| transcript cleavage factors grea and greb act as transient catalytic components of rna polymerase. | prokaryotic transcription elongation factors grea and greb stimulate intrinsic nucleolytic activity of rna polymerase (rnap). the proposed biological role of gre-induced rna hydrolysis includes transcription proofreading, suppression of transcriptional pausing and arrest, and facilitation of rnap transition from transcription initiation to transcription elongation. using an array of biochemical and molecular genetic methods, we mapped the interaction interface between gre and rnap and identified ... | 2003 | 14633991 |
| effect of g-1 on histidine trna microhelix conformation. | histidine trnas (trna(his)) are unique in that they possess an extra 5'-base (g-1) not found in other trnas. deletion of g-1 results in at least a 250-fold reduction in the rate of histidine charging in vitro. to better understand the role of the g-1 nucleotide in defining the structure of trna(his), and to correlate structure with cognate amino acid charging, nmr and molecular dynamics (md) studies were performed on the wild-type and a deltag-1 mutant escherichia coli histidine trna acceptor st ... | 2003 | 14654706 |
| crystal structures that suggest late development of genetic code components for differentiating aromatic side chains. | early forms of the genetic code likely generated "statistical" proteins, with similar side chains occupying the same sequence positions at different ratios. in this scenario, groups of related side chains were treated by aminoacyl-trna synthetases as a single molecular species until a discrimination mechanism developed that could separate them. the aromatic amino acids tryptophan, tyrosine, and phenylalanine likely constituted one of these groups. a crystal structure of human tryptophanyl-trna s ... | 2003 | 14671330 |
| structure of mth11/mth rpp29, an essential protein subunit of archaeal and eukaryotic rnase p. | we have determined the solution structure of mth11 (mth rpp29), an essential subunit of the rnase p enzyme from the archaebacterium methanothermobacter thermoautotrophicus (mth). rnase p is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of trnas in all three domains of life. in eubacteria, this enzyme is made up of two subunits: a large rna ( approximately 120 kda) responsible for mediating catalysis, and a small protein cofactor ... | 2003 | 14673079 |
| 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 |
| grpe, a nucleotide exchange factor for dnak. | the cochaperone grpe functions as a nucleotide exchange factor to promote dissociation of adenosine 5'-diphosphate (adp) from the nucleotide-binding cleft of dnak. grpe and the dnaj cochaperone act in concert to control the flux of unfolded polypeptides into and out of the substrate-binding domain of dnak by regulating the nucleotide-bound state of dnak. dnaj stimulates nucleotide hydrolysis, and grpe promotes the exchange of adp for adenosine triphosphate (atp) and also augments peptide release ... | 2003 | 14984054 |
| efficiency and pattern of uv pulse laser-induced rna-rna cross-linking in the ribosome. | escherichia coli ribosomes were irradiated with a krf excimer laser (248 nm, 22 ns pulse) with incident pulse energies in the range of 10-40 mj for a 1 cm2 area, corresponding to fluences of 4.5 to 18 x 10(9) w m(-2), to determine strand breakage yields and the frequency and pattern of rna-rna cross- linking in the 16s rrna. samples were irradiated in a cuvette with one laser pulse or in a flow cell with an average of 4.6 pulses per sample. the yield of strand breaks per photon was intensity dep ... | 2004 | 14999094 |
| crystal structure of rlmai: implications for understanding the 23s rrna g745/g748-methylation at the macrolide antibiotic-binding site. | the rlma class of enzymes (rlma(i) and rlma(ii)) catalyzes n1-methylation of a guanine base (g745 in gram-negative and g748 in gram-positive bacteria) of hairpin 35 of 23s rrna. we have determined the crystal structure of escherichia coli rlma(i) at 2.8-a resolution, providing 3d structure information for the rlma class of rna methyltransferases. the dimeric protein structure exhibits features that provide new insights into its molecular function. each rlma(i) molecule has a zn-binding domain, r ... | 2004 | 14999102 |
| definition of bases in 23s rrna essential for ribosomal subunit association. | the ribosome is a two-subunit molecular machine, sporting a working cycle that involves coordinated movements of the subunits. recent structural studies of the 70s ribosome describe a rather large number of intersubunit contacts, some of which are dynamic during translocation. we set out to determine which intersubunit contacts are functionally indispensable for the association of ribosome subunits by using a modification interference approach. modification of the n-1 position of a715, a1912, or ... | 2004 | 15037769 |
| probing the q-proton pathway of ba3-cytochrome c oxidase by time-resolved fourier transform infrared spectroscopy. | in cytochrome c oxidase, the terminal respiratory enzyme, electron transfers are strongly coupled to proton movements within the enzyme. two proton pathways (k and d) containing water molecules and hydrophobic amino acids have been identified and suggested to be involved in the proton translocation from the mitochondrial matrix or the bacterial cytoplasm into the active site. in addition to the k and d proton pathways, a third proton pathway (q) has been identified only in ba3-cytochrome c oxida ... | 2004 | 15041681 |
