Publications

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
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
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
regulation through the rna polymerase secondary channel. structural and functional variability of the coiled-coil transcription factors.	gre factors enhance the intrinsic endonucleolytic activity of rna polymerase to rescue arrested transcription complexes and are thought to confer the high fidelity and processivity of rna synthesis. the gre factors insert the extended alpha-helical coiled-coil domains into the rna polymerase secondary channel to position two invariant acidic residues at the coiled-coil tip near the active site to stabilize the catalytic metal ion. gfh1, a grea homolog from thermus thermophilus, inhibits rather t ...	2006	16298991
homology-model-guided site-specific mutagenesis reveals the mechanisms of substrate binding and product-regulation of adenosine kinase from leishmania donovani.	despite designating catalytic roles of asp299 and arg131 during the transfer of gamma-phosphate from atp to ado (adenosine) [r. datta, das, sen, chakraborty, adak, mandal and a. k. datta (2005) biochem. j. 387, 591-600], the mechanisms that determine binding of substrate and cause product inhibition of adenosine kinase from leishmania donovani remained unclear. in the present study, employing homology-model-guided site-specific protein mutagenesis, we show that asp16 is indispensable, since its ...	2006	16271040
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
high precision multi-genome scale reannotation of enzyme function by eficaz.	the functional annotation of most genes in newly sequenced genomes is inferred from similarity to previously characterized sequences, an annotation strategy that often leads to erroneous assignments. we have performed a reannotation of 245 genomes using an updated version of eficaz, a highly precise method for enzyme function prediction.	2006	17166279
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
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
crystallization and preliminary x-ray analysis of a native human trna synthetase whose allelic variants are associated with charcot-marie-tooth disease.	glycyl-trna synthetase (glyrs) is one of a group of enzymes that catalyze the synthesis of aminoacyl-trnas for translation. mutations of human and mouse glyrss are causally associated with charcot-marie-tooth disease, the most common genetic disorder of the peripheral nervous system. as the first step towards a structure-function analysis of this disease, native human glyrs was expressed, purified and crystallized. the crystal belonged to space group p4(3)2(1)2 or its enantiomorphic space group ...	2006	17142907
biochemical and structural characterization of the secreted chorismate mutase (rv1885c) from mycobacterium tuberculosis h37rv: an *aroq enzyme not regulated by the aromatic amino acids.	the gene rv1885c from the genome of mycobacterium tuberculosis h37rv encodes a monofunctional and secreted chorismate mutase (mtcm) with a 33-amino-acid cleavable signal sequence; hence, it belongs to the aroq class of chorismate mutases. consistent with the heterologously expressed mtcm having periplasmic destination in escherichia coli and the absence of a discrete periplasmic compartment in m. tuberculosis, we show here that mtcm secretes into the culture filtrate of m. tuberculosis. *mtc ...	2006	17146044
catalases are nad(p)h-dependent tellurite reductases.	reactive oxygen species damage intracellular targets and are implicated in cancer, genetic disease, mutagenesis, and aging. catalases are among the key enzymatic defenses against one of the most physiologically abundant reactive oxygen species, hydrogen peroxide. the well-studied, heme-dependent catalases accelerate the rate of the dismutation of peroxide to molecular oxygen and water with near kinetic perfection. many catalases also bind the cofactors nadph and nadh tenaciously, but, surprising ...	2006	17183702
experimental rugged fitness landscape in protein sequence space.	the fitness landscape in sequence space determines the process of biomolecular evolution. to plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein d2 domain, which is essential for phage infection. after 20 cycles of random substitution at sites 12-130 of the initial random polypeptide and selection for infectivity, the selected phage s ...	2006	17183728
effect of simulated microgravity on oxidation-sensitive gene expression in pc12 cells.	oxygen utilization by and oxygen dependence of cellular processes may be different in biological systems that are exposed to microgravity (micro-g). a baseline in which cellular changes in oxygen sensitive molecular processes occur during micro-g conditions would be important to pursue this question. the objective of this research is to analyze oxidation-sensitive gene expression in a model cell line [rat pheochromocytoma (pc12)] under simulated micro-g conditions. the pc12 cell line is well cha ...	2006	19081771
