| structure of the pii signal transduction protein of neisseria meningitidis at 1.85 a resolution. | the p(ii) signal transduction proteins glnb and glnk are implicated in the regulation of nitrogen assimilation in escherichia coli and other enteric bacteria. p(ii)-like proteins are widely distributed in bacteria, archaea and plants. in contrast to other bacteria, neisseria are limited to a single p(ii) protein (nmb 1995), which shows a high level of sequence identity to glnb and glnk from escherichia coli (73 and 62%, respectively). the structure of the p(ii) protein from n. meningitidis (sero ... | 2006 | 16754965 |
| structure of xc6422 from xanthomonas campestris at 1.6 a resolution: a small serine alpha/beta-hydrolase. | xc6422 is a conserved hypothetical protein from xanthomonas campestris pathovar campestris (xcc), a gram-negative yellow-pigmented pathogenic bacterium that causes black rot, one of the major worldwide diseases of cruciferous crops. the protein consists of 220 amino acids and its structure has been determined to 1.6 a resolution using the multi-wavelength anomalous dispersion (mad) method. although it has very low sequence identity to protein sequences in the pdb (less than 20%), the determined ... | 2006 | 16754966 |
| simple sequence proteins in prokaryotic proteomes. | the structural and functional features associated with simple sequence proteins (ssps) are non-globularity, disease states, signaling and post-translational modification. ssps are also an important source of genetic and possibly phenotypic variation. analysis of 249 prokaryotic proteomes offers a new opportunity to examine the genomic properties of ssps. | 2006 | 16762057 |
| a base pair at the bottom of the anticodon stem is reciprocally preferred for discrimination of cognate trnas by escherichia coli lysyl- and glutaminyl-trna synthetases. | although the yeast amber suppressor trna(tyr) is a good candidate for a carrier of unnatural amino acids into proteins, slight misacylation with lysine was found to occur in an escherichia coli protein synthesis system. although it was possible to restrain the mislysylation by genetically engineering the anticodon stem region of the amber suppressor trna(tyr), the mutant trna showing the lowest acceptance of lysine was found to accept a trace level of glutamine instead. moreover, the glutamine-a ... | 2006 | 16772402 |
| heterologous expression and biochemical characterization of a polyamine oxidase from arabidopsis involved in polyamine back conversion. | polyamine oxidase (pao) is a flavin adenine dinucleotide-dependent enzyme involved in polyamine catabolism. animal paos oxidize spermine (spm), spermidine (spd), and/or their acetyl derivatives to produce h2o2, an aminoaldehyde, and spd or putrescine, respectively, thus being involved in a polyamine back-conversion pathway. on the contrary, plant paos that have been characterized to date oxidize spm and spd to produce 1,3-diaminopropane, h2o2, and an aminoaldehyde and are therefore involved in t ... | 2006 | 16778015 |
| a genetically encoded fluorescent amino acid. | the ability to introduce fluorophores selectively into proteins provides a powerful tool to study protein structure, dynamics, localization, and biomolecular interactions both in vitro and in vivo. here, we report a strategy for the selective and efficient biosynthetic incorporation of a low-molecular-weight fluorophore into proteins at defined sites. the fluorescent amino acid 2-amino-3-(5-(dimethylamino)naphthalene-1-sulfonamide)propanoic acid (dansylalanine) was genetically encoded in sacchar ... | 2006 | 16785423 |
| comparison of the rpoh-dependent regulon and general stress response in neisseria gonorrhoeae. | in the gammaproteobacteria the rpoh regulon is often equated with the stress response, as the regulon contains many of the genes that encode what have been termed heat shock proteins that deal with the presence of damaged proteins. however, the betaproteobacteria primarily utilize the hrca repressor protein to control genes involved in the stress response. we used genome-wide transcriptional profiling to compare the rpoh regulon and stress response of neisseria gonorrhoeae, a member of the betap ... | 2006 | 16788186 |
| esha accentuates ppgpp accumulation and is conditionally required for antibiotic production in streptomyces coelicolor a3(2). | disruption of esha, which encodes a 52-kda protein that is produced late during the growth of streptomyces coelicolor a3(2), resulted in elimination of actinorhodin production. in contrast, disruption of eshb, a close homologue of esha, had no effect on antibiotic production. the esha disruptant accumulated lower levels of ppgpp than the wild-type strain accumulated. the loss of actinorhodin production in the esha disruptant was restored by expression of a truncated rela gene, which increased th ... | 2006 | 16788203 |
| structure of human tryptophanyl-trna synthetase in complex with trnatrp reveals the molecular basis of trna recognition and specificity. | aminoacyl-trna synthetases (aarss) are a family of enzymes responsible for the covalent link of amino acids to their cognate trnas. the selectivity and species-specificity in the recognitions of both amino acid and trna by aarss play a vital role in maintaining the fidelity of protein synthesis. we report here the first crystal structure of human tryptophanyl-trna synthetase (htrprs) in complex with trna(trp) and trp which, together with biochemical data, reveals the molecular basis of a novel t ... | 2006 | 16798914 |
| the nondiscriminating aspartyl-trna synthetase from helicobacter pylori: anticodon-binding domain mutations that impact trna specificity and heterologous toxicity. | divergent trna substrate recognition patterns distinguish the two distinct forms of aspartyl-trna synthetase (asprs) that exist in different bacteria. in some cases, a canonical, discriminating asprs (d-asprs) specifically generates asp-trna(asp) and usually coexists with asparaginyl-trna synthetase (asnrs). in other bacteria, particularly those that lack asnrs, asprs is nondiscriminating (nd-asprs) and generates both asp-trna(asp) and the noncanonical, misacylated asp-trna(asn); this misacylate ... | 2006 | 16800632 |
| lessons in stability from thermophilic proteins. | studies that compare proteins from thermophilic and mesophilic organisms can provide insights into ability of thermophiles to function at their high habitat temperatures and may provide clues that enable us to better define the forces that stabilize all proteins. most of the comparative studies have focused on thermal stability and show, as expected, that thermophilic proteins have higher tm values than their mesophilic counterparts. although these comparisons are useful, more detailed thermodyn ... | 2006 | 16815912 |
| structure of the synthetase domain of human ctp synthetase, a target for anticancer therapy. | cytidine triphosphate synthetase (ctps) is a key enzyme in nucleic acid and phospholipid biosynthesis and its activity is increased in certain human cancers, making it a promising drug target. the crystal structure of the synthetase domain of human ctps, which represents the first structure of a ctps from an eukaryote, has been determined. the structure is homotetrameric and each active site is formed by three different subunits. sulfate ions bound to the active sites indicate the positions of p ... | 2006 | 16820675 |
| multiple erythroid isoforms of human long-chain acyl-coa synthetases are produced by switch of the fatty acid gate domains. | the formation of acyl-coa by the action of acyl-coa synthetases plays a crucial role in membrane lipid turnover, including the plasma membrane of erythrocytes. in human, five acyl-coa synthetase long-chain (acsl) genes have been identified with as many as 3 different transcript variants for each. | 2006 | 16834775 |