| dna damage recognition of mutated forms of uvrb proteins in nucleotide excision repair. | the dna repair protein uvrb plays an indispensable role in the stepwise and sequential damage recognition of nucleotide excision repair in escherichia coli. our previous studies suggested that uvrb is responsible for the chemical damage recognition only upon a strand opening mediated by uvra. difficulties were encountered in studying the direct interaction of uvrb with adducts due to the presence of uvra. we report herein that a single point mutation of y95w in which a tyrosine is replaced by a ... | 2004 | 15065863 |
| thermodynamic characterization of the interaction of mutant uvrb protein with damaged dna. | during the dna damage recognition of nucleotide excision repair in escherichia coli the interaction of uvrb protein with damaged dna ensures the recognition of differences in the intrinsic chemical structures of a variety of adduct molecules in dna double helix. our earlier study indicated that a single tyrosine-to-tryptophan mutation at residue 95 converted the uvrb to a protein [uvrb(y95w)] that is able to bind to a structure-specific bubble dna substrate, even in the absence of uvra. fluoresc ... | 2004 | 15065864 |
| an aminoacyl-trna synthetase-like protein encoded by the escherichia coli yadb gene glutamylates specifically trnaasp. | the product of the escherichia coli yadb gene is homologous to the n-terminal part of bacterial glutamyl-trna synthetases (glurss), including the rossmann fold with the acceptor-binding domain and the stem-contact fold. this glurs-like protein, which lacks the anticodon-binding domain, does not use trna(glu) as substrate in vitro nor in vivo, but aminoacylates trna(asp) with glutamate. the yadb gene is expressed in wild-type e. coli as an operon with the dksa gene, which encodes a protein involv ... | 2004 | 15096594 |
| a truncated aminoacyl-trna synthetase modifies rna. | aminoacyl-trna synthetases are modular enzymes composed of a central active site domain to which additional functional domains were appended in the course of evolution. analysis of bacterial genome sequences revealed the presence of many shorter aminoacyl-trna synthetase paralogs. here we report the characterization of a well conserved glutamyl-trna synthetase (glurs) paralog (yadb in escherichia coli) that is present in the genomes of >40 species of proteobacteria, cyanobacteria, and actinobact ... | 2004 | 15096612 |
| specific recognition of rpso mrna and 16s rrna by escherichia coli ribosomal protein s15 relies on both mimicry and site differentiation. | the ribosomal protein s15 binds to 16s rrna, during ribosome assembly, and to its own mrna (rpso mrna), affecting autocontrol of its expression. in both cases, the rna binding site is bipartite with a common subsite consisting of a g*u/g-c motif. the second subsite is located in a three-way junction in 16s rrna and in the distal part of a stem forming a pseudoknot in escherichia coli rpso mrna. to determine the extent of mimicry between these two rna targets, we determined which amino acids inte ... | 2004 | 15101974 |
| crystal structures of escherichia coli topoisomerase iv pare subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potency against topoisomerase iv and dna gyrase. | topoisomerase iv and dna gyrase are related bacterial type ii topoisomerases that utilize the free energy from atp hydrolysis to catalyze topological changes in the bacterial genome. the essential function of dna gyrase is the introduction of negative dna supercoils into the genome, whereas the essential function of topoisomerase iv is to decatenate daughter chromosomes following replication. here, we report the crystal structures of a 43-kda n-terminal fragment of escherichia coli topoisomerase ... | 2004 | 15105144 |
| thermal and conformational stability of ssh10b protein from archaeon sulfolobus shibattae. | the secondary structure of the dna binding protein ssh10b is largely unaffected by change in temperature between 25 degrees c and 85 degrees c, indicating that the protein is highly thermostable. here, we report the temperature-dependent equilibrium denaturation of ssh10b in the presence of guanidine hydrochloride (gdnhcl). it was found that the transition midpoint values of the temperature (t(m)), and changes of enthalpy (deltah(m)) and entropy (deltas(m)) of ssh10b unfolding were linearly decr ... | 2004 | 15107015 |
| ring-shaped architecture of recr: implications for its role in homologous recombinational dna repair. | recr, together with recf and reco, facilitates reca loading in the recf pathway of homologous recombinational dna repair in procaryotes. the human rad52 protein is a functional counterpart of recfor. we present here the crystal structure of recr from deinococcus radiodurans (dr recr). a monomer of dr recr has a two-domain structure: the n-terminal domain with a helix-hairpin-helix (hhh) motif and the c-terminal domain with a cys4 zinc-finger motif, a toprim domain and a walker b motif. four such ... | 2004 | 15116069 |
| distinctive protein signatures provide molecular markers and evidence for the monophyletic nature of the deinococcus-thermus phylum. | the deinococcus-thermus group of species is currently recognized as a distinct phylum solely on the basis of their branching in 16s rrna trees. no unique biochemical or molecular characteristics that can distinguish this group from all other bacteria are known at present. in this work, we describe eight conserved indels (viz., inserts or deletions) in seven widely distributed proteins that are distinctive characteristics of the deinococcus-thermus phylum but are not found in any other group of b ... | 2004 | 15126471 |
| comparison of two real-time quantitative assays for detection of severe acute respiratory syndrome coronavirus. | the new severe acute respiratory syndrome (sars) coronavirus (cov), described in february 2003, infected a total of 8,439 people. a total of 812 people died due to respiratory insufficiency. close contact with symptomatic patients appeared to be the main route of transmission. however, potential transmission by blood transfusion could not be definitely excluded. two real-time sars-specific pcr assays were assessed for their sensitivities, agreement of test results, and intra-assay variabilities. ... | 2004 | 15131175 |