modeling of phosphomethyl pyrimidine kinase from leptospira interrogans serovar lai strain 56601.	many microorganisms, as well as plants and fungi, synthesize thiamin, but vertebrates do not produce it. phosphomethyl pyrimidine kinase is an enzyme involved in an intermediary step of thiamin biosynthesis from purine molecules. this enzyme is absent in humans. thus, it is a potential chemotherapeutic target for antileptospiral treatment. structure of this enzyme from leptospira interrogans serovar lai strain 56601 has not yet been elucidated. we used the structural template of phosphomethyl py ...	2006	17597880
paradigm development: comparative and predictive 3d modeling of hiv-1 virion infectivity factor (vif).	obtaining structural information about vif is of interest for several reasons that include the study of the interaction of vif with apobec3g, a resistance factor. vif is a potential drug target and its function is essential for the hiv-1 infectivity process. to study vif mechanism of action, we need to decipher its structure. pivotal in this approach is the painstaking prediction of its protein structure. the three-dimensional (3d) crystal structure for vif has not been established. in order to ...	2006	17597910
kinetic analysis of the metal binding mechanism of escherichia coli manganese superoxide dismutase.	the acquisition of a catalytic metal cofactor is an essential step in the maturation of every metalloenzyme, including manganese superoxide dismutase (mnsod). in this study, we have taken advantage of the quenching of intrinsic protein fluorescence by bound metal ions to continuously monitor the metallation reaction of escherichia coli mnsod in vitro, permitting a detailed kinetic characterization of the uptake mechanism. apo-mnsod metallation kinetics are "gated", zero order in metal ion for bo ...	2006	16258041
kinetic analysis of the metal binding mechanism of escherichia coli manganese superoxide dismutase.	the acquisition of a catalytic metal cofactor is an essential step in the maturation of every metalloenzyme, including manganese superoxide dismutase (mnsod). in this study, we have taken advantage of the quenching of intrinsic protein fluorescence by bound metal ions to continuously monitor the metallation reaction of escherichia coli mnsod in vitro, permitting a detailed kinetic characterization of the uptake mechanism. apo-mnsod metallation kinetics are "gated", zero order in metal ion for bo ...	2006	16258041
domain ii plays a crucial role in the function of ribosome recycling factor.	rrf (ribosome recycling factor) consists of two domains, and in concert with ef-g (elongation factor-g), triggers dissociation of the post-termination ribosomal complex. however, the function of the individual domains of rrf remains unclear. to clarify this, two rrf chimaeras, ecodi/ttedii and ttedi/ecodii, were created by domain swaps between the proteins from escherichia coli and thermoanaerobacter tengcongensis. the ribosome recycling activity of the rrf chimaeras was compared with their wild ...	2006	16262604
crystal structures of the editing domain of escherichia coli leucyl-trna synthetase and its complexes with met and ile reveal a lock-and-key mechanism for amino acid discrimination.	aarss (aminoacyl-trna synthetases) are responsible for the covalent linking of amino acids to their cognate trnas via the aminoacylation reaction and play a vital role in maintaining the fidelity of protein synthesis. leurs (leucyl-trna synthetase) can link not only the cognate leucine but also the nearly cognate residues ile and met to trna(leu). the editing domain of leurs deacylates the mischarged ile-trna(leu) and met-trna(leu). we report here the crystal structures of ecleurs-ed (the editin ...	2006	16277600
asnb is involved in natural resistance of mycobacterium smegmatis to multiple drugs.	mycobacteria are naturally resistant to most common antibiotics and chemotherapeutic agents. the underlying molecular mechanisms are not fully understood. in this paper, we describe a hypersensitive mutant of mycobacterium smegmatis, ms 2-39, which was isolated by screening for transposon insertion mutants of m. smegmatis mc2155 that exhibit increased sensitivity to rifampin, erythromycin, or novobiocin. the mutant ms 2-39 exhibited increased sensitivity to all three of the above mentioned antib ...	2006	16377694
the allosteric transition in dnak probed by infrared difference spectroscopy. concerted atp-induced rearrangement of the substrate binding domain.	the biological activity of dnak, the bacterial representative of the hsp70 protein family, is regulated by the allosteric interaction between its nucleotide and peptide substrate binding domains. despite the importance of the nucleotide-induced cycling of dnak between substrate-accepting and releasing states, the heterotropic allosteric mechanism remains as yet undefined. to further characterize this mechanism, the nucleotide-induced absorbance changes in the vibrational spectrum of wild-type dn ...	2006	16384998