| distinguishing features of delta-proteobacterial genomes. | we analyzed several features of five currently available delta-proteobacterial genomes, including two aerobic bacteria exhibiting predatory behavior and three anaerobic sulfate-reducing bacteria. the delta genomes are distinguished from other bacteria by several properties: (i) the delta genomes contain two "giant" s1 ribosomal protein genes in contrast to all other bacterial types, which encode a single or no s1; (ii) in most delta-proteobacterial genomes the major ribosomal protein (rp) gene c ... | 2006 | 16844781 |
| the yfhq gene of escherichia coli encodes a trna:cm32/um32 methyltransferase. | naturally occurring trnas contain numerous modified nucleosides. they are formed by enzymatic modification of the primary transcripts during the complex rna maturation process. in model organisms escherichia coli and saccharomyces cerevisiae most enzymes involved in this process have been identified. interestingly, it was found that trna methylation, one of the most common modifications, can be introduced by s-adenosyl-l-methionine (adomet)-dependent methyltransferases (mtases) that belong to tw ... | 2006 | 16848900 |
| formation of functional tat translocases from heterologous components. | the tat pathway transports folded proteins across the cytoplasmic membrane of bacteria and the thylakoid membrane of plants. in eschericha coli, tat transport requires the integral membrane proteins tata, tatb and tatc. in this study we have tested the ability of tat genes from the eubacterial species pseudomonas syringae, streptomyces coelicolor and aquifex aeolicus, to compensate for the absence of the cognate e. coli tat gene, and thus to form functional tat translocases with e. coli tat comp ... | 2006 | 16854235 |
| aug sequences are required to sustain nonsense-codon-mediated suppression of splicing. | more than 90% of human genes are rich in intronic latent 5' splice sites whose utilization in pre-mrna splicing would introduce in-frame stop codons into the resultant mrnas. we have therefore hypothesized that suppression of splicing (sos) at latent 5' splice sites regulates alternative 5' splice site selection in a way that prevents the production of toxic nonsense mrnas and verified this idea by showing that the removal of such in-frame stop codons is sufficient to activate latent splicing. s ... | 2006 | 16855285 |
| a protein extension to shorten rna: elongated elongation factor-tu recognizes the d-arm of t-armless trnas in nematode mitochondria. | nematode mitochondria possess extremely truncated trnas. of 22 trnas, 20 lack the entire t-arm. the t-arm is necessary for the binding of canonical trnas and ef (elongation factor)-tu (thermo-unstable). the nematode mitochondrial translation system employs two different ef-tu factors named ef-tu1 and ef-tu2. our previous study showed that nematode caenorhabditis elegans ef-tu1 binds specifically to t-armless trna. c. elegans ef-tu1 has a 57-amino acid c-terminal extension that is absent from can ... | 2006 | 16859488 |
| direct observation of dna rotation during branch migration of holliday junction dna by escherichia coli ruva-ruvb protein complex. | the escherichia coli ruva-ruvb complex promotes branch migration of holliday junction dna, which is the central intermediate of homologous recombination. like many dna motor proteins, it is suggested that ruva-ruvb promotes branch migration by driving helical rotation of the dna. to clarify the ruva-ruvb-mediated branch migration mechanism in more detail, we observed dna rotation during holliday junction branch migration by attaching a bead to one end of cruciform dna that was fixed to a glass s ... | 2006 | 16864792 |
| dihydrodipicolinate synthase from thermotoga maritima. | dhdps (dihydrodipicolinate synthase) catalyses the branch point in lysine biosynthesis in bacteria and plants and is feedback inhibited by lysine. dhdps from the thermophilic bacterium thermotoga maritima shows a high level of heat and chemical stability. when incubated at 90 degrees c or in 8 m urea, the enzyme showed little or no loss of activity, unlike the escherichia coli enzyme. the active site is very similar to that of the e. coli enzyme, and at mesophilic temperatures the two enzymes ha ... | 2006 | 16872276 |
| identification of smtb/arsr cis elements and proteins in archaea using the prokaryotic intergenic exploration database (piged). | microbial genome sequencing projects have revealed an apparently wide distribution of smtb/arsr metal-responsive transcriptional regulators among prokaryotes. using a position-dependent weight matrix approach, prokaryotic genome sequences were screened for smtb/arsr dna binding sites using data derived from intergenic sequences upstream of orthologous genes encoding these regulators. sixty smtb/arsr operators linked to metal detoxification genes, including nine among various archaeal species, ar ... | 2006 | 16877320 |
| structure of mycobacterium tuberculosis ruva, a protein involved in recombination. | the process of recombinational repair is crucial for maintaining genomic integrity and generating biological diversity. in association with ruvb and ruvc, ruva plays a central role in processing and resolving holliday junctions, which are a critical intermediate in homologous recombination. here, the cloning, purification and structure determination of the ruva protein from mycobacterium tuberculosis (mtruva) are reported. analysis of the structure and comparison with other known ruva proteins r ... | 2006 | 16880543 |
| peptide deformylase is a potential target for anti-helicobacter pylori drugs: reverse docking, enzymatic assay, and x-ray crystallography validation. | colonization of human stomach by the bacterium helicobacter pylori is a major causative factor for gastrointestinal illnesses and gastric cancer. however, the discovery of anti-h. pylori agents is a difficult task due to lack of mature protein targets. therefore, identifying new molecular targets for developing new drugs against h. pylori is obviously necessary. in this study, the in-house potential drug target database (pdtd, http://www.dddc.ac.cn/tarfisdock/) was searched by the reverse dockin ... | 2006 | 16882991 |
| a novel branching enzyme of the gh-57 family in the hyperthermophilic archaeon thermococcus kodakaraensis kod1. | branching enzyme (be) catalyzes formation of the branch points in glycogen and amylopectin by cleavage of the alpha-1,4 linkage and its subsequent transfer to the alpha-1,6 position. we have identified a novel be encoded by an uncharacterized open reading frame (tk1436) of the hyperthermophilic archaeon thermococcus kodakaraensis kod1. tk1436 encodes a conserved protein showing similarity to members of glycoside hydrolase family 57 (gh-57 family). at the c terminus of the tk1436 protein, two cop ... | 2006 | 16885460 |
| the essential gtpase yphc displays a major domain rearrangement associated with nucleotide binding. | the structure of a bacillus subtilis yphc/gdp complex shows that it contains two gtpase domains that pack against a central domain whose fold resembles that of an rna binding kh-domain. comparisons of this structure to that of a homologue in thermotoga maritima reveals a dramatic rearrangement in the position of the n-terminal gtpase domain with a shift of up to 60 a and the formation of a totally different interface to the central domain. this rearrangement appears to be triggered by conformati ... | 2006 | 16894162 |