| thermus thermophilus genome analysis: benefits and implications. | the genome sequence analysis of thermus thermophilus hb27, a microorganism with high biotechnological potential, has recently been published. in that report, the chromosomal and the megaplasmid sequence were compared to those of other organisms and discussed on the basis of their physiological and metabolic features. out of the 2,218 putative genes identified through the large genome sequencing project, a significant number has potential interest for biotechnology. the present communication will ... | 2004 | 15134584 |
| mycobacterium tuberculosis dnaa initiator protein: purification and dna-binding requirements. | the mycobacterium tuberculosis oric (the origin of chromosomal replication) region contains 13 non-perfect dnaa boxes. the m. tuberculosis initiator protein, dnaa, was overexpressed in escherichia coli as a soluble his-tagged fusion protein. the purified protein his6mtdnaa was investigated for its binding properties to dnaa boxes from the oric region. gel retardation demonstrated that the dnaa from m. tuberculosis requires two dnaa boxes for efficient binding. electron microscopy as well as dnas ... | 2004 | 15137907 |
| resistance of rumen bacteria murein to bovine gastric lysozyme. | lysozymes, enzymes mostly associated with defence against bacterial infections, are mureinolytic. ruminants have evolved a gastric c type lysozyme as a digestive enzyme, and profit from digestion of foregut bacteria, after most dietary components, including protein, have been fermented in the rumen. in this work we characterized the biological activities of bovine gastric secretions against membranes, purified murein and bacteria. | 2004 | 15137912 |
| mapping of the second tetracycline binding site on the ribosomal small subunit of e.coli. | tetracycline blocks stable binding of aminoacyl-trna to the bacterial ribosomal a-site. various tetracycline binding sites have been identified in crystals of the 30s ribosomal small subunit of thermus thermophilus. here we describe a direct photo- affinity modification of the ribosomal small subunits of escherichia coli with 7-[3h]-tetracycline. to select for specific interactions, an excess of the 30s subunits over tetracycline has been used. primer extension analysis of the 16s rrna revealed ... | 2004 | 15141029 |
| the structure of a ribosomal protein s8/spc operon mrna complex. | in bacteria, translation of all the ribosomal protein cistrons in the spc operon mrna is repressed by the binding of the product of one of them, s8, to an internal sequence at the 5' end of the l5 cistron. the way in which the first two genes of the spc operon are regulated, retroregulation, is mechanistically distinct from translational repression by s8 of the genes from l5 onward. a 2.8 a resolution crystal structure has been obtained of escherichia coli s8 bound to this site. despite sequence ... | 2004 | 15146079 |
| a minimalist glutamyl-trna synthetase dedicated to aminoacylation of the trnaasp quc anticodon. | escherichia coli encodes yadb, a protein displaying 34% identity with the catalytic core of glutamyl-trna synthetase but lacking the anticodon-binding domain. we show that yadb is a trna modifying enzyme that evidently glutamylates the queuosine residue, a modified nucleoside at the wobble position of the trna(asp) quc anticodon. this conclusion is supported by a variety of biochemical data and by the inability of the enzyme to glutamylate trna(asp) isolated from an e.coli trna-guanosine transgl ... | 2004 | 15150343 |
| simulation, experiment, and evolution: understanding nucleation in protein s6 folding. | in this study, we explore nucleation and the transition state ensemble of the ribosomal protein s6 using a monte carlo (mc) go model in conjunction with restraints from experiment. the results are analyzed in the context of extensive experimental and evolutionary data. the roles of individual residues in the folding nucleus are identified, and the order of events in the s6 folding mechanism is explored in detail. interpretation of our results agrees with, and extends the utility of, experiments ... | 2004 | 15150413 |
| new enzymes from environmental cassette arrays: functional attributes of a phosphotransferase and an rna-methyltransferase. | by targeting gene cassettes by polymerase chain reaction (pcr) directly from environmentally derived dna, we are able to amplify entire open reading frames (orfs) independently of prior sequence knowledge. approximately 10% of the mobile genes recovered by these means can be attributed to known protein families. here we describe the characterization of two orfs which show moderate homology to known proteins: (1) an aminoglycoside phosphotransferase displaying 25% sequence identity with aph(7") f ... | 2004 | 15152095 |
| crystal structure of escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/atp-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets. | cytidine triphosphate synthetases (ctpss) produce ctp from utp and glutamine, and regulate intracellular ctp levels through interactions with the four ribonucleotide triphosphates. we solved the 2.3-a resolution crystal structure of escherichia coli ctps using hg-mad phasing. the structure reveals a nearly symmetric 222 tetramer, in which each bifunctional monomer contains a dethiobiotin synthetase-like amidoligase n-terminal domain and a type 1 glutamine amidotransferase c-terminal domain. for ... | 2004 | 15157079 |