production of recombinant and tagged proteins in the hyperthermophilic archaeon sulfolobus solfataricus.	many systems are available for the production of recombinant proteins in bacterial and eukaryotic model organisms, which allow us to study proteins in their native hosts and to identify protein-protein interaction partners. in contrast, only a few transformation systems have been developed for archaea, and no system for high-level gene expression existed for hyperthermophilic organisms. recently, a virus-based shuttle vector with a reporter gene was developed for the crenarchaeote sulfolobus sol ...	2006	16391031
involvement of nark1 and nark2 proteins in transport of nitrate and nitrite in the denitrifying bacterium pseudomonas aeruginosa pao1.	two transmembrane proteins were tentatively classified as nark1 and nark2 in the pseudomonas genome project and hypothesized to play an important physiological role in nitrate/nitrite transport in pseudomonas aeruginosa. the nark1 and nark2 genes are located in a cluster along with the structural genes for the nitrate reductase complex. our studies indicate that the transcription of all these genes is initiated from a single promoter and that the gene complex nark1k2ghji constitutes an operon. u ...	2006	16391109
bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of n-acetylated intermediates in prokaryotes.	the n-acetylation of l-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. until recently, this reaction was thought to be catalyzed by either of two enzymes: (i) the classical n-acetylglutamate synthase (nags, gene arga) first characterized in escherichia coli and pseudomonas aeruginosa several decades ago and also present in vertebrates, or (ii) the bifunctional version of ornithine acetyltransferase (oat, gene argj) present in bacteria, a ...	2006	16409639
comparative genomics of multidrug resistance in acinetobacter baumannii.	acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found in water and soil. this organism was susceptible to most antibiotics in the 1970s. it has now become a major cause of hospital-acquired infections worldwide due to its remarkable propensity to rapidly acquire resistance determinants to a wide range of antibacterial agents. here we use a comparative genomic approach to identify the complete repertoire of resistance genes exhibited by the multidrug-resist ...	2006	16415984
structure-function analysis of the kinase-cpd domain of yeast trna ligase (trl1) and requirements for complementation of trna splicing by a plant trl1 homolog.	trl1 is an essential 827 amino acid enzyme that executes the end-healing and end-sealing steps of trna splicing in saccharomyces cerevisiae. trl1 consists of two domains--an n-terminal ligase component and a c-terminal 5'-kinase/2',3'-cyclic phosphodiesterase (cpd) component--that can function in trna splicing in vivo when expressed as separate polypeptides. to understand the structural requirements for the kinase-cpd domain, we performed an alanine scan of 30 amino acids that are conserved in t ...	2006	16428247
function and evolution of plasmid-borne genes for pyrimidine biosynthesis in borrelia spp.	the thyx gene for thymidylate synthase of the lyme borreliosis (lb) agent borrelia burgdorferi is located in a 54-kb linear plasmid. in the present study, we identified an orthologous thymidylate synthase gene in the relapsing fever (rf) agent borrelia hermsii, located it in a 180-kb linear plasmid, and demonstrated its expression. the functions of the b. hermsii and b. burgdorferi thyx gene products were evaluated both in vivo, by complementation of a thymidylate synthase-deficient escherichia ...	2006	16428394
characterization of the biosynthetic pathway of glucosylglycerate in the archaeon methanococcoides burtonii.	the pathway for the synthesis of the organic solute glucosylglycerate (gg) is proposed based on the activities of the recombinant glucosyl-3-phosphoglycerate synthase (gpgs) and glucosyl-3-phosphoglycerate phosphatase (gpgp) from methanococcoides burtonii. a mannosyl-3-phosphoglycerate phosphatase gene homologue (mpgp) was found in the genome of m. burtonii (http://www.jgi.doe.gov), but an mpgs gene coding for mannosyl-3-phosphoglycerate synthase (mpgs) was absent. the gene upstream of the mpgp ...	2006	16428406
crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover.	nitroalkane oxidase (nao) from fusarium oxysporum catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones with the production of h(2)o(2) and nitrite. the flavoenzyme is a new member of the acyl-coa dehydrogenase (acad) family, but it does not react with acyl-coa substrates. we present the 2.2 a resolution crystal structure of nao trapped during the turnover of nitroethane as a covalent n5-fad adduct (es). the homotetrameric structure of es was solved by mad p ...	2006	16430210