| investigation of the mechanism of proton translocation by nadh:ubiquinone oxidoreductase (complex i) from bovine heart mitochondria: does the enzyme operate by a q-cycle mechanism? | complex i (nadh:ubiquinone oxidoreductase) is the first enzyme of the membrane-bound electron transport chain in mitochondria. it conserves energy, from the reduction of ubiquinone by nadh, as a protonmotive force across the inner membrane, but the mechanism of energy transduction is not known. the structure of the hydrophilic arm of thermophilic complex i supports the idea that proton translocation is driven at (or close to) the point of quinone reduction, rather than at the point of nadh oxida ... | 2006 | 16895522 |
| analyses of variant human papillomavirus type-16 e5 proteins for their ability to induce mitogenesis of murine fibroblasts. | human papillomavirus type 16 (hpv-16) e5 protein co-operates with epidermal growth factor to stimulate mitogenesis of murine fibroblasts. currently, little is known about which viral amino acids are involved in this process. using sequence variants of hpv-16 e5 we have investigated their effects upon e5 transcription, cell-cycling and cell-growth of murine fibroblasts. | 2006 | 16899131 |
| crystal structure of the moloney murine leukemia virus rnase h domain. | a crystallographic study of the moloney murine leukemia virus (mo-mlv) rnase h domain was performed to provide information about its structure and mechanism of action. these efforts resulted in the crystallization of a mutant mo-mlv rnase h lacking the putative helix c (deltac). the 1.6-angstroms resolution structure resembles the known structures of the human immunodeficiency virus type 1 (hiv-1) and escherichia coli rnase h. the structure revealed the coordination of a magnesium ion within the ... | 2006 | 16912289 |
| isolation of a single-stranded dna-binding protein from the methylotrophic yeast, pichia pastoris and its identification as zeta crystallin. | a single-stranded dna (ssdna)-binding protein (ssb) that binds to specific upstream sequences of alcohol oxidase (aox1) promoter of the methylotrophic yeast pichia pastoris has been isolated and identified as zeta crystallin (zta1). the cdna encoding p.pastoris zta1 (ppzta1) was cloned into an escherichia coli expression vector, the recombinant ppzta1 was expressed and purified from e.coli cell lysates. the dna-binding properties of recombinant ppzta1 are identical to those of the ssb present in ... | 2006 | 16914438 |
| elongation complexes of thermus thermophilus rna polymerase that possess distinct translocation conformations. | we have characterized elongation complexes (ecs) of rna polymerase from the extremely thermophilic bacterium, thermus thermophilus. we found that complexes assembled on nucleic acid scaffolds are transcriptionally competent at high temperature (50-80 degrees c) and, depending upon the organization of the scaffold, possess distinct translocation conformations. ecs assembled on scaffolds with a 9 bp rna:dna hybrid are highly stable, resistant to pyrophosphorolysis, and are in the posttranslocated ... | 2006 | 16914440 |
| the "bridging" aspartate 178 in phthalate dioxygenase facilitates interactions between the rieske center and the iron(ii)--mononuclear center. | phthalate dioxygenase (pdo) and its reductase are parts of a two-component rieske dioxygenase system that initiates the aerobic breakdown of phthalate by forming cis-4,5-dihydro-4,5-dihydroxyphthalate (dhd). aspartate d178 in pdo, located near its ferrous mononuclear center, is highly conserved among rieske dioxygenases. the analogous aspartate has been implicated in electron transfer between the mononuclear iron and rieske center in naphthalene dioxygenase [parales et al. (1999) j. bacteriol. 1 ... | 2006 | 16922496 |
| two genes encoding new carotenoid-modifying enzymes in the green sulfur bacterium chlorobium tepidum. | the green sulfur bacterium chlorobium tepidum produces chlorobactene as its primary carotenoid. small amounts of chlorobactene are hydroxylated by the enzyme crtc and then glucosylated and acylated to produce chlorobactene glucoside laurate. the genes encoding the enzymes responsible for these modifications of chlorobactene, ct1987, and ct0967, have been identified by comparative genomics, and these genes were insertionally inactivated in c. tepidum to verify their predicted function. the gene e ... | 2006 | 16923888 |
| antimutator role of the dna glycosylase muty gene in helicobacter pylori. | helicobacter pylori has a highly variable genome with ongoing diversification via inter- and intragenomic recombination and spontaneous mutation. dna repair genes modulating mutation and recombination rates that influence diversification have not been well characterized for h. pylori. to examine the role of putative base excision repair ung and muty glycosylase and xtha apurinic/apyrimidinic endonuclease genes in h. pylori, mutants of each were constructed in strain jp26 by allelic exchange. spo ... | 2006 | 16923889 |
| 23s rrna 2058a-->g alteration mediates ketolide resistance in combination with deletion in l22. | resistance to macrolides and ketolides occurs mainly via alterations in rna moieties of the drug-binding site. using an a2058g mutant of mycobacterium smegmatis, additional telithromycin resistance was acquired via deletion of 15 residues from protein l22. molecular modeling, based on the crystal structure of the large ribosomal subunit from deinococcus radiodurans complexed with telithromycin, shows that the telithromycin carbamate group is located in the proximity of the tip of the l22 hairpin ... | 2006 | 16923950 |
| sit down, relax and unwind: structural insights into recq helicase mechanisms. | helicases are specialized molecular motors that separate duplex nucleic acids into single strands. the recq family of helicases functions at the interface of dna replication, recombination and repair in bacterial and eukaryotic cells. they are key, multifunctional enzymes that have been linked to three human diseases: bloom's, werner's and rothmund-thomson's syndromes. this review summarizes recent studies that relate the structures of recq proteins to their biochemical activities. | 2006 | 16935877 |
| role and timing of gtp binding and hydrolysis during ef-g-dependent trna translocation on the ribosome. | the translocation of trna and mrna through the ribosome is promoted by elongation factor g (ef-g), a gtpase that hydrolyzes gtp during the reaction. recently, it was reported that, in contrast to previous observations, the affinity of ef-g was much weaker for gtp than for gdp and that ribosome-catalyzed gdp-gtp exchange would be required for translocation [zavialov av, hauryliuk vv, ehrenberg m (2005) j biol 4:9]. we have reinvestigated gtp/gdp binding and show that ef-g binds gtp and gdp with a ... | 2006 | 16940356 |
| structure of the stand-alone ram-domain protein from thermus thermophilus hb8. | the stand-alone ram (regulation of amino-acid metabolism) domain protein sraa from thermus thermophilus hb8 (ttha0845) was crystallized in the presence of zinc ions. the x-ray crystal structure was determined using a multiple-wavelength anomalous dispersion technique and was refined at 2.4 a resolution to a final r factor of 25.0%. the monomeric structure is a betaalphabetabetaalphabeta fold and it dimerizes mainly through interactions between the antiparallel beta-sheets. furthermore, five sraa ... | 2006 | 16946463 |