| crystal structure of the deinococcus radiodurans single-stranded dna-binding protein suggests a mechanism for coping with dna damage. | single-stranded dna (ssdna)-binding (ssb) proteins are uniformly required to bind and protect single-stranded intermediates in dna metabolic pathways. all bacterial and eukaryotic ssb proteins studied to date oligomerize to assemble four copies of a conserved domain, called an oligonucleotide/oligosaccharide-binding (ob) fold, that cooperate in nonspecific ssdna binding. the vast majority of bacterial ssb family members function as homotetramers, with each monomer contributing a single ob fold. ... | 2004 | 15159541 |
| the ribosomal protein rps15p is required for nuclear exit of the 40s subunit precursors in yeast. | we have conducted a genetic screen in order to identify ribosomal proteins of saccharomyces cerevisiae involved in nuclear export of the small subunit precursors. this has led us to distinguish rps15p as a protein dispensable for maturation of the pre-40s particles, but whose assembly into the pre-ribosomes is a prerequisite to their nuclear exit. upon depletion of rps15p, 20s pre-rrna is released from the nucleolus and retained in the nucleus, without alteration of the pre-rrna early cleavages. ... | 2004 | 15167894 |
| identification of active site residues in mevalonate diphosphate decarboxylase: implications for a family of phosphotransferases. | a combination of sequence homology analyses of mevalonate diphosphate decarboxylase (mdd) proteins and structural information for mdd leads to the hypothesis that asp 302 and lys 18 are active site residues in mdd. these residues were mutated to replace acidic/basic side chains and the mutant proteins were isolated and characterized. binding and competitive displacement studies using trinitrophenyl-atp, a fluorescent analog of substrate atp, indicate that these mutant enzymes (d302a, d302n, k18m ... | 2004 | 15169949 |
| visualization of ribosome-recycling factor on the escherichia coli 70s ribosome: functional implications. | after the termination step of protein synthesis, a deacylated trna and mrna remain associated with the ribosome. the ribosome-recycling factor (rrf), together with elongation factor g (ef-g), disassembles this posttermination complex into mrna, trna, and the ribosome. we have obtained a three-dimensional cryo-electron microscopic map of a complex of the escherichia coli 70s ribosome and rrf. we find that rrf interacts mainly with the segments of the large ribosomal subunit's (50s) rrna helices t ... | 2004 | 15178758 |
| cloning, sequencing, and characterization of a heat- and alkali-stable type i pullulanase from anaerobranca gottschalkii. | the gene encoding a type i pullulanase was identified from the genome sequence of the anaerobic thermoalkaliphilic bacterium anaerobranca gottschalkii. in addition, the homologous gene was isolated from a gene library of anaerobranca horikoshii and sequenced. the proteins encoded by these two genes showed 39% amino acid sequence identity to the pullulanases from the thermophilic anaerobic bacteria fervidobacterium pennivorans and thermotoga maritima. the pullulanase gene from a. gottschalkii (en ... | 2004 | 15184138 |
| interaction of horse heart and thermus thermophilus type c cytochromes with phospholipid vesicles and hydrophobic surfaces. | the binding of horse heart cytochrome c (cyt-c) and thermus thermophilus cytochrome c(552) (cyt-c(552)) to dioleoyl phosphatidylglycerol (dopg) vesicles was investigated using fourier transform infrared (ftir) spectroscopy and turbidity measurements. ftir spectra revealed that the tertiary structures of both cytochromes became more open when bound to dopg vesicles, but this was more pronounced for cyt-c. their secondary structures were unchanged. turbidity measurements showed important differenc ... | 2004 | 15189883 |
| interactions between uvra and uvrb: the role of uvrb's domain 2 in nucleotide excision repair. | nucleotide excision repair (ner) is a highly conserved dna repair mechanism present in all kingdoms of life. uvrb is a central component of the bacterial ner system, participating in damage recognition, strand excision and repair synthesis. none of the three presently available crystal structures of uvrb has defined the structure of domain 2, which is critical for the interaction with uvra. we have solved the crystal structure of the uvrb y96a variant, which reveals a new fold for domain 2 and i ... | 2004 | 15192705 |
| thiostrepton-resistant mutants of thermus thermophilus. | ribosomal protein l11 and its associated binding site on 23s rrna together comprise one of the principle components that mediate interactions of translation factors with the ribosome. this site is also the target of the antibiotic thiostrepton, which has been proposed to act by preventing important structural transitions that occur in this region of the ribosome during protein synthesis. here, we describe the isolation and characterization of spontaneous thiostrepton-resistant mutants of the ext ... | 2004 | 15199170 |
| the role of bacterial antizyme: from an inhibitory protein to atoc transcriptional regulator. | this review considers the role of bacterial antizyme in the regulation of polyamine biosynthesis and gives new perspectives on the involvement of antizyme in other significant cellular mechanisms. antizyme is a protein molecule induced by the end product of the enzymic reaction that it inhibits, in a non-competitive manner. the bacterial ornithine decarboxylase is regulated by nucleotides, phosphorylation and antizyme. the inhibition of ornithine decarboxylase by antizyme can be relieved to diff ... | 2004 | 15200682 |