identification and characterization of rsme, the founding member of a new rna base methyltransferase family.	a variety of rna methyltransferases act during ribosomal rna maturation to modify nucleotides in a site-specific manner. however, of the 10 base-methylated nucleotides present in the small ribosomal subunit of escherichia coli, only three enzymes responsible for modification of four bases are known. here, we show that the protein encoded by yggj, a member of the uncharacterized duf558 protein family of predicted alpha/beta (trefoil) knot methyltransferases is responsible for methylation at u1498 ...	2006	16431987
mutations conferring aminoglycoside and spectinomycin resistance in borrelia burgdorferi.	we have isolated and characterized in vitro mutants of the lyme disease agent borrelia burgdorferi that are resistant to spectinomycin, kanamycin, gentamicin, or streptomycin, antibiotics that target the small subunit of the ribosome. 16s rrna mutations a1185g and c1186u, homologous to escherichia coli nucleotides a1191 and c1192, conferred >2,200-fold and 1,300-fold resistance to spectinomycin, respectively. a 16s rrna a1402g mutation, homologous to e. coli a1408, conferred >90-fold resistance ...	2006	16436695
two conformational states in the crystal structure of the homo sapiens cytoplasmic ribosomal decoding a site.	the decoding a site of the small ribosomal subunit is an rna molecular switch, which monitors codon-anticodon interactions to guarantee translation fidelity. we have solved the crystal structure of an rna fragment containing two homo sapiens cytoplasmic a sites. each of the two a sites presents a different conformational state. in one state, adenines a1492 and a1493 are fully bulged-out with c1409 forming a wobble-like pair to a1491. in the second state, adenines a1492 and a1493 form non-watson- ...	2006	16452297
structure of the tetrahymena thermophila telomerase rna helix ii template boundary element.	telomere addition by telomerase requires an internal templating sequence located in the rna subunit of telomerase. the correct boundary definition of this template sequence is essential for the proper addition of the nucleotide repeats. incorporation of incorrect telomeric repeats onto the ends of chromosomes has been shown to induce chromosomal instability in ciliate, yeast and human cells. a 5' template boundary defining element (tbe) has been identified in human, yeast and ciliate telomerase ...	2006	16452301
molecular dynamics simulations of sarcin-ricin rrna motif.	explicit solvent molecular dynamics (md) simulations were carried out for sarcin-ricin domain (srd) motifs from 23s (escherichia coli) and 28s (rat) rrnas. the srd motif consists of gaga tetraloop, g-bulged cross-strand a-stack, flexible region and duplex part. detailed analysis of the overall dynamics, base pairing, hydration, cation binding and other srd features is presented. the srd is surprisingly static in multiple 25 ns long simulations and lacks any non-local motions, with root mean squa ...	2006	16456030
type a and b rnase p rnas are interchangeable in vivo despite substantial biophysical differences.	we show that structural type a and b bacterial ribonuclease p (rnase p) rnas can fully replace each other in vivo despite the many reported differences in their biogenesis, biochemical/biophysical properties and enzyme function in vitro. our findings suggest that many of the reported idiosyncrasies of type a and b enzymes either do not reflect the in vivo situation or are not crucial for rnase p function in vivo, at least under standard growth conditions. the discrimination of mature trna by rna ...	2006	16470227
isolation of a site-specifically modified rna from an unmodified transcript.	natural rnas contain many base modifications that have specific biological functions. the ability to functionally dissect individual modifications is facilitated by the identification and cloning of enzymes responsible for these modifications, but is hindered by the difficulty of isolating site-specifically modified rnas away from unmodified transcripts. using the m1g37 and m1a58 methyl modifications of trna as two examples, we demonstrate that non-pairing base modifications protect rnas against ...	2006	16473844
trna properties help shape codon pair preferences in open reading frames.	translation elongation is an accurate and rapid process, dependent upon efficient juxtaposition of trnas in the ribosomal a- and p-sites. here, we sought evidence of a- and p-site trna interaction by examining bias in codon pair choice within open reading frames from a range of genomes. three distinct and marked effects were revealed once codon and dipeptide biases had been subtracted. first, in the majority of genomes, codon pair preference is primarily determined by a tetranucleotide combinati ...	2006	16473853
crystal structures of two putative phosphoheptose isomerases.		2006	16477602
