Publications

domain stability in the aaa+ atpase clpb from escherichia coli.	clpb is a heat-shock protein that reactivates aggregated proteins in cooperation with the dnak chaperone system. clpb belongs to the family of aaa+ atpases and forms ring-shaped oligomers: heptamers in the absence of nucleotides and hexamers in the presence of nucleotides. we investigated the thermodynamic stability of clpb in its monomeric and oligomeric forms. clpb contains six distinct structural domains: the n-terminal domain involved in substrate binding, two aaa+ atp-binding modules, each ...	2006	16615934
prions adhere to soil minerals and remain infectious.	an unidentified environmental reservoir of infectivity contributes to the natural transmission of prion diseases (transmissible spongiform encephalopathies [tses]) in sheep, deer, and elk. prion infectivity may enter soil environments via shedding from diseased animals and decomposition of infected carcasses. burial of tse-infected cattle, sheep, and deer as a means of disposal has resulted in unintentional introduction of prions into subsurface environments. we examined the potential for soil t ...	2006	16617377
the three-dimensional structure of complex i from yarrowia lipolytica: a highly dynamic enzyme.	the structure of complex i from yarrowia lipolytica was determined by three-dimensional electron microscopy. a random conical data set was collected from deep stain embedded particles. more than 14000 image pairs were analyzed. through extensive classification combined with three-dimensional reconstruction, it was possible for the first time to show a much more detailed substructure of the complex. the peripheral arm is subdivided in at least six domains. the membrane arm shows two major protrus ...	2006	16621601
trnahis guanylyltransferase adds g-1 to the 5' end of trnahis by recognition of the anticodon, one of several features unexpectedly shared with trna synthetases.	all eukaryotic trna(his) molecules are unique among trna species because they require addition of a guanine nucleotide at the -1 position by trna(his) guanylyltransferase, encoded in yeast by thg1. this g(-1) residue is both necessary and sufficient for aminoacylation of trna by histidyl-trna synthetase in vitro and is required for aminoacylation in vivo. although thg1 is presumed to be highly specific for trna(his) to prevent misacylation of trnas, the source of this specificity is unknown. we ...	2006	16625026
ph-dependent conformational switch activates the inhibitor of transcription elongation.	gfh1, a transcription factor from thermus thermophilus, inhibits all catalytic activities of rna polymerase (rnap). we characterized the gfh1 structure, function and possible mechanism of action and regulation. gfh1 inhibits rnap by competing with ntps for coordinating the active site mg2+ ion. this coordination requires at least two aspartates at the tip of the gfh1 n-terminal coiled-coil domain (ntd). the overall structure of gfh1 is similar to that of the escherichia coli transcript cleavage ...	2006	16628221
differential gene transfers and gene duplications in primary and secondary endosymbioses.	most genes introduced into phototrophic eukaryotes during the process of endosymbiosis are either lost or relocated into the host nuclear genome. in contrast, groel homologues are found in different genome compartments among phototrophic eukaryotes. comparative sequence analyses of recently available genome data, have allowed us to reconstruct the evolutionary history of these genes and propose a hypothesis that explains the unusual genome distribution of groel homologues.	2006	16640777
crystal structure of hypothetical protein tthb192 from thermus thermophilus hb8 reveals a new protein family with an rna recognition motif-like domain.	we have determined the crystal structure of hypothetical protein tthb192 from thermus thermophilus hb8 at 1.9 a resolution. this protein is a member of the escherichia coli ygch sequence family, which contains approximately 15 sequence homologs of bacterial origin. these homologs have a high isoelectric point. the crystal structure reveals that tthb192 consists of two independently folded domains, and that each domain exhibits a ferredoxin-like fold with a four-stranded antiparallel beta-sheet p ...	2006	16672237
effect of biofilm growth on expression of surface proteins of actinomyces naeslundii genospecies 2.	the predominant surface proteins of biofilm and planktonic actinomyces naeslundii, a primary colonizer of the tooth surface, were examined. seventy-nine proteins (the products of 52 genes) were identified in biofilm cells, and 30 of these, including adhesins, chaperones, and stress-response proteins, were significantly up-regulated relative to planktonic cells.	2006	16672534