| a gene from the mesophilic bacterium dehalococcoides ethenogenes encodes a novel mannosylglycerate synthase. | mannosylglycerate (mg) is a common compatible solute found in thermophilic and hyperthermophilic prokaryotes. in this study we characterized a mesophilic and bifunctional mannosylglycerate synthase (mgsd) encoded in the genome of the bacterium dehalococcoides ethenogenes. mgsd encodes two domains with extensive homology to mannosyl-3-phosphoglycerate synthase (mpgs, ec 2.4.1.217) and to mannosyl-3-phosphoglycerate phosphatase (mpgp, ec 3.1.3.70), which catalyze the consecutive synthesis and deph ... | 2004 | 15205409 |
| two distinct domains of the beta subunit of aquifex aeolicus leucyl-trna synthetase are involved in trna binding as revealed by a three-hybrid selection. | the aquifex aeolicus alphabeta-leurs is the only known heterodimeric class ia aminoacyl-trna synthetase. in this study, we investigated the function of the beta subunit which is believed to bind trna(leu). a yeast three-hybrid system was constructed on the basis of the interaction of the beta subunit with its cognate trna(leu). then, seven mutated beta subunits exhibiting impaired trna binding capacities were selected out from a randomly mutated library. two mutations were identified in the clas ... | 2004 | 15208367 |
| direct evidence that a conserved arginine in ruvb aaa+ atpase acts as an allosteric effector for the atpase activity of the adjacent subunit in a hexamer. | the escherichia coli ruva and ruvb protein complex promotes branch migration of holliday junctions during recombinational repair and homologous recombination and at stalled replication forks. the ruvb protein belongs to the aaa(+) (atpase associated with various cellular activities) atpase family and forms a hexameric ring in an atp-dependent manner. studies on the oligomeric aaa(+) class atpases suggest that a conserved arginine residue is located in close proximity to the atpase site of the ad ... | 2004 | 15210950 |
| crystal structure of elongation factor p from thermus thermophilus hb8. | translation elongation factor p (ef-p) stimulates ribosomal peptidyltransferase activity. ef-p is conserved in bacteria and is essential for cell viability. eukarya and archaea have an ef-p homologue, eukaryotic initiation factor 5a (eif-5a). in the present study, we determined the crystal structure of ef-p from thermus thermophilus hb8 at a 1.65-a resolution. ef-p consists of three beta-barrel domains (i, ii, and iii), whereas eif-5a has only two domains (n and c domains). domain i of ef-p is t ... | 2004 | 15210970 |
| molecular characterization of benzimidazole resistance in helicobacter pylori. | a family of benzimidazole derivatives (bi) was shown to possess potent and selective activity against helicobacter pylori, although the precise cellular target of the bis is unknown. spontaneous h. pylori mutants were isolated as resistant to a representative bi (compound a). genomic dna was isolated from a bi-resistant mutant, transformed into a bi-sensitive strain, and found to be sufficient to confer bi resistance. the resistance determinant was localized to a 17-kb clone after screening a la ... | 2004 | 15215104 |
| the crystal structure of human endonuclease viii-like 1 (neil1) reveals a zincless finger motif required for glycosylase activity. | in prokaryotes, two dna glycosylases recognize and excise oxidized pyrimidines: endonuclease iii (nth) and endonuclease viii (nei). the oxidized purine 8-oxoguanine, on the other hand, is recognized by fpg (also known as mutm), a glycosylase that belongs to the same family as nei. the recent availability of the human genome sequence allowed the identification of three human homologs of escherichia coli nei. we report here the crystal structure of a human nei-like (neil) enzyme, neil1. the struct ... | 2004 | 15232006 |
| thermus thermophilus as a cell factory for the production of a thermophilic mn-dependent catalase which fails to be synthesized in an active form in escherichia coli. | thermostable mn-dependent catalases are promising enzymes in biotechnological applications as h(2)o(2)-detoxifying systems. we cloned the genes encoding mn-dependent catalases from thermus thermophilus hb27 and hb8 and a less thermostable mutant carrying two amino acid replacements (m129v and e293g). when the wild-type and mutant genes were overexpressed in escherichia coli, unmodified or six-his-tagged proteins of the expected size were overproduced as inactive proteins. several attempts to obt ... | 2004 | 15240253 |
| identification of a bifunctional enzyme mnmc involved in the biosynthesis of a hypermodified uridine in the wobble position of trna. | the gene encoding the bifunctional enzyme mnmc that catalyzes the two last steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm5s2u) in trna has been previously mapped at about 50 min on the escherichia coli k12 chromosome, but to date the identity of the corresponding enzyme has not been correlated with any of the known open reading frames (orfs). using the protein fold-recognition approach, we predicted that the 74-kda product of the yfck orf located at 52.6 min and annotated as ... | 2004 | 15247431 |
| the phosphoenolpyruvate carboxylase from methanothermobacter thermautotrophicus has a novel structure. | in methanothermobacter thermautotrophicus, oxaloacetate synthesis is a major and essential co(2)-fixation reaction. this methanogenic archaeon possesses two oxaloacetate-synthesizing enzymes, pyruvate carboxylase and phosphoenolpyruvate carboxylase. the phosphoenolpyruvate carboxylase from this organism was purified to homogeneity. the subunit size of this homotetrameric protein was 55 kda, which is about half that of all known bacterial and eukaryotic phosphoenolpyruvate carboxylases (ppcs). th ... | 2004 | 15262949 |
| discrimination against deoxyribonucleotide substrates by bacterial rna polymerase. | nucleic acid polymerases have evolved elaborate mechanisms that prevent incorporation of the non-cognate substrates, which are distinguished by both the base and the sugar moieties. while the mechanisms of substrate selection have been studied in single-subunit dna and rna polymerases (dnaps and rnaps, respectively), the determinants of substrate binding in the multisubunit rnaps are not yet known. molecular modeling of thermus thermophilus rnap-substrate ntp complex identified a conserved beta' ... | 2004 | 15262972 |