| cloning, expression, purification, crystallization and initial crystallographic analysis of the preprotein translocation atpase seca from thermus thermophilus. | the thermus thermophilus gene encoding the preprotein translocation atpase seca was cloned and expressed and the purified protein was crystallized by the hanging-drop vapour-diffusion technique in two different space groups p3(1(2))21 (a = b = 168.6, c = 149.8 a) and p6(1(5))22 (a = b = 130.9, c = 564.6 a). the crystals, improved by macroseeding, diffracted to beyond 2.8 and 3.5 a resolution for the trigonal and hexagonal crystal forms, respectively. structure determination using the multiple is ... | 2006 | 16946477 |
| a counterintuitive mg2+-dependent and modification-assisted functional folding of mitochondrial trnas. | mitochondrial trnas (mtrnas) often lack domains and posttranscriptional modifications that are found in cytoplasmic trnas. these structural and chemical elements normally stabilize the folding of cytoplasmic trnas into canonical structures that are competent for aminoacylation and translation. for example, the dihydrouridine (d) stem and loop domain is involved in the tertiary structure of cytoplasmic trnas through hydrogen bonds and a mg2+ bridge to the ribothymidine (t) stem and loop domain. t ... | 2006 | 16949614 |
| easi--enrichment of alternatively spliced isoforms. | alternative splicing produces more than one protein from the majority of genes and the rarer forms can have dominant functions. instability of alternative transcripts can also hinder the study of regulation of gene expression by alternative splicing. to investigate the true extent of alternative splicing we have developed a simple method of enriching alternatively spliced isoforms (easi) from pcrs using beads charged with thermus aquaticus single-stranded dna-binding protein (t.aq ssb). this dir ... | 2006 | 16951290 |
| tungsten transport protein a (wtpa) in pyrococcus furiosus: the first member of a new class of tungstate and molybdate transporters. | a novel tungstate and molybdate binding protein has been discovered from the hyperthermophilic archaeon pyrococcus furiosus. this tungstate transport protein a (wtpa) is part of a new abc transporter system selective for tungstate and molybdate. wtpa has very low sequence similarity with the earlier-characterized transport proteins moda for molybdate and tupa for tungstate. its structural gene is present in the genome of numerous archaea and some bacteria. the identification of this new tungstat ... | 2006 | 16952940 |
| mlc of thermus thermophilus: a glucose-specific regulator for a glucose/mannose abc transporter in the absence of the phosphotransferase system. | we report the presence of mlc in a thermophilic bacterium. mlc is known as a global regulator of sugar metabolism in gram-negative enteric bacteria that is controlled by sequestration to a glucose-transporting eii(glc) of the phosphotransferase system (pts). since thermophilic bacteria do not possess pts, mlc in thermus thermophilus must be differently controlled. dna sequence alignments between mlc from t. thermophilus (mlc(tth)) and mlc from e. coli (mlc(eco)) revealed that mlc(tth) conserved ... | 2006 | 16952948 |
| molecular characterization of disease-associated streptococci of the mitis group that are optochin susceptible. | eight optochin-susceptible (opt(s)) alpha-hemolytic (viridans) streptococcus isolates were characterized at the molecular level. these isolates showed phenotypic characteristics typical of both viridans streptococci and streptococcus pneumoniae. comparison of the sequence of housekeeping genes from these isolates with those of s. pneumoniae, streptococcus mitis, streptococcus oralis, and streptococcus pseudopneumoniae suggested that the opt(s) isolates corresponded to streptococci of the mitis g ... | 2006 | 16971639 |
| conservation and variation between rhodobacter capsulatus and escherichia coli tat systems. | the tat system allows the translocation of folded and often cofactor-containing proteins across biological membranes. here, we show by an interspecies transfer of a complete tat translocon that tat systems are largely, but not fully, interchangeable even between different classes of proteobacteria. the tat apparatus from the alpha-proteobacterium rhodobacter capsulatus was transferred to a tat-deficient escherichia coli strain, which is a gamma-proteobacterium. similar to that of e. coli, the r. ... | 2006 | 16980457 |
| colocation of genes encoding a trna-mrna hybrid and a putative signaling peptide on complementary strands in the genome of the hyperthermophilic bacterium thermotoga maritima. | in the genome of the hyperthermophilic bacterium thermotoga maritima, tm0504 encodes a putative signaling peptide implicated in population density-dependent exopolysaccharide formation. although not noted in the original genome annotation, tm0504 was found to colocate, on the opposite strand, with the gene encoding ssra, a hybrid of trna and mrna (tmrna), which is involved in a trans-translation process related to ribosome rescue and is ubiquitous in bacteria. specific dna probes were designed a ... | 2006 | 16980482 |
| analysis of rnase p protein (rnpa) expression in bacillus subtilis utilizing strains with suppressible rnpa expression. | bacterial rnase p is composed of an rna subunit and a single protein subunit (encoded by the rnpb and rnpa genes, respectively). we constructed bacillus subtilis mutant strains that conditionally express the rnase p protein under control of the xylose promoter (p(xyl)). in one strain (d7), rnpa expression was efficiently repressed in the absence of the inducer xylose, leading to cell growth arrest. growth could be restored by a second functional rnpa allele. this is the first rnase p protein kno ... | 2006 | 16980484 |
| characterization of adhesion threads of deinococcus geothermalis as type iv pili. | deinococcus geothermalis e50051 forms tenuous biofilms on paper machine surfaces. field emission electron microscopy analysis revealed peritrichous appendages which mediated cell-to-surface and cell-to-cell interactions but were absent in planktonically grown cells. the major protein component of the extracellular extract of d. geothermalis had an n-terminal sequence similar to the fimbrial protein pilin annotated in the d. geothermalis dsm 11300 draft sequence. it also showed similarity to the ... | 2006 | 16980504 |
| effects of protein-ligand associations on the subunit interactions of phosphofructokinase from b. stearothermophilus. | differences between the crystal structures of inhibitor-bound and uninhibited forms of phosphofructokinase (pfk) from b. stearothermophilus have led to a structural model for allosteric inhibition by phosphoenolpyruvate (pep) wherein a dimer-dimer interface within the tetrameric enzyme undergoes a quaternary shift. we have developed a labeling and hybridization technique to generate a tetramer with subunits simultaneously containing two different extrinsic fluorophores in known subunit orientati ... | 2006 | 16981693 |
| structural and functional conversion of molecular chaperone clpb from the gram-positive halophilic lactic acid bacterium tetragenococcus halophilus mediated by atp and stress. | in this study, we report the purification, initial structural characterization, and functional analysis of the molecular chaperone clpb from the gram-positive, halophilic lactic acid bacterium tetragenococcus halophilus. a recombinant t. halophilus clpb (clpb(tha)) was overexpressed in escherichia coli and purified by affinity chromatography, hydroxyapatite chromatography, and gel filtration chromatography. as demonstrated by gel filtration chromatography, chemical cross-linking with glutaraldeh ... | 2006 | 16997952 |