compositional discordance between prokaryotic plasmids and host chromosomes.	most plasmids depend on the host replication machinery and possess partitioning genes. these properties confine plasmids to a limited range of hosts, yielding a close and presumably stable relationship between plasmid and host. hence, it is anticipated that due to amelioration the dinucleotide composition of plasmids is similar to that of the genome of their hosts. however, plasmids are also thought to play a major role in horizontal gene transfer and thus are frequently exchanged between hosts, ...	2006	16480495
effects of streptomycin resistance mutations on posttranslational modification of ribosomal protein s12.	ribosomal protein s12 contains a highly conserved aspartic acid residue that is posttranslationally beta-methylthiolated. using mass spectrometry, we have determined the modification states of several s12 mutants of thermus thermophilus and conclude that beta-methylthiolation is not a determinant of the streptomycin phenotype.	2006	16484214
the molecular architecture of the metalloprotease ftsh.	the atp-dependent integral membrane protease ftsh is universally conserved in bacteria. orthologs exist in chloroplasts and mitochondria, where in humans the loss of a close ftsh-homolog causes a form of spastic paraplegia. ftsh plays a crucial role in quality control by degrading unneeded or damaged membrane proteins, but it also targets soluble signaling factors like sigma(32) and lambda-cii. we report here the crystal structure of a soluble ftsh construct that is functional in caseinolytic an ...	2006	16484367
dependency map of proteins in the small ribosomal subunit.	the assembly of the ribosome has recently become an interesting target for antibiotics in several bacteria. in this work, we extended an analytical procedure to determine native state fluctuations and contact breaking to investigate the protein stability dependence in the 30s small ribosomal subunit of thermus thermophilus. we determined the causal influence of the presence and absence of proteins in the 30s complex on the binding free energies of other proteins. the predicted dependencies are i ...	2006	16485038
recj exonuclease: substrates, products and interaction with ssb.	the recj exonuclease from escherichia coli degrades single-stranded dna (ssdna) in the 5'-3' direction and participates in homologous recombination and mismatch repair. the experiments described here address recj's substrate requirements and reaction products. recj complexes on a variety of 5' single-strand tailed substrates were analyzed by electrophoretic mobility shift in the absence of mg2+ ion required for substrate degradation. recj required single-stranded tails of 7 nt or greater for rob ...	2006	16488881
molecular localization of a ribosome-dependent atpase on escherichia coli ribosomes.	we have previously isolated and described an escherichia coli ribosome-bound atpase, rbba, that is required for protein synthesis in the presence of atp, gtp and the elongation factors, ef-tu and ef-g. the gene encoding rbba, yhih, has been cloned and the deduced protein sequence harbors two atp-motifs and one rna-binding motif and is homologous to the fungal ef-3. here, we describe the isolation and assay of a truncated form of the rbba protein that is stable to overproduction and purification. ...	2006	16495476
identification of hepta- and octo-uridine stretches as sole signals for programmed +1 and -1 ribosomal frameshifting during translation of sars-cov orf 3a variants.	programmed frameshifting is one of the translational recoding mechanisms that read the genetic code in alternative ways. this process is generally programmed by signals at defined locations in a specific mrna. in this study, we report the identification of hepta- and octo-uridine stretches as sole signals for programmed +1 and -1 ribosomal frameshifting during translation of severe acute respiratory syndrome coronavirus (sars-cov) orf 3a variants. sars-cov orf 3a encodes a minor structural prote ...	2006	16500894
a structural model for the large subunit of the mammalian mitochondrial ribosome.	protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. evolutionary changes in protein and rna sequences can affect the 3d organization of structural features in ribosomes in different species. the most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. the rna component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. ...	2006	16510155
specific functional interactions of nucleotides at key -3 and +4 positions flanking the initiation codon with components of the mammalian 48s translation initiation complex.	eukaryotic initiation factor (eif) 1 maintains the fidelity of initiation codon selection and enables mammalian 43s preinitiation complexes to discriminate against aug codons with a context that deviates from the optimum sequence gcc(a/g)ccaugg, in which the purines at (-)3 and (+)4 positions are most important. we hypothesize that eif1 acts by antagonizing conformational changes that occur in ribosomal complexes upon codon-anticodon base-pairing during 48s initiation complex formation, and that ...	2006	16510876