| heteronuclear nmr investigations of dynamic regions of intact escherichia coli ribosomes. | 15n-(1)h nmr spectroscopy has been used to probe the dynamic properties of uniformly (15)n labeled escherichia coli ribosomes. despite the high molecular weight of the complex ( approximately 2.3 mda), [(1)h-(15)n] heteronuclear single-quantum correlation spectra contain approximately 100 well resolved resonances, the majority of which arise from two of the four c-terminal domains of the stalk proteins, l7/l12. heteronuclear pulse-field gradient nmr experiments show that the resonances arise fro ... | 2004 | 15263071 |
| formation and characterization of an all-ferrous rieske cluster and stabilization of the [2fe-2s]0 core by protonation. | the all-ferrous rieske cluster, [2fe-2s](0), has been produced in solution and characterized by protein-film voltammetry and uv-visible, epr, and mössbauer spectroscopies. the [2fe-2s](0) cluster, in the overexpressed soluble domain of the rieske protein from the bovine cytochrome bc(1) complex, is formed at -0.73 v at ph 7. therefore, at ph 7, the [2fe-2s](1+/0) couple is 1.0 v below the [2fe-2s](2+/1+) couple. the two cluster-bound ferrous irons are both high spin (s = 2), and they are coupled ... | 2004 | 15263097 |
| insights into the dna repair process by the formamidopyrimidine-dna glycosylase investigated by molecular dynamics. | formamidopyrimidine-dna glycosylase (fpg) identifies and removes 8-oxoguanine from dna. all of the x-ray structures of fpg complexed to an abasic site containing dna exhibit a common disordered region present in the c-terminal domain of the enzyme. however, this region is believed to be involved in the damaged base binding site when the initial protein/dna complex is formed. the dynamic behavior of the disordered polypeptide (named loop) in relation to the supposed scenario for the dna repair me ... | 2004 | 15273302 |
| staphylococcus aureus dna ligase: characterization of its kinetics of catalysis and development of a high-throughput screening compatible chemiluminescent hybridization protection assay. | dna ligases are key enzymes involved in the repair and replication of dna. prokaryotic dna ligases uniquely use nad+ as the adenylate donor during catalysis, whereas eukaryotic enzymes use atp. this difference in substrate specificity makes the bacterial enzymes potential targets for therapeutic intervention. we have developed a homogeneous chemiluminescence-based hybridization protection assay for staphylococcus aureus dna ligase that uses novel acridinium ester technology and demonstrate that ... | 2004 | 15283677 |
| a single-amino-acid lid renders a gas-tight compartment within a membrane-bound transporter. | proteins undergo structural fluctuations between nearly isoenergetic substates. such fluctuations are often intimately linked with the functional properties of proteins. however, in some cases, such as in transmembrane ion transporters, the control of the ion transport requires that the protein is designed to restrict the motions in specific regions. in this study, we have investigated the dynamics of a membrane-bound respiratory oxidase, which acts both as an enzyme catalyzing reduction of o(2) ... | 2004 | 15289603 |
| targeting the a site rna of the escherichia coli ribosomal 30 s subunit by 2'-o-methyl oligoribonucleotides: a quantitative equilibrium dialysis binding assay and differential effects of aminoglycoside antibiotics. | the bacterial ribosome comprises 30 s and 50 s ribonucleoprotein subunits, contains a number of binding sites for known antibiotics and is an attractive target for selection of novel antibacterial agents. on the 30 s subunit, for example, the a site (aminoacyl site) close to the 3'-end of 16 s rrna is highly important in the decoding process. binding by some aminoglycoside antibiotics to the a site leads to erroneous protein synthesis and is lethal for bacteria. we targeted the a site on purifie ... | 2004 | 15294017 |
| construction of a chimeric thermostable pyrophosphatase to facilitate its purification and immobilization by using the choline-binding tag. | the thermophilic inorganic pyrophosphatase (pyr) from thermus thermophilus has been produced in escherichia coli fused to the c terminus of the choline-binding tag (chb tag) derived from the choline-binding domain (chbd) of pneumococcal lyta autolysin. the chimeric chbd-pyr protein retains its thermostable activity and can be purified in a single step by deae-cellulose affinity chromatography. pyr can be further released from the chbd by thrombin, using the specific protease recognition site inc ... | 2004 | 15294797 |
| stabilizing roles of residual structure in the empty heme binding pockets and unfolded states of microsomal and mitochondrial apocytochrome b5. | the microsomal (mc) and mitochondrial (om) isoforms of mammalian cytochrome b5 are the products of different genes, which likely arose via duplication of a primordial gene and subsequent functional divergence. despite sharing essentially identical folds, heme-polypeptide interactions are stronger in om b5s than in mc b5s due to the presence of two conserved patches of hydrophobic amino acid side chains in the om heme binding pockets. this is of fundamental interest in terms of understanding heme ... | 2004 | 15295112 |