| identification of pyruvate carboxylase genes in pseudomonas aeruginosa pao1 and development of a p. aeruginosa-based overexpression system for alpha4- and alpha4beta4-type pyruvate carboxylases. | pyruvate carboxylase (pyc) is an ecologically, medically, and industrially important enzyme. it is widespread in all three domains of life, the archaea, bacteria, and eukarya. pyc catalyzes atp-dependent carboxylation of pyruvate to oxaloacetate. detailed structure-function studies of this enzyme have been hampered due to the unavailability of a facile recombinant overexpression system. except for the alpha4 enzyme from a thermophilic bacillus species, escherichia coli has been unsuitable for ov ... | 2006 | 16997990 |
| genetic characterization of the phenylacetyl-coenzyme a oxygenase from the aerobic phenylacetic acid degradation pathway of escherichia coli. | we show here that the paaabcde genes of the paa cluster responsible for phenylacetate degradation in escherichia coli w encode a five-component oxygenase that hydroxylates phenylacetyl-coenzyme a (coa), the first intermediate of the pathway. the primary structure of the subunits of bacterial phenylacetyl-coa oxygenases revealed that these enzymes constitute the prototype of a new and distinct group of the large bacterial diiron multicomponent oxygenase family. | 2006 | 16997993 |
| structural analysis of kasugamycin inhibition of translation. | the prokaryotic ribosome is an important target of antibiotic action. we determined the x-ray structure of the aminoglycoside kasugamycin (ksg) in complex with the escherichia coli 70s ribosome at 3.5-a resolution. the structure reveals that the drug binds within the messenger rna channel of the 30s subunit between the universally conserved g926 and a794 nucleotides in 16s ribosomal rna, which are sites of ksg resistance. to our surprise, ksg resistance mutations do not inhibit binding of the dr ... | 2006 | 16998486 |
| characterization of the particulate methane monooxygenase metal centers in multiple redox states by x-ray absorption spectroscopy. | the integral membrane enzyme particulate methane monooxygenase (pmmo) converts methane, the most inert hydrocarbon, to methanol under ambient conditions. the 2.8-a resolution pmmo crystal structure revealed three metal sites: a mononuclear copper center, a dinuclear copper center, and a nonphysiological mononuclear zinc center. although not found in the crystal structure, solution samples of pmmo also contain iron. we have used x-ray absorption spectroscopy to analyze the oxidation states and co ... | 2006 | 16999437 |
| crystal structures of the dna-binding domain of escherichia coli proline utilization a flavoprotein and analysis of the role of lys9 in dna recognition. | puta (proline utilization a) from escherichia coli is a 1320-amino-acid residue protein that is both a bifunctional proline catabolic enzyme and an autogenous transcriptional repressor. here, we report the first crystal structure of a puta dna-binding domain along with functional analysis of a mutant puta defective in dna binding. crystals were grown using a polypeptide corresponding to residues 1-52 of e. coli puta (puta52). the 2.1 angstrom resolution structure of puta52 mutant lys9met was det ... | 2006 | 17001030 |
| the nmr structure of an internal loop from 23s ribosomal rna differs from its structure in crystals of 50s ribosomal subunits. | internal loops play an important role in structure and folding of rna and in recognition of rna by other molecules such as proteins and ligands. an understanding of internal loops with propensities to form a particular structure will help predict rna structure, recognition, and function. the structures of internal loops 5' 1009cuaag1013 3'/3' 1168gaagc1164 5' and 5' 998cuaag1002 3'/3' 1157gaagc1153 5' from helix 40 of the large subunit rrna in deinococcus radiodurans and escherichia coli, respec ... | 2006 | 17002278 |
| evolution of new function in the gtp cyclohydrolase ii proteins of streptomyces coelicolor. | the genome sequence of streptomyces coelicolor contains three open reading frames (sco1441, sco2687, and sco6655) that encode proteins with significant (>40%) amino acid identity to gtp cyclohydrolase ii (gch ii), which catalyzes the committed step in the biosynthesis of riboflavin. the physiological significance of the redundancy of these proteins in s. coelicolor is not known. however, the gene contexts of the three proteins are different, suggesting that they may serve alternate biological ni ... | 2006 | 17002314 |
| structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-trna synthetase. | to achieve accurate aminoacylation of trnas with their cognate amino acids, errors in aminoacylation are corrected by the "editing" mechanism in several aminoacyl-trna synthetases. phenylalanyl-trna synthetase (phers) hydrolyzes, or edits, misformed tyrosyl-trna with its editing domain in the beta subunit. we report the crystal structure of an n-terminal fragment of the phers beta subunit (phers-beta(n)) from the archaeon, pyrococcus horikoshii, at 1.94-a resolution. phers-beta(n) includes the e ... | 2006 | 17003130 |
| thermostable rnase p rnas lacking p18 identified in the aquificales. | the rnase p rna (rnpb) and protein (rnpa) genes were identified in the two aquificales sulfurihydrogenibium azorense and persephonella marina. in contrast, neither of the two genes has been found in the sequenced genome of their close relative, aquifex aeolicus. as in most bacteria, the rnpa genes of s. azorense and p. marina are preceded by the rpmh gene coding for ribosomal protein l34. this genetic region, including several genes up- and downstream of rpmh, is uniquely conserved among all thr ... | 2006 | 17005927 |
| heat shock proteins, end effectors of myocardium ischemic preconditioning? | the purpose of this study was to investigate (1) whether ischemia-reperfusion increased the content of heat shock protein 72 (hsp72) transcripts and (2) whether myocardial content of hsp72 is increased by ischemic preconditioning so that they can be considered as end effectors of preconditioning. twelve male minipigs (8 protocol, 4 sham) were used, with the following ischemic preconditioning protocol: 3 ischemia and reperfusion 5-minute alternative cycles and last reperfusion cycle of 3 hours. i ... | 2006 | 17009598 |
| substrate recognition, protein dynamics, and iron-sulfur cluster in pseudomonas aeruginosa adenosine 5'-phosphosulfate reductase. | aps reductase catalyzes the first committed step of reductive sulfate assimilation in pathogenic bacteria, including mycobacterium tuberculosis, and is a promising target for drug development. we report the 2.7 a resolution crystal structure of pseudomonas aeruginosa aps reductase in the thiosulfonate intermediate form of the catalytic cycle and with substrate bound. the structure, high-resolution fourier transform ion cyclotron resonance (ft-icr) mass spectrometry, and quantitative kinetic anal ... | 2006 | 17010373 |
| oligomeric states of the seca and secyeg core components of the bacterial sec translocon. | many proteins synthesized in the cytoplasm ultimately function in non-cytoplasmic locations. in escherichia coli, the general secretory (sec) pathway transports the vast majority of these proteins. two fundamental components of the sec transport pathway are the secyeg heterotrimeric complex that forms the channel through the cytoplasmic membrane, and seca, the atpase that drives the preprotein to and across the membrane. this review focuses on what is known about the oligomeric states of these c ... | 2007 | 17011510 |
