method, support vector machines (svm) ...	2004	14970381
the trna world.		2004	14970379
the acetate switch.	to succeed, many cells must alternate between life-styles that permit rapid growth in the presence of abundant nutrients and ones that enhance survival in the absence of those nutrients. one such change in life-style, the "acetate switch," occurs as cells deplete their environment of acetate-producing carbon sources and begin to rely on their ability to scavenge for acetate. this review explains why, when, and how cells excrete or dissimilate acetate. the central components of the "switch" (phos ...	2005	15755952
the tyra family of aromatic-pathway dehydrogenases in phylogenetic context.	the tyra protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to l-tyrosine and a third reaction that is not part of tyrosine biosynthesis. family members share a catalytic core region of about 30 kda, where inhibitors operate competitively by acting as substrate mimics. this protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size.	2005	15888209
the archaeal origins of the eukaryotic translational system.	among the 78 eukaryotic ribosomal proteins, eleven are specific to eukarya, 33 are common only to archaea and eukarya and 34 are homologous (at least in part) to those of both bacteria and archaea. several other translational proteins are common only to eukarya and archaea (e.g., if2a, srp19, etc.), whereas others are shared by the three phyla (e.g., eftu/ef1a and srp54). although this and other analyses strongly support an archaeal origin for a substantial fraction of the eukaryotic translation ...	2005	16877317
the archaeal origins of the eukaryotic translational system.	among the 78 eukaryotic ribosomal proteins, eleven are specific to eukarya, 33 are common only to archaea and eukarya and 34 are homologous (at least in part) to those of both bacteria and archaea. several other translational proteins are common only to eukarya and archaea (e.g., if2a, srp19, etc.), whereas others are shared by the three phyla (e.g., eftu/ef1a and srp54). although this and other analyses strongly support an archaeal origin for a substantial fraction of the eukaryotic translation ...	2005	16877317
inhibition of bacterial rna polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.	we define the target, mechanism, and structural basis of inhibition of bacterial rna polymerase (rnap) by the tetramic acid antibiotic streptolydigin (stl). stl binds to a site adjacent to but not overlapping the rnap active center and stabilizes an rnap-active-center conformational state with a straight-bridge helix. the results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix rnap-active-center conformations exist and that cycling between st ...	2005	16122422
enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of epsilonproteobacteria.	the carbon and energy metabolisms of a variety of cultured chemolithoautotrophic epsilonproteobacteria from deep-sea hydrothermal environments were characterized by both enzymatic and genetic analyses. all the epsilonproteobacteria tested had all three key reductive tricarboxylic acid (rtca) cycle enzymatic activities--atp-dependent citrate lyase, pyruvate:ferredoxin oxidoreductase, and 2-oxoglutarate:ferredoxin oxidoreductase--while they had no ribulose 1,5-bisphosphate carboxylase (rubisco) ac ...	2005	16269773
comparative genomic analyses of the bacterial phosphotransferase system.	we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ...	2005	16339738
protein subunit interfaces: heterodimers versus homodimers.	protein dimers are either homodimers (complexation of identical monomers) or heterodimers (complexation of non-identical monomers). these dimers are common in catalysis and regulation. however, the molecular principles of protein dimer interactions are difficult to understand mainly due to the geometrical and chemical characteristics of proteins. nonetheless, the principles of protein dimer interactions are often studied using a dataset of 3d structural complexes determined by x-ray crystallogra ...	2005	17597849
predicted highly expressed genes in archaeal genomes.	based primarily on 16s rrna sequence comparisons, life has been broadly divided into the three domains of bacteria, archaea, and eukarya. archaea is further classified into crenarchaea and euryarchaea. archaea generally thrive in extreme environments as assessed by temperature, ph, and salinity. for many prokaryotic organisms, ribosomal proteins (rp), transcription/translation factors, and chaperone genes tend to be highly expressed. a gene is predicted highly expressed (phx) if its codon usage ...	2005	15883368
transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in is element gene expression.	transcription slippage occurs on certain patterns of repeat mononucleotides, resulting in synthesis of a heterogeneous population of mrnas. individual mrna molecules within this population differ in the number of nucleotides they contain that are not specified by the template. when transcriptional slippage occurs in a coding sequence, translation of the resulting mrnas yields more than one protein product. except where the products of the resulting mrnas have distinct functions, transcription sl ...	2005	15774026
clustering the annotation space of proteins.	current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas.	2005	15703069
structural basis for transcription inhibition by tagetitoxin.	tagetitoxin (tgt) inhibits transcription by an unknown mechanism. a structure at a resolution of 2.4 a of the thermus thermophilus rna polymerase (rnap)-tgt complex revealed that the tgt-binding site within the rnap secondary channel overlaps that of the stringent control effector ppgpp, which partially protects rnap from tgt inhibition. tgt binding is mediated exclusively through polar interactions with the beta and beta' residues whose substitutions confer resistance to tgt in vitro. important ...	2005	16273103
bacterial chromosome segregation: structure and dna binding of the soj dimer--a conserved biological switch.	soj and spo0j of the gram-negative hyperthermophile thermus thermophilus belong to the conserved parab family of bacterial proteins implicated in plasmid and chromosome partitioning. spo0j binds to dna near the replication origin and localises at the poles following initiation of replication. soj oscillates in the nucleoid region in an atp- and spo0j-dependent fashion. here, we show that soj undergoes atp-dependent dimerisation in solution and forms nucleoprotein filaments with dna. crystal stru ...	2005	15635448
high-level overproduction of his-tagged tth dna polymerase in thermus thermophilus.	a new plasmid for the overexpression of his-tagged thermozymes in thermus thermophilus was developed. with this plasmid, soluble and active histidine-tagged dna polymerase from t. thermophilus was overproduced in larger amounts in the thermophile than in escherichia coli. the protein purified from the thermophile was active in pcr.	2005	15640243
isolation and characterization of a thermostable rna ligase 1 from a thermus scotoductus bacteriophage ts2126 with good single-stranded dna ligation properties.	we have recently sequenced the genome of a novel thermophilic bacteriophage designated as ts2126 that infects the thermophilic eubacterium thermus scotoductus. one of the annotated open reading frames (orfs) shows homology to t4 rna ligase 1, an enzyme of great importance in molecular biology, owing to its ability to ligate single-stranded nucleic acids. the orf was cloned, and recombinant protein was expressed, purified and characterized. the recombinant enzyme ligates single-stranded nucleic a ...	2005	15642699
crystal structure of mil (mth680): internal duplication and similarity between the imp4/brix domain and the anticodon-binding domain of class iia aminoacyl-trna synthetases.	proteins of the imp4/brix superfamily are involved in ribosomal rna processing, an essential function in all cells. we report the first structure of an imp4/brix superfamily protein, the mil (for methanothermobacter thermautotrophicus imp4-like) protein (gene product mth680), from the archaeon m. thermautotrophicus. the amino- and carboxy-terminal halves of mil show significant structural similarity to one another, suggesting an origin by means of an ancestral duplication. both halves show the s ...	2005	15654320
breaking sieve for steric exclusion of a noncognate amino acid from active site of a trna synthetase.	the genetic code is fixed in aminoacylation reactions catalyzed by aminoacyl-trna synthetases. amino acid discrimination occurs at two sites: one for amino acid activation and aminoacylation and one for editing misactivated amino acids. although the active site sieves out bulkier amino acids, misactivation occurs with substrates whose side chains are smaller than the cognate one. paradoxically, although alanyl-trna synthetase activates glycine as well as alanine, the sterically larger (than alan ...	2005	15657145