cloning, expression, purification, crystallization and initial crystallographic analysis of transcription elongation factors greb from escherichia coli and gfh1 from thermus thermophilus.	the escherichia coli gene encoding the transcription cleavage factor greb and the thermus thermophilus gene encoding the anti-grea transcription factor gfh1 were cloned and expressed and the purified proteins were crystallized by the sitting-drop vapor-diffusion technique. the greb and gfh1 crystals, which were improved by macroseeding, belong to space group p4(1)2(1)2 (or p4(3)2(1)2), with unit-cell parameters a = b = 148, c = 115.2 a and a = b = 59.3, c = 218.9 a, respectively. complete diffra ...	2006	16511259
expression, purification, crystallization and preliminary x-ray analysis of the human ruvb-like protein ruvbl1.	ruvbl1, an evolutionary highly conserved protein related to the aaa+ family of atpases, has been crystallized using the hanging-drop vapour-diffusion method at 293 k. the crystals are hexagonal and belong to space group p6, with unit-cell parameters a = b = 207.1, c = 60.7 a and three molecules in the asymmetric unit.	2006	16511264
expression, purification, crystallization and preliminary x-ray analysis of the human ruvb-like protein ruvbl1.	ruvbl1, an evolutionary highly conserved protein related to the aaa+ family of atpases, has been crystallized using the hanging-drop vapour-diffusion method at 293 k. the crystals are hexagonal and belong to space group p6, with unit-cell parameters a = b = 207.1, c = 60.7 a and three molecules in the asymmetric unit.	2006	16511264
purification, crystallization and preliminary characterization of a putative lmbe-like deacetylase from bacillus cereus.	the bacillus cereus bc1534 protein, a putative deacetylase from the lmbe family, has been purified to homogeneity and crystallized using the hanging-drop vapour-diffusion method. crystals of the 26 kda protein grown from mpd and acetate buffer belong to space group r32, with unit-cell parameters a = b = 76.7, c = 410.5 a (in the hexagonal setting). a complete native data set was collected to a resolution of 2.5 a from a single cryoprotected crystal using synchrotron radiation. as bc1534 shows si ...	2006	16511317
crystallization and preliminary x-ray crystallographic analysis of biodegradative threonine deaminase (tdcb) from salmonella typhimurium.	biodegradative threonine deaminase (tdcb) catalyzes the deamination of l-threonine to alpha-ketobutyrate, the first reaction in the anaerobic breakdown of l-threonine to propionate. unlike the biosynthetic threonine deaminase, tdcb is insensitive to l-isoleucine and is activated by amp. here, the cloning of tdcb (molecular weight 36 kda) from salmonella typhimurium with an n-terminal hexahistidine affinity tag and its overexpression in escherichia coli is reported. tdcb was purified to homogenei ...	2006	16511321
use of single-point genome signature tags as a universal tagging method for microbial genome surveys.	we developed single-point genome signature tags (sp-gsts), a generally applicable, high-throughput sequencing-based method that targets specific genes to generate identifier tags from well-defined points in a genome. the technique yields identifier tags that can distinguish between closely related bacterial strains and allow for the identification of microbial community members. sp-gsts are determined by three parameters: (i) the primer designed to recognize a conserved gene sequence, (ii) the a ...	2006	16517658
comparison of conventional pcr with real-time pcr and branched dna-based assays for hepatitis c virus rna quantification and clinical significance for genotypes 1 to 5.	the key parameter for diagnosis and management of hepatitis c virus (hcv) infection is hcv rna. standardization of hcv rna assays to iu is mainly based on genotype 1 panels. little is known about the variability of commercially available hcv rna assays for quantification of different genotypes. two real-time reverse transcription (rt)-pcr assays (cobas taqman hcv test for use with the high-pure system [hps/ctm] and cobas ampliprep/cobas taqman hcv test [cap/ctm]), one standard rt-pcr assay (coba ...	2006	16517847
structural and evolutionary classification of g/u wobble basepairs in the ribosome.	we present a comprehensive structural, evolutionary and molecular dynamics (md) study of the g/u wobble basepairs in the ribosome based on high-resolution crystal structures, including the recent escherichia coli structure. these basepairs are classified according to their tertiary interactions, and sequence conservation at their positions is determined. g/u basepairs participating in tertiary interactions are more conserved than those lacking any interactions. specific interactions occurring in ...	2006	16522645
computer-aided nmr assay for detecting natively folded structural domains.	structural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. for large proteins, this strategy includes the dissection of proteins into structural domains that form stable native structures. however, protein dissection essentially remains an empirical and often a tedious process. here, we describe a simple strategy for rapidly identifying structural domains and assessing their structures. this approach combines the com ...	2006	16522794