| creating ribosomes with an all-rna 30s subunit p site. | ribosome crystal structures have revealed that two small subunit proteins, s9 and s13, have c-terminal tails, which, together with several features of 16s rrna, contact the anticodon stem-loop of p-site trna. to test the functional importance of these protein tails, we created genomic deletions of the c-terminal regions of s9 and s13. all of the tail deletions, including double mutants containing deletions in both s9 and s13, were viable, showing that escherichia coli cells can synthesize all of ... | 2004 | 15308780 |
| thermus thermophilus l11 methyltransferase, prma, is dispensable for growth and preferentially modifies free ribosomal protein l11 prior to ribosome assembly. | the ribosomal protein l11 in bacteria is posttranslationally trimethylated at multiple amino acid positions by the l11 methyltransferase prma, the product of the prma gene. the role of l11 methylation in ribosome function or assembly has yet to be determined, although the deletion of escherichia coli prma has no apparent phenotype. we have constructed a mutant of the extreme thermophile thermus thermophilus in which the prma gene has been disrupted with the htk gene encoding a heat-stable kanamy ... | 2004 | 15317787 |
| substrate-induced asymmetry and channel closure revealed by the apoenzyme structure of mycobacterium tuberculosis phosphopantetheine adenylyltransferase. | phosphopantetheine adenylyltransferase (ppat) catalyzes the penultimate step in prokaryotic coenzyme a (coa) biosynthesis, directing the transfer of an adenylyl group from atp to 4'-phosphopantetheine (ppant) to yield dephospho-coa (dpcoa). the crystal structures of escherichia coli ppat bound to its substrates, product, and inhibitor revealed an allosteric hexameric enzyme with half-of-sites reactivity, and established an in-line displacement catalytic mechanism. to provide insight into the mec ... | 2004 | 15322293 |
| incidence of antibiotic resistance in campylobacter jejuni isolated in alberta, canada, from 1999 to 2002, with special reference to tet(o)-mediated tetracycline resistance. | of 203 human clinical isolates of campylobacter jejuni from alberta, canada (1999 to 2002), 101 isolates (50%) were resistant to at least 64 microg of tetracycline/ml, with four isolates exhibiting higher levels of tetracycline resistance (512 microg/ml). in total, the mics for 37% of tetracycline-resistant isolates (256 to 512 microg/ml) were higher than those previously reported in c. jejuni (64 to 128 microg/ml). in the tetracycline-resistant clinical isolates, 67% contained plasmids and all ... | 2004 | 15328109 |
| dna ligases ensure fidelity by interrogating minor groove contacts. | dna ligases, found in both prokaryotes and eukaryotes, covalently link the 3'-hydroxyl and 5'-phosphate ends of duplex dna segments. this reaction represents a completion step for dna replication, repair and recombination. it is well established that ligases are sensitive to mispairs present on the 3' side of the ligase junction, but tolerant of mispairs on the 5' side. while such discrimination would increase the overall accuracy of dna replication and repair, the mechanisms by which this fidel ... | 2004 | 15328364 |
| photolabile anticodon stem-loop analogs of trnaphe as probes of ribosomal structure and structural fluctuation at the decoding center. | with the recent availability of high-resolution structures of bacterial ribosomes, studies of ribosome-catalyzed protein biosynthesis are now focusing on the nature of conformational changes that occur as the ribosome exerts its complex catalytic function. photocrosslinking can be relevant for this purpose by providing clues to ribosomal structural fluctuations and dynamics. here we describe crosslinking experiments on 70s ribosomes using two photolabile anticodon stem-loop derivatives of escher ... | 2004 | 15337844 |
| crystal structure of ribosomal protein l27 from thermus thermophilus hb8. | ribosomal protein l27 is located near the peptidyltransferase center at the interface of ribosomal subunits, and is important for ribosomal assembly and function. we report the crystal structure of ribosomal protein l27 from thermus thermophilus hb8, which was determined by the multiwavelength anomalous dispersion method and refined to an r-factor of 19.7% (r(free) = 23.6%) at 2.8 a resolution. the overall fold is an all beta-sheet hybrid. it consists of two sets of four-stranded beta-sheets for ... | 2004 | 15340170 |
| x-ray crystal structure of ornithine acetyltransferase from the clavulanic acid biosynthesis gene cluster. | the orf6 gene from the clavulanic acid biosynthesis gene cluster encodes an oat (ornithine acetyltransferase). similar to other oats the enzyme has been shown to catalyse the reversible transfer of an acetyl group from n-acetylornithine to glutamate. oats are ntn (n-terminal nucleophile) enzymes, but are distinct from the better-characterized ntn hydrolase enzymes as they catalyse acetyl transfer rather than a hydrolysis reaction. in the present study, we describe the x-ray crystal structure of ... | 2005 | 15352873 |
| reverse transcriptase activity innate to dna polymerase i and dna topoisomerase i proteins of streptomyces telomere complex. | replication of streptomyces linear chromosomes and plasmids proceeds bidirectionally from a central origin, leaving recessed 5' termini that are extended by a telomere binding complex. this complex contains both a telomere-protecting terminal protein (tpg) and a telomere-associated protein that interacts with tpg and the dna ends of linear streptomyces replicons. by using histidine-tagged telomere-associated protein (tap) as a scaffold, we identified dna polymerase (pola) and topoisomerase i (to ... | 2004 | 15353591 |
| biochemical characterization of cdc6/orc1 binding to the replication origin of the euryarchaeon methanothermobacter thermoautotrophicus. | archaeal cell division cycle protein 6 (cdc6)/origin replication complex subunit 1 (orc1) proteins share sequence homology with eukaryotic dna replication initiation factors but are also structurally similar to the bacterial initiator dnaa. to better understand whether cdc6/orc1 functions in an eukaryotic or bacterial-like manner, we have characterized the interaction of two cdc6/orc1 paralogs (mthcdc6-1 and mthcdc6-2) with the replication origin from methanothermobacter thermoautotrophicus. we ... | 2004 | 15358831 |