the snrnp 15.5k protein folds its cognate k-turn rna: a combined theoretical and biochemical study.	the human 15.5k protein binds to the 5' stem-loop of u4 snrna, promotes the assembly of the spliceosomal u4/u6 snrnp, and is required for the recruitment of the 61k protein and the 20/60/90k protein complex to the u4 snrna. in the crystallographic structure of the 15.5k-u4 snrna complex, the conformation of the rna corresponds to the family of kink-turn (k-turn) structural motifs. we simulated the complex and the free rna, showing how the protein binding and the intrinsic flexibility contribute ...	2005	15659359
genetic analysis reveals domain interactions of arabidopsis hsp100/clpb and cooperation with the small heat shock protein chaperone system.	we have defined amino acids important for function of the arabidopsis thaliana hsp100/clpb chaperone (athsp101) in acquired thermotolerance by isolating recessive, loss-of-function mutations and a novel semidominant, gain-of-function allele [hot1-4 (a499t)]. the hot1-4 allele is unusual in that it not only fails to develop thermotolerance to 45 degrees c after acclimation at 38 degrees c, but also is sensitive to 38 degrees c, which is a permissive temperature for wild-type and loss-of-function ...	2005	15659638
biogenesis of a putative channel protein, comec, required for dna uptake: membrane topology, oligomerization and formation of disulphide bonds.	comec is a putative channel protein for dna uptake in bacillus subtilis and other genetically transformable bacteria. membrane topology studies suggest a model of comec as a multispanning membrane protein with seven transmembrane segments (tmss), and possibly with one laterally inserted amphipathic helix. we show that comec contains an intramolecular disulphide bond in its n-terminal extracellular loop (between the residues c131 and c172), which is required for the stability of the protein, and ...	2005	15661011
interaction of rrf and ef-g from e. coli and t. thermophilus with ribosomes from both origins--insight into the mechanism of the ribosome recycling step.	ribosome recycling factor (rrf), elongation factor-g (ef-g), and ribosomes from thermus thermophilus (tt-) and escherichia coli (ec-) were used to study the disassembly mechanism of post-termination ribosomal complexes by these factors. with tt-rrf, ec-ef-g can release bound-trna from ec-model post-termination complexes. however, tt-rrf is not released by ec-ef-g from ec-ribosomes. this complex with tt-rrf and ec-ribosomes after the trna release by ec-ef-g is regarded as an intermediate of the d ...	2005	15661844
the diversity of dolichol-linked precursors to asn-linked glycans likely results from secondary loss of sets of glycosyltransferases.	the vast majority of eukaryotes (fungi, plants, animals, slime mold, and euglena) synthesize asn-linked glycans (alg) by means of a lipid-linked precursor dolichol-pp-glcnac2man9glc3. knowledge of this pathway is important because defects in the glycosyltransferases (alg1-alg12 and others not yet identified), which make dolichol-pp-glycans, lead to numerous congenital disorders of glycosylation. here we used bioinformatic and experimental methods to characterize alg glycosyltransferases and doli ...	2005	15665075
stabilization of nucleic acids by unusual polyamines produced by an extreme thermophile, thermus thermophilus.	extreme thermophiles produce two types of unusual polyamine: long linear polyamines such as caldopentamine and caldohexamine, and branched polyamines such as quaternary ammonium compounds [e.g. tetrakis(3-aminopropyl)ammonium]. to clarify the physiological roles of long linear and branched polyamines in thermophiles, we synthesized them chemically and tested their effects on the stability of ds (double-stranded) and ss (single-stranded) dnas and trna in response to thermal denaturation, as measu ...	2005	15673283
the high-affinity maltose/trehalose abc transporter in the extremely thermophilic bacterium thermus thermophilus hb27 also recognizes sucrose and palatinose.	we have studied the transport of trehalose and maltose in the thernophilic bacterium thermus thermophilus hb27, which grows optimally in the range of 70 to 75 degrees c. the k(m) values at 70 degrees c were 109 nm for trehalose and 114 nm for maltose; also, a high k(m) (424 nm) was found for the uptake of sucrose. competition studies showed that a single transporter recognizes trehalose, maltose, and sucrose, while d-galactose, d-fucose, l-rhamnose, l-arabinose, and d-mannose were not competitiv ...	2005	15687184
dna binding: a novel function of pseudomonas aeruginosa type iv pili.	the opportunistic pathogen pseudomonas aeruginosa produces multifunctional, polar, filamentous appendages termed type iv pili. type iv pili are involved in colonization during infection, twitching motility, biofilm formation, bacteriophage infection, and natural transformation. electrostatic surface analysis of modeled pilus fibers generated from p. aeruginosa strain pak, k122-4, and kb-7 pilin monomers suggested that a solvent-exposed band of positive charge may be a common feature of all type ...	2005	15687210