| oligomeric states of the seca and secyeg core components of the bacterial sec translocon. | many proteins synthesized in the cytoplasm ultimately function in non-cytoplasmic locations. in escherichia coli, the general secretory (sec) pathway transports the vast majority of these proteins. two fundamental components of the sec transport pathway are the secyeg heterotrimeric complex that forms the channel through the cytoplasmic membrane, and seca, the atpase that drives the preprotein to and across the membrane. this review focuses on what is known about the oligomeric states of these c ... | 2007 | 17011510 |
| the methanothermobacter thermautotrophicus exoiii homologue mth212 is a dna uridine endonuclease. | the genome of methanothermobacter thermautotrophicus, as a hitherto unique case, is apparently devoid of genes coding for general uracil dna glycosylases, the universal mediators of base excision repair following hydrolytic deamination of dna cytosine residues. we have now identified protein mth212, a member of the exoiii family of nucleases, as a possible initiator of dna uracil repair in this organism. this enzyme, in addition to bearing all the enzymological hallmarks of an exoiii homologue, ... | 2006 | 17012282 |
| an evolutionary 'intermediate state' of mitochondrial translation systems found in trichinella species of parasitic nematodes: co-evolution of trna and ef-tu. | ef-tu delivers aminoacyl-trnas to ribosomes in the translation system. however, unusual truncations found in some animal mitochondrial trnas seem to prevent recognition by a canonical ef-tu. we showed previously that the chromadorean nematode has two distinct ef-tus, one of which (ef-tu1) binds only to t-armless aminoacyl-trnas and the other (ef-tu2) binds to d-armless ser-trnas. neither of the ef-tus can bind to canonical cloverleaf trnas. in this study, by analyzing the translation system of e ... | 2006 | 17012285 |
| preparation, crystallization and preliminary x-ray analysis of protein ytlp from bacillus subtilis. | bacillus subtilis ytlp is a protein that is predicted to belong to the bacterial and archael 2'-5' rna-ligase family. it contains 183 residues and two copies of the hxtx sequence motif conserved among proteins belonging to this family. in order to determine the structure of ytlp and to compare it with the paralogue yjcg and identified 2'-5' rna ligases, the gene ytlp was amplified from b. subtilis genomic dna and cloned into expression vector pet-21a. the soluble protein was produced in escheric ... | 2006 | 17012785 |
| cloning, purification and preliminary crystallographic analysis of a putative pyridoxal kinase from bacillus subtilis. | pyridoxal kinases (pdxk) are able to catalyse the phosphorylation of three vitamin b(6) precursors, pyridoxal, pyridoxine and pyridoxamine, to their 5'-phosphates and play an important role in the vitamin b(6) salvage pathway. recently, the thid gene of bacillus subtilis was found to encode an enzyme which has the activity expected of a pyridoxal kinase despite its previous assignment as an hmpp kinase owing to higher sequence similarity. as such, this enzyme would appear to represent a new clas ... | 2006 | 17012797 |
| intrinsic and selected resistance to antibiotics binding the ribosome: analyses of brucella 23s rrn, l4, l22, ef-tu1, ef-tu2, efflux and phylogenetic implications. | brucella spp. are highly similar, having identical 16s rna. however, they have important phenotypic differences such as differential susceptibility to antibiotics binding the ribosome. neither the differential susceptibility nor its basis has been rigorously studied. differences found among other conserved ribosomal loci could further define the relationships among the classical brucella spp. | 2006 | 17014718 |
| physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, thermus thermophilus. | guanosine tetraphosphate (ppgpp) is a key mediator of stringent control, an adaptive response of bacteria to amino acid starvation, and has thus been termed a bacterial alarmone. previous x-ray crystallographic analysis has provided a structural basis for the transcriptional regulation of rna polymerase activity by ppgpp in the thermophilic bacterium thermus thermophilus. here we investigated the physiological basis of the stringent response by comparing the changes in intracellular ppgpp levels ... | 2006 | 17015650 |
| thermus thermophilus bacteriophage phiys40 genome and proteomic characterization of virions. | we determined the sequence of the 152,372 bp genome of phiys40, a lytic tailed bacteriophage of thermus thermophilus. the genome contains 170 putative open reading frames and three trna genes. functions for 25% of phiys40 gene products were predicted on the basis of similarity to proteins of known function from diverse phages and bacteria. phiys40 encodes a cluster of proteins involved in nucleotide salvage, such as flavin-dependent thymidylate synthase, thymidylate kinase, ribonucleotide reduct ... | 2006 | 17027029 |
| atomic force microscopy reveals dna bending during group ii intron ribonucleoprotein particle integration into double-stranded dna. | the mobile lactococcus lactis ll.ltrb group ii intron integrates into dna target sites by a mechanism in which the intron rna reverse splices into one dna strand while the intron-encoded protein uses a c-terminal dna endonuclease domain to cleave the opposite strand and then uses the cleaved 3' end to prime reverse transcription of the inserted intron rna. these reactions are mediated by an rnp particle that contains the intron-encoded protein and the excised intron lariat rna, with both the pro ... | 2006 | 17029398 |
| the key dna-binding residues in the c-terminal domain of mycobacterium tuberculosis dna gyrase a subunit (gyra). | as only the type ii topoisomerase is capable of introducing negative supercoiling, dna gyrase is involved in crucial cellular processes. although the other domains of dna gyrase are better understood, the mechanism of dna binding by the c-terminal domain of the dna gyrase a subunit (gyra-ctd) is less clear. here, we investigated the dna-binding sites in the gyra-ctd of mycobacterium tuberculosis gyrase through site-directed mutagenesis. the results show that y577, r691 and r745 are among the key ... | 2006 | 17038336 |
| structural basis for mrna and trna positioning on the ribosome. | protein synthesis requires the accurate positioning of mrna and trna in the peptidyl-trna site of the ribosome. here we describe x-ray crystal structures of the intact bacterial ribosome from escherichia coli in a complex with mrna and the anticodon stem-loop of p-site trna. at 3.5-a resolution, these structures reveal rearrangements in the intact ribosome that clamp p-site trna and mrna on the small ribosomal subunit. binding of the anticodon stem-loop of p-site trna to the ribosome is sufficie ... | 2006 | 17038497 |
| expression of the pyr operon of lactobacillus plantarum is regulated by inorganic carbon availability through a second regulator, pyrr2, homologous to the pyrimidine-dependent regulator pyrr1. | inorganic carbon (ic), such as bicarbonate or carbon dioxide, stimulates the growth of lactobacillus plantarum. at low ic levels, one-third of natural isolated l. plantarum strains are nutritionally dependent on exogenous arginine and pyrimidine, a phenotype previously defined as high-co2-requiring (hcr) prototrophy. ic enrichment significantly decreased the amounts of the enzymes in the pyrimidine biosynthetic pathway encoded by the pyrr1bcaa1ab1dfe operon, as demonstrated by proteomic analysis ... | 2006 | 17041052 |
| crystal structure of laao from calloselasma rhodostoma with an l-phenylalanine substrate: insights into structure and mechanism. | l-amino acid oxidase is a dimeric glycosylated flavoenzyme, a major constituent of the venom-from the snake calloselasma rhodostoma. the enzyme exhibits apoptosis inducing effects as well as antibacterial and anti-hiv activities. the structure of l-amino acid oxidase with its substrate (l-phenylalanine) has been refined to a resolution of 1.8 a. the complex structure reveals the substrate bound to the reduced flavin (fadred). alternative conformations for the key residues his223 and arg322 are e ... | 2006 | 17046020 |
| structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool. | electron transfer flavoprotein-ubiquinone oxidoreductase (etf-qo) is a 4fe4s flavoprotein located in the inner mitochondrial membrane. it catalyzes ubiquinone (uq) reduction by etf, linking oxidation of fatty acids and some amino acids to the mitochondrial respiratory chain. deficiencies in etf or etf-qo result in multiple acyl-coa dehydrogenase deficiency, a human metabolic disease. crystal structures of etf-qo with and without bound uq were determined, and they are essentially identical. the m ... | 2006 | 17050691 |
| a novel single amino acid change in small subunit ribosomal protein s5 has profound effects on translational fidelity. | s5 is a small subunit ribosomal protein (r-protein) linked to the functional center of the 30s ribosomal subunit. in this study we have identified a unique amino acid mutation in escherichia coli s5 that produces spectinomycin-resistance and cold sensitivity. this mutation significantly alters cell growth, folding of 16s ribosomal rna, and translational fidelity. while translation initiation is not affected, both +1 and -1 frameshifting and nonsense suppression are greatly enhanced in the mutant ... | 2006 | 17053085 |
| bioinformatic, genetic, and biochemical evidence that some glycoside hydrolase family 42 beta-galactosidases are arabinogalactan type i oligomer hydrolases. | glycoside hydrolases are organized into glycoside hydrolase families (ghfs) and within this larger group, the beta-galactosidases are members of four families: 1, 2, 35, and 42. most genes encoding ghf 42 enzymes are from prokaryotes unlikely to encounter lactose, suggesting a different substrate for these enzymes. in search of this substrate, we analyzed genes neighboring ghf 42 genes in databases and detected an arrangement implying that these enzymes might hydrolyze oligosaccharides released ... | 2006 | 17056685 |
| coordinate expression of the acetyl coenzyme a carboxylase genes, accb and accc, is necessary for normal regulation of biotin synthesis in escherichia coli. | transcription of the biotin (bio) biosynthetic operon of escherichia coli is negatively regulated by the bira protein, an atypical repressor protein in that it is also an enzyme. the bira-catalyzed reaction involves the covalent attachment of biotin to accb, a subunit of acetyl coenzyme (acetyl-coa) carboxylase. the two functions of bira allow regulation of the bio operon to respond to the intracellular concentrations of both biotin and unbiotinylated accb. we report here that bio operon express ... | 2007 | 17056747 |
| coordinate expression of the acetyl coenzyme a carboxylase genes, accb and accc, is necessary for normal regulation of biotin synthesis in escherichia coli. | transcription of the biotin (bio) biosynthetic operon of escherichia coli is negatively regulated by the bira protein, an atypical repressor protein in that it is also an enzyme. the bira-catalyzed reaction involves the covalent attachment of biotin to accb, a subunit of acetyl coenzyme (acetyl-coa) carboxylase. the two functions of bira allow regulation of the bio operon to respond to the intracellular concentrations of both biotin and unbiotinylated accb. we report here that bio operon express ... | 2007 | 17056747 |
| identification of a histidine-tyrosine cross-link in the active site of the cbb3-type cytochrome c oxidase from rhodobacter sphaeroides. | the heme-copper oxidases constitute a superfamily of terminal dioxygen-reducing enzymes located in the inner mitochondrial or in the bacterial cell membrane. the presence of a mechanistically important covalent bond between a histidine ligand of the copper ion (cu(b)) in the active site and a generally conserved tyrosine residue nearby has been shown to exist in the canonical cytochrome c oxidases. however, according to sequence alignment studies, this critical tyrosine is missing from the subfa ... | 2006 | 17060620 |
| structural and biochemical characterization of human orphan dhrs10 reveals a novel cytosolic enzyme with steroid dehydrogenase activity. | to this day, a significant proportion of the human genome remains devoid of functional characterization. in this study, we present evidence that the previously functionally uncharacterized product of the human dhrs10 gene is endowed with 17beta-hsd (17beta-hydroxysteroid dehydrogenase) activity. 17beta-hsd enzymes are primarily involved in the metabolism of steroids at the c-17 position and also of other substrates such as fatty acids, prostaglandins and xenobiotics. in vitro, dhrs10 converts na ... | 2007 | 17067289 |
| biosynthesis of phosphoserine in the methanococcales. | methanococcus maripaludis and methanocaldococcus jannaschii produce cysteine for protein synthesis using a trna-dependent pathway. these methanogens charge trna(cys) with l-phosphoserine, which is also an intermediate in the predicted pathways for serine and cystathionine biosynthesis. to establish the mode of phosphoserine production in methanococcales, cell extracts of m. maripaludis were shown to have phosphoglycerate dehydrogenase and phosphoserine aminotransferase activities. the heterologo ... | 2007 | 17071763 |
| biosynthesis of phosphoserine in the methanococcales. | methanococcus maripaludis and methanocaldococcus jannaschii produce cysteine for protein synthesis using a trna-dependent pathway. these methanogens charge trna(cys) with l-phosphoserine, which is also an intermediate in the predicted pathways for serine and cystathionine biosynthesis. to establish the mode of phosphoserine production in methanococcales, cell extracts of m. maripaludis were shown to have phosphoglycerate dehydrogenase and phosphoserine aminotransferase activities. the heterologo ... | 2007 | 17071763 |
| crystallization, preliminary crystallographic analysis and phasing of the thiosulfate-binding protein soxy from chlorobium limicola f. thiosulfatophilum. | the 22 kda soxyz protein complex from the green sulfur bacterium chlorobium limicola f. thiosulfatophilum is a central player in the sulfur-oxidizing (sox) enzyme system of the organism by activating thiosulfate for oxidation by soxxa and soxb. it has been proposed that soxyz exists as a heterodimer or heterotetramer, but the properties and role of the individual components of the complex thus far remain unknown. here, the heterologous expression, purification, and the crystallization of stable ... | 2006 | 17077486 |
| overexpression, crystallization and preliminary x-ray crystallographic analysis of phosphopantetheine adenylyltransferase from enterococcus faecalis. | phosphopantetheine adenylyltransferase, an essential enzyme in the coenzyme a biosynthetic pathway, catalyzes the reversible transfer of an adenylyl group from atp to 4'-phosphopantetheine, yielding 3'-dephospho-coa and pyrophosphate. enterococcus faecalis ppat has been overexpressed in escherichia coli as a fusion with a c-terminal purification tag and crystallized at 297 k using a reservoir solution consisting of 0.1 m sodium hepes ph 7.5, 0.8 m sodium dihydrogen phosphate and 0.8 m potassium ... | 2006 | 17077496 |
| carotenoid biosynthesis in the primitive red alga cyanidioschyzon merolae. | cyanidioschyzon merolae is considered to be one of the most primitive of eukaryotic photosynthetic organisms. to obtain insights into the origin and evolution of the pathway of carotenoid biosynthesis in eukaryotic plants, the carotenoid content of c. merolae was ascertained, genes encoding enzymes of carotenoid biosynthesis in this unicellular red alga were identified, and the activities of two candidate pathway enzymes of particular interest, lycopene cyclase and beta-carotene hydroxylase, wer ... | 2007 | 17085635 |