structural and functional analysis of rv3214 from mycobacterium tuberculosis, a protein with conflicting functional annotations, leads to its characterization as a phosphatase.	the availability of complete genome sequences has highlighted the problems of functional annotation of the many gene products that have only limited sequence similarity with proteins of known function. the predicted protein encoded by open reading frame rv3214 from the mycobacterium tuberculosis h37rv genome was originally annotated as entd through sequence similarity with the escherichia coli entd, a 4'-phosphopantetheinyl transferase implicated in siderophore biosynthesis. an alternative annot ...	2006	16672613
structure of the unusual seryl-trna synthetase reveals a distinct zinc-dependent mode of substrate recognition.	methanogenic archaea possess unusual seryl-trna synthetase (serrs), evolutionarily distinct from the serrss found in other archaea, eucaryotes and bacteria. the two types of serrss show only minimal sequence similarity, primarily within class ii conserved motifs 1, 2 and 3. here, we report a 2.5 a resolution crystal structure of the atypical methanogenic methanosarcina barkeri serrs and its complexes with atp, serine and the nonhydrolysable seryl-adenylate analogue 5'-o-(n-serylsulfamoyl)adenosi ...	2006	16675947
hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation.	we used a high flux synchrotron x-ray beam to map the structure of 16s rrna and rnase p in viable bacteria in situ. a 300 ms exposure to the x-ray beam was sufficient for optimal cleavage of the phosphodiester backbone. the in vivo footprints of the 16s rrna in frozen cells were similar to those obtained in vitro and were consistent with the predicted accessibility of the rna backbone to hydroxyl radical. protection or enhanced cleavage of certain nucleotides in vivo can be explained by interact ...	2006	16682443
30s ribosomal subunits can be assembled in vivo without primary binding ribosomal protein s15.	assembly of 30s ribosomal subunits from escherichia coli has been dissected in detail using an in vitro system. such studies have allowed characterization of the role for ribosomal protein s15 in the hierarchical assembly of 30s subunits; s15 is a primary binding protein that orchestrates the assembly of ribosomal proteins s6, s11, s18, and s21 with the central domain of 16s ribosomal rna to form the platform of the 30s subunit. in vitro s15 is the sole primary binding protein in this cascade, p ...	2006	16682557
the mechanism of superoxide production by nadh:ubiquinone oxidoreductase (complex i) from bovine heart mitochondria.	nadh:ubiquinone oxidoreductase (complex i) is a major source of reactive oxygen species in mitochondria and a significant contributor to cellular oxidative stress. here, we describe the kinetic and molecular mechanism of superoxide production by complex i isolated from bovine heart mitochondria and confirm that it produces predominantly superoxide, not hydrogen peroxide. redox titrations and electron paramagnetic resonance spectroscopy exclude the iron-sulfur clusters and flavin radical as the s ...	2006	16682634
structure of ribose 5-phosphate isomerase from plasmodium falciparum.	the structure of ribose 5-phosphate isomerase from plasmodium falciparum, pfe0730c, has been determined by molecular replacement at 2.09 angstroms resolution. the enzyme, which catalyzes the isomerization reaction that interconverts ribose 5-phosphate and ribulose 5-phosphate, is a member of the pentose phosphate pathway. the p. falciparum enzyme belongs to the ribose 5-phosphate isomerase a family, pfam family pf06562 (duf1124), and is structurally similar to other members of the family.	2006	16682767
preliminary x-ray crystallographic analysis of the secreted chorismate mutase from mycobacterium tuberculosis: a tricky crystallization problem solved.	chorismate mutase catalyzes the conversion of chorismate to prephenate in the biosynthesis of the aromatic amino acids tyrosine and phenylalanine in bacteria, fungi and plants. here, the crystallization of the unusual secreted chorismate mutase from mycobacterium tuberculosis (encoded by rv1885c), a 37.2 kda dimeric protein belonging to the aroq(gamma) subclass of mutases, is reported. crystal optimization was non-trivial and is discussed in detail. to obtain crystals of sufficient quality, it w ...	2006	16682771
alterations in expression and chromatin configuration of the alpha hemoglobin-stabilizing protein gene in erythroid kruppel-like factor-deficient mice.	erythroid krüppel-like factor (eklf) is an erythroid zinc finger protein identified by its interaction with a caccc sequence in the beta-globin promoter, where it establishes local chromatin structure permitting beta-globin gene transcription. we sought to identify other eklf target genes and determine the chromatin status of these genes in the presence and absence of eklf. we identified alpha hemoglobin-stabilizing protein (ahsp) by subtractive hybridization and demonstrated a 95 to 99.9% reduc ...	2006	16705186