contribution of the atp binding site of pare to susceptibility to novobiocin and quinolones in streptococcus pneumoniae.	in streptococcus pneumoniae, an h103y substitution in the atp binding site of the pare subunit of topoisomerase iv was shown to confer quinolone resistance and hypersensitivity to novobiocin when associated with an s84f change in the a subunit of dna gyrase. we reconstituted in vitro the wild-type topoisomerase iv and its pare mutant. the pare mutant enzyme showed a decreased activity for decatenation at subsaturating atp levels and was more sensitive to inhibition by novobiocin but was as sensi ...	2005	15687222
crystal structure of a predicted phosphoribosyltransferase (tt1426) from thermus thermophilus hb8 at 2.01 a resolution.	tt1426, from thermus thermophilus hb8, is a conserved hypothetical protein with a predicted phosphoribosyltransferase (prtase) domain, as revealed by a pfam database search. the 2.01 a crystal structure of tt1426 has been determined by the multiwavelength anomalous dispersion (mad) method. tt1426 comprises a core domain consisting of a central five-stranded beta sheet surrounded by four alpha-helices, and a subdomain in the c terminus. the core domain structure resembles those of the type i prta ...	2005	15689504
analysis of subsecond protein dynamics by amide hydrogen exchange and mass spectrometry using a quenched-flow setup.	amide hydrogen exchange (hx) in combination with mass spectrometry (ms) is a powerful tool to analyze the folding and dynamics of proteins. in the traditional methodology the exchange time is controlled by manual pipetting, thereby limiting the time resolution to several seconds. some conformational changes in proteins, however, occur in the subsecond time scale, making it desirable to perform hx at shorter time intervals down to the limit set by the intrinsic chemical exchange rate. we now repo ...	2005	15689511
processivity clamp gp45 and ssdna-binding-protein gp32 modulate the fidelity of bacteriophage rb69 dna polymerase in a sequence-specific manner, sometimes enhancing and sometimes compromising accuracy.	numerous studies of the impact of accessory proteins upon the fidelity of dna synthesis have provided a complex and sometimes discordant picture. we previously described such an analysis conducted in vitro using various bacteriophage rb69 gp43 mutator dna polymerases with or without the accessory proteins gp32 (which binds single-stranded dna) plus gp45/44/62 (processivity clamp and its loaders). mutations were scored at many sites in the laczalpha mutation reporter sequence. unexpectedly, the a ...	2005	15695359
a previously uncharacterized role for small protein b (smpb) in transfer messenger rna-mediated trans-translation.	ssra is a versatile rna molecule found in all bacteria that functions as both a trna and an mrna. ssra rescues ribosomes stalled on damaged mrnas and directs the tagging and degradation of their aberrant protein products. small protein b (smpb) is required for all known activities of ssra. the two known functions of smpb are binding ssra rna and promoting stable association of the smpb.ssra complex with 70s ribosomes. using mutational analysis and biochemical experiments, we have discovered a pr ...	2005	15699355
quantitative pcr-enhanced immunoassay for measurement of enteroviral immunoglobulin m antibody and diagnosis of aseptic meningitis.	a pcr-enhanced immunoassay (pia) to detect enterovirus (ev) immunoglobulin m (igm) for diagnosis of recent ev infection was recently developed. this test was compared with another ev igm capture technique, the solid-phase reverse immunosorbent test (sprist). fourteen of 43 serum samples from aseptic meningitis patients were positive by pia, whereas 10 were positive by sprist. one of 39 control serum samples was weakly positive by pia. a single-serum-dilution real-time pcr-based pia for ev igm (q ...	2005	15699416
complete genome sequence of the hyperthermophilic archaeon thermococcus kodakaraensis kod1 and comparison with pyrococcus genomes.	the genus thermococcus, comprised of sulfur-reducing hyperthermophilic archaea, belongs to the order thermococcales in euryarchaeota along with the closely related genus pyrococcus. the members of thermococcus are ubiquitously present in natural high-temperature environments, and are therefore considered to play a major role in the ecology and metabolic activity of microbial consortia within hot-water ecosystems. to obtain insight into this important genus, we have determined and annotated the c ...	2005	15710748