kinetics and product analysis of the reaction catalysed by recombinant homoaconitase from thermus thermophilus.	hacn (homoaconitase) is a member of a family of [4fe-4s] cluster-dependent enzymes that catalyse hydration/dehydration reactions. the best characterized example of this family is the ubiquitous acn (aconitase), which catalyses the dehydration of citrate to cis-aconitate, and the subsequent hydration of cis-aconitate to isocitrate. hacn is an enzyme from the alpha-aminoadipate pathway of lysine biosynthesis, and has been identified in higher fungi and several archaea and one thermophilic species ...	2006	16524361
adaptor protein controlled oligomerization activates the aaa+ protein clpc.	the aaa+ protein clpc is not only involved in the removal of misfolded and aggregated proteins but also controls, through regulated proteolysis, key steps of several developmental processes in the gram-positive bacterium bacillus subtilis. in contrast to other aaa+ proteins, clpc is unable to mediate these processes without an adaptor protein like meca. here, we demonstrate that the general activation of clpc is based upon the ability of meca to participate in the assembly of an active and subst ...	2006	16525504
discrimination of cognate and noncognate substrates at the active site of class i lysyl-trna synthetase.	the aminoacyl-trna synthetases are divided into two unrelated structural classes, with lysyl-trna synthetase (lysrs) being the only enzyme represented in both classes. on the basis of the structure of l-lysine complexed with pyrococcus horikoshii class i lysrs (lysrs1) and homology to glutamyl-trna synthetase (glurs), residues implicated in amino acid recognition and noncognate substrate discrimination were systematically replaced in borrelia burgdorferi lysrs1. the catalytic efficiency of stead ...	2006	16533047
pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine crenarchaeota.	marine crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. we report here analysis of fosmid sequences derived from the uncultivated mar ...	2006	16533068
nabp1, a novel rorgamma-regulated gene encoding a single-stranded nucleic-acid-binding protein.	rorgamma2 (retinoid-related orphan receptor gamma2) plays a critical role in the regulation of thymopoiesis. microarray analysis was performed in order to uncover differences in gene expression between thymocytes of wild-type and rorgamma-/- mice. this analysis identified a novel gene encoding a 22 kda protein, referred to as nabp1 (nucleic-acid-binding protein 1). this subsequently led to the identification of an additional protein, closely related to nabp1, designated nabp2. both proteins cont ...	2006	16533169
explanation of the stability of thermophilic proteins based on unique micromorphology.	two mesophilic/thermophilic variants of the g-domain of the elongation factor tu were studied via molecular dynamics simulations. by analyzing the simulation data via the voronoi space tessellation, we have found that the two proteins have the same macromolecular packing, while the water-exposed surface area is larger for the thermophile. a larger coordination with water is probably due to a peculiar corrugation of the exposed surface of this species. from an enthalpic point of view, the thermop ...	2006	16533850
residues in substrate proteins that interact with groel in the capture process are buried in the native state.	we have used a bioinformatic approach to predict the natural substrate proteins for the escherichia coli chaperonin groel based on two simple criteria. natural substrate proteins should contain binding motifs similar in sequence to the mobile loop peptide of groes that displaces the binding motif during the chaperonin cycle. secondly, each substrate protein should contain multiple copies of the binding motif so that the chaperonin can perform "work" on the substrate protein. to validate these cr ...	2006	16537402
score-based prediction of genomic islands in prokaryotic genomes using hidden markov models.	horizontal gene transfer (hgt) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. it is the difference in speed enabling the rapid adaptation to changing environmental demands that distinguishes hgt from gene genesis, duplications or mutations. for a precise characterization, algorithms are needed that identify transfer events with high reliability. frequently, the transferred pieces of dna have a considerable length, comprise several gene ...	2006	16542435
liberation of zinc-containing l31 (rpme) from ribosomes by its paralogous gene product, ytia, in bacillus subtilis.	we have found that alternative localization of two types of l31 ribosomal protein, rpme and ytia, is controlled by the intracellular concentration of zinc in bacillus subtilis. the detailed mechanisms for the alternation of l31 proteins under zinc-deficient conditions were previously unknown. to obtain further information about this regulatory mechanism, we have studied the stability of rpme in vivo and the binding affinity of these proteins to ribosomes in vitro, and we have found that liberati ...	2006	16547061