improvements of rolling circle amplification (rca) efficiency and accuracy using thermus thermophilus ssb mutant protein.	rolling circle amplification (rca) of plasmid or genomic dna using random hexamers and bacteriophage phi29 dna polymerase has become increasingly popular in the amplification of template dna in dna sequencing. we have found that the mutant protein of single-stranded dna binding protein (ssb) from thermus thermophilus (tth) hb8 enhances the efficiency of amplification of dna templates. in addition, the tthssb mutant protein increased the specificity of phi29 dna polymerase. we have overexpressed ...	2006	16707659
use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes.	amino acids in proteins are not used equally. some of the differences in the amino acid composition of proteins are between species (mainly due to nucleotide composition and lifestyle) and some are between proteins from the same species (related to protein function, expression or subcellular localization, for example). as several factors contribute to the different amino acid usage in proteins, it is difficult both to analyze these differences and to separate the contributions made by each facto ...	2006	16709240
predicting shine-dalgarno sequence locations exposes genome annotation errors.	in prokaryotes, shine-dalgarno (sd) sequences, nucleotides upstream from start codons on messenger rnas (mrnas) that are complementary to ribosomal rna (rrna), facilitate the initiation of protein synthesis. the location of sd sequences relative to start codons and the stability of the hybridization between the mrna and the rrna correlate with the rate of synthesis. thus, accurate characterization of sd sequences enhances our understanding of how an organism's transcriptome relates to its cellul ...	2006	16710451
the potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases.	aberrant forms of proteins ubiquitin b and beta-amyloid precusor protein, ubb+1 and app+1, are implicated in human neurodegenerative diseases. they have their carboxyl-terminal regions derived from an alternative reading frame. transcription slippage has been invoked to explain the production of these proteins from abnormal mrna. however, ribosomal frameshifting on wild-type mrna may account for the great majority of the aberrant protein. ribosomal frameshifting may also be involved in the progr ...	2006	16714280
the obligate human pathogen, neisseria gonorrhoeae, is polyploid.	we show using several methodologies that the gram-negative, diplococcal-bacterium neisseria gonorrhoeae has more than one complete genome copy per cell. gene dosage measurements demonstrated that only a single replication initiation event per chromosome occurs per round of cell division, and that there is a single origin of replication. the region containing the origin does not encode any genes previously associated with bacterial origins of replication. quantitative pcr results showed that ther ...	2006	16719561
finding the region of pseudo-periodic tandem repeats in biological sequences.	the genomes of many species are dominated by short sequences repeated consecutively. it is estimated that over 10% of the human genome consists of tandemly repeated sequences. finding repeated regions in long sequences is important in sequence analysis. we develop a software, locrepeat, that finds regions of pseudo-periodic repeats in a long sequence. we use the definition of li et al. 1 for the pseudo-periodic partition of a region and extend the algorithm that can select the repeated region fr ...	2006	16722520
functional, biophysical, and structural bases for antibacterial activity of tigecycline.	tigecycline is a novel glycylcycline antibiotic that possesses broad-spectrum activity against many clinically relevant species of bacterial pathogens. the mechanism of action of tigecycline was delineated using functional, biophysical, and molecular modeling experiments in this study. functional assays showed that tigecycline specifically inhibits bacterial protein synthesis with potency 3- and 20-fold greater than that of minocycline and tetracycline, respectively. biophysical analyses demonst ...	2006	16723578
two conformations of a crystalline human trna synthetase-trna complex: implications for protein synthesis.	aminoacylation of trna is the first step of protein synthesis. here, we report the co-crystal structure of human tryptophanyl-trna synthetase and trnatrp. this enzyme is reported to interact directly with elongation factor 1alpha, which carries charged trna to the ribosome. crystals were generated from a 50/50% mixture of charged and uncharged trnatrp. these crystals captured two conformations of the complex, which are nearly identical with respect to the protein and a bound tryptophan. they are ...	2006	16724112