increasing stability of water-soluble pqq glucose dehydrogenase by increasing hydrophobic interaction at dimeric interface.	water-soluble quinoprotein glucose dehydrogenase (pqqgdh-b) from acinetobacter calcoaceticus has a great potential for application as a glucose sensor constituent. because this enzyme shows no activity in its monomeric form, correct quaternary structure is essential for the formation of active enzyme. we have previously reported on the increasing of the stability of pqqgdh-b by preventing the subunit dissociation. previous studies were based on decreasing the entropy of quaternary structure diss ...	2005	15715904
genomic analysis of anaerobic respiration in the archaeon halobacterium sp. strain nrc-1: dimethyl sulfoxide and trimethylamine n-oxide as terminal electron acceptors.	we have investigated anaerobic respiration of the archaeal model organism halobacterium sp. strain nrc-1 by using phenotypic and genetic analysis, bioinformatics, and transcriptome analysis. nrc-1 was found to grow on either dimethyl sulfoxide (dmso) or trimethylamine n-oxide (tmao) as the sole terminal electron acceptor, with a doubling time of 1 day. an operon, dmsreabcd, encoding a putative regulatory protein, dmsr, a molybdopterin oxidoreductase of the dmso reductase family (dmseabc), and a ...	2005	15716436
structure of the nucleotide complex of pyrr, the pyr attenuation protein from bacillus caldolyticus, suggests dual regulation by pyrimidine and purine nucleotides.	pyrr is a protein that regulates the expression of genes and operons of pyrimidine nucleotide biosynthesis (pyr genes) in many bacteria. pyrr acts by binding to specific sequences on pyr mrna and causing transcriptional attenuation when intracellular levels of uridine nucleotides are elevated. pyrr from bacillus subtilis has been purified and extensively studied. in this work, we describe the purification to homogeneity and characterization of recombinant pyrr from the thermophile bacillus caldo ...	2005	15716449
characterization of the atpase and unwinding activities of the yeast dead-box protein has1p and the analysis of the roles of the conserved motifs.	the yeast dead-box protein has1p is required for the maturation of 18s rrna, the biogenesis of 40s r-subunits and for the processing of 27s pre-rrnas during 60s r-subunit biogenesis. we purified recombinant has1p and characterized its biochemical activities. we show that has1p is an rna-dependent atpase in vitro and that it is able to unwind rna/dna duplexes in an atp-dependent manner. we also report a mutational analysis of the conserved residues in motif i (86aktgsgkt93), motif iii (228sat230) ...	2005	15718299
crystal structure and dna-binding analysis of reco from deinococcus radiodurans.	the recfor pathway has been shown to be essential for dna repair through the process of homologous recombination in bacteria and, recently, to be important in the recovery of stalled replication forks following uv irradiation. reco, along with recr, recf, recq and recj, is a principal actor in this fundamental dna repair pathway. here we present the three-dimensional structure of a member of the reco family. the crystal structure of deinococcus radiodurans reco (drreco) reveals possible binding ...	2005	15719017
identification of a new family of putative pd-(d/e)xk nucleases with unusual phylogenomic distribution and a new type of the active site.	prediction of structure and function for uncharacterized protein families by identification of evolutionary links to characterized families and known structures is one of the cornerstones of genomics. theoretical assignment of three-dimensional folds and prediction of protein function even at a very general level can facilitate the experimental determination of the molecular mechanism of action and the role that members of a given protein family fulfill in the cell. here, we predict the three-di ...	2005	15720711
hinge-like motions in rna kink-turns: the role of the second a-minor motif and nominally unpaired bases.	kink-turn (k-turn) motifs are asymmetric internal loops found at conserved positions in diverse rnas, with sharp bends in phosphodiester backbones producing v-shaped structures. explicit-solvent molecular dynamics simulations were carried out for three k-turns from 23s rrna, i.e., kt-38 located at the base of the a-site finger, kt-42 located at the base of the l7/l12 stalk, and kt-58 located in domain iii, and for the k-turn of human u4 snrna. the simulations reveal hinge-like k-turn motions on ...	2005	15722438