| reaction cycle of the yeast isw2 chromatin remodeling complex. | members of the iswi family of chromatin remodeling factors hydrolyze atp to reposition nucleosomes along dna. here we show that the yeast isw2 complex interacts with dna in a nucleotide-dependent manner at physiological ionic strength. isw2 efficiently binds dna in the absence of nucleotides and in the presence of a nonhydrolyzable atp analog. conversely, adp promotes the dissociation of isw2 from dna. in contrast, isw2 remains bound to mononucleosomes through multiple cycles of atp hydrolysis. ... | 2004 | 15359274 |
| structure and dna-binding properties of the cytolysin regulator cylr2 from enterococcus faecalis. | enterococcus faecalis is one of the major causes for hospital-acquired antibiotic-resistant infections. it produces an exotoxin, called cytolysin, which is lethal for a wide range of gram-positive bacteria and is toxic to higher organisms. recently, the regulation of the cytolysin operon was connected to autoinduction by a quorum-sensing mechanism involving the cylr1/cylr2 two-component regulatory system. we report here the crystal structure of cylr2 and its properties in solution as determined ... | 2004 | 15359276 |
| theoretical identification of proton channels in the quinol oxidase aa3 from acidianus ambivalens. | heme-copper oxidases are membrane proteins found in the respiratory chain of aerobic organisms. they are the terminal electron acceptors coupling the translocation of protons across the membrane with the reduction of oxygen to water. because the catalytic process occurs in the heme cofactors positioned well inside the protein matrix, proton channels must exist. however, due to the high structural divergence among this kind of proteins, the proton channels previously described are not necessarily ... | 2004 | 15377522 |
| liver portal fibrosis in dioxin receptor-null mice that overexpress the latent transforming growth factor-beta-binding protein-1. | mice lacking aryl hydrocarbon (dioxin) receptor (ahr) had variable degree of hepatic fibrosis and altered liver architecture. transforming growth factor-beta (tgf-beta), a major profibrogenic molecule in the liver, is localized to the extracellular matrix by its association to the latent tgf-beta-binding protein-1 (ltbp-1). very recently, ltbp-1 has been shown to be negatively regulated by the ahr. embryonic fibroblasts from ahr-null (ahr(-/-)) mice overexpress ltbp-1 and secrete four times more ... | 2004 | 15379962 |
| efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides. | evidence is presented that morpholino, 2'-o-methyl, phosphorothioate, and rna antisense oligonucleotides can direct site-specific -1 translational frameshifting when annealed to mrna downstream from sequences where the p- and a-site trnas are both capable of repairing with -1 frame codons. the efficiency of ribosomes shifting into the new frame can be as high as 40%, determined by the sequence of the frameshift site, as well as the location, sequence composition, and modification of the antisens ... | 2004 | 15383681 |
| selectivity and specificity of substrate binding in methionyl-trna synthetase. | the accuracy of in vivo incorporation of amino acids during protein biosynthesis is controlled to a significant extent by aminoacyl-trna synthetases (aars). this paper describes the application of the hierdock computational method to study the molecular basis of amino acid binding to the escherichia coli methionyl trna synthetase (metrs). starting with the protein structure from the metrs cocrystal, the hierdock calculations predict the binding site of methionine in metrs to a root mean square d ... | 2004 | 15388861 |
| atomic model of the thermus thermophilus 70s ribosome developed in silico. | the ribosome is a large molecular complex that consists of at least three ribonucleic acid molecules and a large number of proteins. it translates genetic information from messenger ribonucleic acid and makes protein accordingly. to better understand ribosomal function and provide information for designing biochemical experiments require knowledge of the complete structure of the ribosome. for expanding the structural information of the ribosome, we took on the challenge of developing a detailed ... | 2004 | 15454463 |
| crystal structures of possible lysine decarboxylases from thermus thermophilus hb8. | tt1887 and tt1465 from thermus thermophilus hb8 are conserved hypothetical proteins, and are annotated as possible lysine decarboxylases in the pfam database. here we report the crystal structures of tt1887 and tt1465 at 1.8 a and 2.2 a resolutions, respectively, as determined by the multiwavelength anomalous dispersion (mad) method. tt1887 is a homotetramer, while tt1465 is a homohexamer in the crystal and in solution. the structures of the tt1887 and tt1465 monomers contain single domains with ... | 2004 | 15459330 |
| complete genome sequence of the genetically tractable hydrogenotrophic methanogen methanococcus maripaludis. | the genome sequence of the genetically tractable, mesophilic, hydrogenotrophic methanogen methanococcus maripaludis contains 1,722 protein-coding genes in a single circular chromosome of 1,661,137 bp. of the protein-coding genes (open reading frames [orfs]), 44% were assigned a function, 48% were conserved but had unknown or uncertain functions, and 7.5% (129 orfs) were unique to m. maripaludis. of the unique orfs, 27 were confirmed to encode proteins by the mass spectrometric identification of ... | 2004 | 15466049 |