how initiation factors tune the rate of initiation of protein synthesis in bacteria.	the kinetics of initiator transfer rna (trna) interaction with the messenger rna (mrna)-programmed 30s subunit and the rate of 50s subunit docking to the 30s preinitiation complex were measured for different combinations of initiation factors in a cell-free escherichia coli system for protein synthesis with components of high purity. the major results are summarized by a michaelis-menten scheme for initiation. all three initiation factors are required for maximal efficiency (kcat/km) of initiati ...	2006	16724118
crystal structure of the yeast his6 enzyme suggests a reaction mechanism.	the saccharomyces cerevisiae his6 gene codes for the enzyme phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxamide isomerase, catalyzing the fourth step in histidine biosynthesis. to get an insight into the structure and function of this enzyme, we determined its x-ray structure at a resolution of 1.30 a using the anomalous diffraction signal of the protein's sulphur atoms at 1.77 a wavelength. his6 folds in an (alpha/beta)8 barrel similar to hisa, which performs the same function in bac ...	2006	16731983
native state energetics of the src sh2 domain: evidence for a partially structured state in the denatured ensemble.	we have defined the free-energy profile of the src sh2 domain using a variety of biophysical techniques. equilibrium and kinetic experiments monitored by tryptophan fluorescence show that src sh2 is quite stable and folds rapidly by a two-state mechanism, without populating any intermediates. native state hydrogen-deuterium exchange confirms this two-state behavior; we detect no cooperative partially unfolded forms in equilibrium with the native conformation under any conditions. interestingly, ...	2006	16751610
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
overproduction and preliminary crystallographic study of a human kynurenine aminotransferase ii homologue from pyrococcus horikoshii ot3.	the pyrococcus horikoshii ot3 genome contains a gene encoding a human kynurenine aminotransferase ii (kat ii) homologue, which consists of 428 amino-acid residues and shows an amino-acid sequence identity of 30% to human kat ii. this gene was overexpressed in escherichia coli and the recombinant protein (ph-kat ii) was purified. gel-filtration chromatography showed that ph-kat ii exists as a homodimer. ph-kat ii exhibited enzymatic activity that catalyzes the transamination of l-kynurenine to pr ...	2005	16511030
structure of the pseudouridine synthase rsua from haemophilus influenzae.	the structure of the pseudouridine synthase rsua from haemophilus influenza, which catalyzes the conversion of uridine to pseudouridine at a single position within 16s ribosomal rna, has been determined at 1.59 a resolution and compared with that of escherichia coli rsua. the h. influenza enzyme contains an n-terminal s4-like alpha3beta4 domain followed by a catalytic domain, as observed in the structure of e. coli rsua. whereas the individual domains of e. coli and h. influenza rsua are structu ...	2005	16511038
crystallization and preliminary x-ray crystallographic analysis of a conserved domain in plants and prokaryotes from pyrococcus horikoshii ot3.	a plant- and prokaryote-conserved domain (ppc) has previously been found in at-hook motif nuclear localized protein 1 (ahl1) localized in the nuclear matrix of arabidopsis thaliana (atahl1). atahl1 has a dna-binding function. mutation analyses of atahl1 has previously revealed that the hydrophobic region of the ppc domain is essential for its nuclear localization. in this study, the ppc of the hyperthermophilic archaebacterium pyrococcus horikoshii (phppc) was crystallized using the hanging-drop ...	2005	16511056
structure of purine nucleoside phosphorylase (deod) from bacillus anthracis.	protein structures from the causative agent of anthrax (bacillus anthracis) are being determined as part of a structural genomics programme. amongst initial candidates for crystallographic analysis are enzymes involved in nucleotide biosynthesis, since these are recognized as potential targets in antibacterial therapy. purine nucleoside phosphorylase is a key enzyme in the purine-salvage pathway. the crystal structure of purine nucleoside phosphorylase (deod) from b. anthracis has been solved by ...	2005	16511068
crystallization and preliminary x-ray crystallographic analysis of yeast nad+-specific isocitrate dehydrogenase.	nad+-specific isocitrate dehydrogenase (idh; ec 1.1.1.41) is a complex allosterically regulated enzyme in the tricarboxylic acid cycle. yeast idh is believed to be an octamer containing four catalytic idh2 and four regulatory idh1 subunits. crystals of yeast idh have been obtained and optimized using sodium citrate, a competitive inhibitor of the enzyme, as the precipitating agent. the crystals belong to space group r3, with unit-cell parameters a = 302.0, c = 112.1 a. diffraction data were coll ...	2005	16511075