| carotenoid biosynthesis in the primitive red alga cyanidioschyzon merolae. | cyanidioschyzon merolae is considered to be one of the most primitive of eukaryotic photosynthetic organisms. to obtain insights into the origin and evolution of the pathway of carotenoid biosynthesis in eukaryotic plants, the carotenoid content of c. merolae was ascertained, genes encoding enzymes of carotenoid biosynthesis in this unicellular red alga were identified, and the activities of two candidate pathway enzymes of particular interest, lycopene cyclase and beta-carotene hydroxylase, wer ... | 2007 | 17085635 |
| an inserted gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases h. | dynamic processes are inherent properties of proteins and are crucial for a wide range of biological functions. to address how changes in protein sequence and structure affect dynamic processes, a quantitative comparison of microsecond-to-microsecond time scale conformational changes, measured by solution nmr spectroscopy, within homologous mesophilic and thermophilic ribonuclease h (rnase h) enzymes is presented. kinetic transitions between the observed major state (high population) and alterna ... | 2006 | 17088323 |
| mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent dna polymerase. | numerous template-dependent dna polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end dna. such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. here, we employed pre-steady state kinetics and x-ray crystallography to establish a mechanism for blunt-end additions catalyzed by sulfolobus solfataricus dpo4. our kinetic studies indicated that the first blunt-end dat ... | 2007 | 17095011 |
| mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent dna polymerase. | numerous template-dependent dna polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end dna. such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. here, we employed pre-steady state kinetics and x-ray crystallography to establish a mechanism for blunt-end additions catalyzed by sulfolobus solfataricus dpo4. our kinetic studies indicated that the first blunt-end dat ... | 2007 | 17095011 |
| mutagenesis of rat acyl-coa synthetase 4 indicates amino acids that contribute to fatty acid binding. | although each of the five mammalian long-chain acyl-coa synthetases (acsl) can bind saturated and unsaturated fatty acids ranging from 12 to 22 carbons, acsl4 prefers longer chain polyunsaturated fatty acids. in order to gain a better understanding of acsl4 fatty acid binding, we based a mutagenesis approach on sequence alignments related to ttlc-facs crystallized from thermus thermophilus hb8. four residues selected for mutagenesis corresponded to residues in ttlc-facs that comprise the fatty a ... | 2007 | 17110164 |
| emergence of the universal genetic code imprinted in an rna record. | the molecular basis of the genetic code manifests itself in the interaction of the aminoacyl-trna synthetases and their cognate trnas. the fundamental biological question regarding these enzymes' role in the evolution of the genetic code remains open. here we probe this question in a system in which the same trna species is aminoacylated by two unrelated synthetases. should this trna possess major identity elements common to both enzymes, this would favor a scenario where the aminoacyl-trna synt ... | 2006 | 17110438 |
| a thin-layer electrophoretic assay for asp-trnaasn/glu-trnagln amidotransferase. | | 2007 | 17113030 |
| a thin-layer electrophoretic assay for asp-trnaasn/glu-trnagln amidotransferase. | | 2007 | 17113030 |
| interpretation of electron density with stereographic roadmap projections. | the program rivem (radial interpretation of viral electron density maps) was developed to project density radially onto a sphere that is then presented as a stereographic diagram. this permits features resulting from an asymmetric reconstruction to be projected and positioned onto an icosahedral virus surface. the features that constitute the viral surface can also be simultaneously represented in terms of atoms, amino acid residues, potential charge distribution, and surface topology. the proce ... | 2007 | 17116403 |
| interpretation of electron density with stereographic roadmap projections. | the program rivem (radial interpretation of viral electron density maps) was developed to project density radially onto a sphere that is then presented as a stereographic diagram. this permits features resulting from an asymmetric reconstruction to be projected and positioned onto an icosahedral virus surface. the features that constitute the viral surface can also be simultaneously represented in terms of atoms, amino acid residues, potential charge distribution, and surface topology. the proce ... | 2007 | 17116403 |
| time-dependent translational response of e. coli to excess zn(ii). | zinc homeostasis is not well understood beyond methods of import and export. in order to better understand zinc homeostasis in escherichia coli by identifying zn(ii)-responsive proteins, a proteomic approach was taken. through the use of two-dimensional gel electrophoresis, we were able to show that the levels of ompf, aspc, ycdo, eno, and cyse increased after 30 min of zn(ii) stress, while the levels of tig, tufa, sela, and leuc decreased relative to non-stressed controls. after 4 h of zn(ii) s ... | 2006 | 17122063 |
| biochemical characterisation of lign, an nad+-dependent dna ligase from the halophilic euryarchaeon haloferax volcanii that displays maximal in vitro activity at high salt concentrations. | dna ligases are required for dna strand joining in all forms of cellular life. nad+-dependent dna ligases are found primarily in eubacteria but also in some eukaryotic viruses, bacteriophage and archaea. among the archaeal nad+-dependent dna ligases is the lign enzyme of the halophilic euryarchaeon haloferax volcanii, the gene for which was apparently acquired by hfx. volcanii through lateral gene transfer (lgt) from a halophilic eubacterium. genetic studies show that the lgt-acquired lign enzym ... | 2006 | 17132163 |
| the precursor trna 3'-cca interaction with escherichia coli rnase p rna is essential for catalysis by rnase p in vivo. | the l15 region of escherichia coli rnase p rna forms two watson-crick base pairs with precursor trna 3'-cca termini (g292-c75 and g293-c74). here, we analyzed the phenotypes associated with disruption of the g292-c75 or g293-c74 pair in vivo. mutant rnase p rna alleles (rnpbc292 and rnpbc293) caused severe growth defects in the e. coli rnpb mutant strain dw2 and abolished growth in the newly constructed mutant strain bw, in which chromosomal rnpb expression strictly depended on the presence of a ... | 2006 | 17135488 |
| the structure of pyrococcus horikoshii 2'-5' rna ligase at 1.94 a resolution reveals a possible open form with a wider active-site cleft. | bacterial and archaeal 2'-5' rna ligases, members of the 2h phosphoesterase superfamily, catalyze the linkage of the 5' and 3' exons via a 2'-5'-phosphodiester bond during trna-precursor splicing. the crystal structure of the 2'-5' rna ligase ph0099 from pyrococcus horikoshii ot3 was solved at 1.94 a resolution (pdb code 1vgj). the molecule has a bilobal alpha+beta arrangement with two antiparallel beta-sheets constituting a v-shaped active-site cleft, as found in other members of the 2h phospho ... | 2006 | 17142895 |