separation of mutation avoidance and antirecombination functions in an escherichia coli muts mutant.	dna mismatch repair in escherichia coli has been shown to be involved in two distinct processes: mutation avoidance, which removes potential mutations arising as replication errors, and antirecombination which prevents recombination between related, but not identical (homeologous), dna sequences. we show that cells with the mutsdelta800 mutation (which removes the c-terminal 53 amino acids of muts) on a multicopy plasmid are proficient for mutation avoidance. in interspecies genetic crosses, how ...	2005	15731339
tolerance of the rieske-type [2fe-2s] cluster in recombinant ferredoxin bpha3 from pseudomonas sp. kks102 to histidine ligand mutations.	bpha3 from pseudomonas sp. kks102 is a rieske-type [2fe-2s] ferredoxin that transfers electrons from an nadh-dependent oxidoreductase, bpha4, to a biphenyl dioxygenase complex. a high-level expression and purification system for the recombinant bpha3 in escherichia coli was constructed. two histidine ligands of the rieske-type cluster in bpha3, were each replaced with serine, cysteine, asparagine and tyrosine. the single mutants, in which either his44 or his65 was replaced with a cysteine residu ...	2005	15733056
crystal structure of a novel polyisoprenoid-binding protein from thermus thermophilus hb8.	the isoprenoid quinones exist widely among prokaryotes and eukaryotes. they play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. in the isoprenoid quinone biosynthetic pathway, polyprenyl pyrophosphates are used as isoprenoid side-chain precursors. here we report the crystal structure of a novel polyprenyl pyrophosphate binding protein, tt1927b, from thermus thermophilus hb8, complexed with its ligand. this protein belongs to the ycei-li ...	2005	15741337
a mutation in the decoding center of thermus thermophilus 16s rrna suggests a novel mechanism of streptomycin resistance.	a spontaneous kanamycin resistance and capreomycin resistance mutation, a1408g, in the decoding center of 16s rrna, was identified in the extreme thermophile thermus thermophilus. unexpectedly, this mutation also confers resistance to streptomycin. we propose a novel mechanism of streptomycin resistance by which a1408g influences conformational changes in 16s rrna during trna selection.	2005	15743969
modular rna architecture revealed by computational analysis of existing pseudoknots and ribosomal rnas.	modular architecture is a hallmark of rna structures, implying structural, and possibly functional, similarity among existing rnas. to systematically delineate the existence of smaller topologies within larger structures, we develop and apply an efficient rna secondary structure comparison algorithm using a newly developed two-dimensional rna graphical representation. our survey of similarity among 14 pseudoknots and subtopologies within ribosomal rnas (rrnas) uncovers eight pairs of structurall ...	2005	15745998
the interaction between sigma70 and the beta-flap of escherichia coli rna polymerase inhibits extension of nascent rna during early elongation.	the sigma-subunit of bacterial rna polymerase (rnap) is required for promoter-specific transcription initiation. this function depends on specific intersubunit interactions that occur when sigma associates with the rnap core enzyme to form rnap holoenzyme. among these interactions, that between conserved region 4 of sigma and the flap domain of the rnap beta-subunit (beta-flap) is critical for recognition of the major class of bacterial promoters. here, we describe the isolation of amino acid su ...	2005	15761057
molecular analysis of a synthetic tetracycline-binding riboswitch.	riboswitches are newly discovered regulatory elements that consist solely of rna, sense their ligand in a preformed binding pocket, and perform a conformational switch in response to ligand binding, resulting in altered gene expression. regulation by a tetracycline (tc)-binding aptamer when inserted into the 5' untranslated region (utr) of a reporter gene exhibits all characteristics of a riboswitch. chemical and enzymatic probing reveals that the aptamer consists of two stems, p1 and p2, which ...	2005	15769877
leucyl-trna synthetase from the ancestral bacterium aquifex aeolicus contains relics of synthetase evolution.	the editing reactions catalyzed by aminoacyl-trna synthetases are critical for the faithful protein synthesis by correcting misactivated amino acids and misaminoacylated trnas. we report that the isolated editing domain of leucyl-trna synthetase from the deep-rooted bacterium aquifex aeolicus (alphabeta-leurs) catalyzes the hydrolytic editing of both mischarged trna(leu) and minihelix(leu). within the domain, we have identified a crucial 20-amino-acid peptide that confers editing capacity when t ...	2005	15775966