preparation, crystallization and preliminary x-ray analysis of yjcg protein from bacillus subtilis.	bacillus subtilis yjcg is a functionally uncharacterized protein with 171 residues that has no structural homologue in the protein data bank. however, it shows sequence homology to bacterial and archaeal 2'-5' rna ligases. in order to identify its exact function via structural studies, the yjcg gene was amplified from b. subtilis genomic dna and cloned into the expression vector pet21-dest. the protein was expressed in a soluble form in escherichia coli and was purified to homogeneity. crystals ...	2005	16511078
crystallization and preliminary crystallographic analysis of a flavoprotein nadh oxidase from lactobacillus brevis.	nadh oxidase (nox) from lactobacillus brevis is a homotetrameric flavoenzyme composed of 450 amino acids per subunit. the molecular weight of each monomer is 48.8 kda. the enzyme catalyzes the oxidation of two equivalents of nadh and reduces one equivalent of oxygen to yield two equivalents of water, without releasing hydrogen peroxide after the reduction of the first equivalent of nadh. crystals of this protein were grown in the presence of 34% polyethylene glycol monomethyl ether 2000, 0.1 m s ...	2005	16511087
overexpression, purification and crystallographic analysis of a unique adenosine kinase from mycobacterium tuberculosis.	adenosine kinase from mycobacterium tuberculosis is the only prokaryotic adenosine kinase that has been isolated and characterized. the enzyme catalyzes the phosphorylation of adenosine to adenosine monophosphate and is involved in the activation of 2-methyladenosine, a compound that has demonstrated selective activity against m. tuberculosis. the mechanism of action of 2-methyladenosine is likely to be different from those of current tuberculosis treatments and this compound (or other adenosine ...	2005	16511094
expression, purification, crystallization and preliminary x-ray analysis of a nucleoside kinase from the hyperthermophile methanocaldococcus jannaschii.	methanocaldococcus jannaschii nucleoside kinase (mjnk) is an atp-dependent non-allosteric phosphotransferase that shows high catalytic activity for guanosine, inosine and cytidine. mjnk is a member of the phosphofructokinase b family, but participates in the biosynthesis of nucleoside monophosphates rather than in glycolysis. mjnk was crystallized as the apoenzyme as well as in complex with an atp analogue and mg2+. the latter crystal form was also soaked with fructose-6-phosphate. synchrotron-r ...	2005	16511104
crystallization and avoiding the problem of hemihedral twinning in crystals of delta1-pyrroline-5-carboxylate dehydrogenase from thermus thermophilus.	delta1-pyrroline-5-carboxylate dehydrogenase from thermus thermophilus (ttp5cdh) has been crystallized in a citrate-bound form (ttp5cdh-cit). the crystals diffracted to well beyond 2 a resolution, but exhibited perfect or near-perfect hemihedral twinning. variation of crystallization conditions resulted in the growth of larger untwinned crystals or crystals with significantly reduced twin content, all with similar unit-cell parameters. the soaking of ttp5cdh-cit crystals in citrate-free solution ...	2005	16511109
a double mutation of escherichia coli2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase disrupts six hydrogen bonds with, yet fails to prevent binding of, an isoprenoid diphosphate.	the essential enzyme 2c-methyl-d-erythritol-2,4-cyclodiphosphate (mecp) synthase, found in most eubacteria and the apicomplexan parasites, participates in isoprenoid-precursor biosynthesis and is a validated target for the development of broad-spectrum antimicrobial drugs. the structure and mechanism of the enzyme have been elucidated and the recent exciting finding that the enzyme actually binds diphosphate-containing isoprenoids at the interface formed by the three subunits that constitute the ...	2005	16511114
structure of a class ii trmh trna-modifying enzyme from aquifex aeolicus.	biological rnas contain a variety of post-transcriptional modifications that facilitate their efficient function in the cellular environment. one of the two most common forms of modification is methylation of the 2'-hydroxyl group of the ribose sugar, which is performed by a number of s-adenosylmethionine (sam) dependent methyltransferases. in bacteria, many of these modifications in trna and rrna are carried out by the alpha/beta-knot superfamily of enzymes, whose sam-binding pocket is created ...	2005	16511140
cloning, purification and crystallization of thermus thermophilus proline dehydrogenase.	nature recycles l-proline by converting it to l-glutamate. this four-electron oxidation process is catalyzed by the two enzymes: proline dehydrogenase (prodh) and delta1-pyrroline-5-carboxylate dehydrogenase. this note reports the cloning, purification and crystallization of thermus thermophilus prodh, which is the prototype of a newly discovered superfamily of bacterial monofunctional prodhs. the results presented here include production of a monodisperse protein solution through use of the det ...	2005	16511143