ldpa: a component of the circadian clock senses redox state of the cell.	the endogenous 24-h (circadian) rhythms exhibited by the cyanobacterium synechococcus elongatus pcc 7942 and other organisms are entrained by a variety of environmental factors. in cyanobacteria, the mechanism that transduces environmental input signals to the central oscillator of the clock is not known. an earlier study identified ldpa as a gene involved in light-dependent modulation of the circadian period, and a candidate member of a clock-entraining input pathway. here, we report that the l ...	2005	15775978
modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial trnas lacking the entire t-arm.	the mitochondria of the nematode ascaris suum have trnas with unusual secondary structures that lack either the t-arm or d-arm found in most other organisms. of the twenty-two trna species present in the mitochondria of a.suum, twenty lack the entire t-arm and two serine trnas lack the d-arm. to understand how such unusual trnas work in the nematode mitochondrial translation system, we analyzed post-transcriptional modifications of 11 mitochondrial trna species purified from a.suum, 10 of which ...	2005	15781491
single-stranded dna-binding protein of deinococcus radiodurans: a biophysical characterization.	the highly conserved bacterial single-stranded dna-binding (ssb) proteins play an important role in dna replication, repair and recombination and are essential for the survival of the cell. they are functional as tetramers, in which four ob(oligonucleotide/oligosaccharide binding)-folds act as dna-binding domains. the protomer of the ssb protein from the extremely radiation-resistant organism deinococcus radiodurans (drassb) has twice the size of the other bacterial ssb proteins and contains two ...	2005	15781492
the thermophilic, homohexameric aminopeptidase of borrelia burgdorferi is a member of the m29 family of metallopeptidases.	proteases are implicated in several aspects of the physiology of microorganisms, as well as in host-pathogen interactions. aminopeptidases are also emerging as novel drug targets in infectious agents. in this study, we have characterized an aminopeptidase from the spirochete borrelia burgdorferi, the causative agent of lyme disease. the aminopeptidolytic activity was identified in cell extracts from b. burgdorferi by using the substrate leucine-7-amido-4-methylcoumarin. a protein displaying this ...	2005	15784569
structure of p-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia.	the crystal structure of the p-protein of the glycine cleavage system from thermus thermophilus hb8 has been determined. this is the first reported crystal structure of a p-protein, and it reveals that p-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (plp)-dependent enzymes. instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally simila ...	2005	15791207
crystal structure of yeast yhr049w/fsh1, a member of the serine hydrolase family.	yhr049w/fsh1 was recently identified in a combined computational and experimental proteomics analysis for the detection of active serine hydrolases in yeast. this analysis suggested that fsh1 might be a serine-type hydrolase belonging to the broad functional alphabeta-hydrolase superfamily. in order to get insight into the molecular function of this gene, it was targeted in our yeast structural genomics project. the crystal structure of the protein confirms that it contains a ser/his/asp catalyt ...	2005	15802654
identification of pilus-like structures and genes in microcystis aeruginosa pcc7806.	four putative type iv pilus genes from the toxic, naturally transformable microcystis aeruginosa pcc7806 were identified. three of these genes were clustered in an arrangement which is identical to that from other cyanobacterial genomes. type iv pilus-like appendages were also observed by electron microscopy.	2005	16269818
structure of a central stalk subunit f of prokaryotic v-type atpase/synthase from thermus thermophilus.	the crystal structure of subunit f of vacuole-type atpase/synthase (prokaryotic v-atpase) was determined to of 2.2 a resolution. the subunit reveals unexpected structural similarity to the response regulator proteins that include the escherichia coli chemotaxis response regulator chey. the structure was successfully placed into the low-resolution em structure of the prokaryotic holo-v-atpase at a location indicated by the results of crosslinking experiments. the crystal structure, together with ...	2005	16281059