a pathway branching in transcription initiation in escherichia coli.	in transcription initiation, all rna polymerase molecules bound to a promoter have been conventionally supposed to proceed into elongation of transcript. however, for escherichia coli rna polymerase, evidence has been accumulated for a view that only its fraction can proceed into elongation and the rest is retained at a promoter in non-productive form: a pathway branching in transcription initiation. proteins such as grea and greb affect these fractions at several promoters in vitro. to reveal t ...	2006	16553885
identification of nucleotides in e. coli 16s rrna essential for ribosome subunit association.	the ribosome consists of two unequal subunits, which associate via numerous intersubunit contacts. medium-resolution structural studies have led to grouping of the intersubunit contacts into 12 directly visualizable intersubunit bridges. most of the intersubunit interactions involve rna. we have used an rna modification interference approach to determine escherichia coli 16s rrna positions that are essential for the association of functionally active 70s ribosomes. modification of the n1 positio ...	2006	16556933
structural basis for altering the stability of homologous rnas from a mesophilic and a thermophilic bacterium.	tertiary rna structures from thermophilic bacteria generally are more stable than their mesophilic homologs. to understand the structural basis of the increase in stability, we investigated equilibrium folding of the specificity domain (s-domain) of rnase p rna from a mesophilic (escherichia coli) and a thermophilic (thermus thermophilus) bacterium. equilibrium folding of both s-domains is described by a minimal, three-state folding scheme, u-to-i-to-n. in the i-to-n transition of the thermophil ...	2006	16581805
purification, crystallization and preliminary x-ray diffraction of secdf, a translocon-associated membrane protein, from thermus thermophilus.	thermus thermophilus has a multi-path membrane protein, tsecdf, as a single-chain homologue of escherichia coli secd and secf, which form a translocon-associated complex required for efficient preprotein translocation and membrane-protein integration. here, the cloning, expression in e. coli, purification and crystallization of tsecdf are reported. overproduced tsecdf was solubilized with dodecylmaltoside, chromatographically purified and crystallized by vapour diffusion in the presence of polye ...	2006	16582489
two putative c-type multiheme cytochromes required for the expression of omcb, an outer membrane protein essential for optimal fe(iii) reduction in geobacter sulfurreducens.	deletion of two homologous geobacter sulfurreducens c-type cytochrome genes, omcg and omch, decreased the rate of fe(iii) reduction and decreased the level of an outer membrane cytochrome critical for fe(iii) reduction, omcb, without affecting its transcription. expression of either gene restored fe(iii) reduction and omcb expression, suggesting functional similarity.	2006	16585776
nmr structure of the aquifex aeolicus tmrna pseudoknot pk1: new insights into the recoding event of the ribosomal trans-translation.	the transfer-messenger rna (tmrna) pseudoknot pk1 is essential for bacterial trans-translation, a ribosomal rescue mechanism. we report the solution structure of pk1 from aquifex aeolicus, which despite an unprecedented small number of nucleotides and thus an unprecented compact size, displays a very high thermal stability. several unusual structural features account for these properties and indicate that pk1 belongs to the class of ribosomal frameshift pseudoknots. this suggests a similarity be ...	2006	16595798
crystal structure of the conserved protein ttha0727 from thermus thermophilus hb8 at 1.9 a resolution: a cmd family member distinct from carboxymuconolactone decarboxylase (cmd) and ahpd.	ttha0727 is a conserved hypothetical protein from thermus thermophilus hb8, with a molecular mass of 12.6 kda. ttha0727 belongs to the carboxymuconolactone decarboxylase (cmd) family (pfam 02627). a sequence comparison with its homologs suggested that ttha0727 is a distinct protein from alkylhydroperoxidase ahpd and gamma-carboxymuconolactone decarboxylase in the cmd family. here we report the 1.9 a crystal structure of ttha0727 (pdb id: 2cwq) determined by the multiwavelength anomalous dispersi ...	2006	16597838
characteristic signatures of the lyta gene provide a basis for rapid and reliable diagnosis of streptococcus pneumoniae infections.	the nucleotide sequences of the lyta gene from 29 pneumococcal isolates of various serotypes and 22 additional streptococci of the mitis group (including two streptococcus pseudopneumoniae strains) have been compared and found to correspond to 19 typical (927-bp-long) and 20 atypical (921-bp-long) alleles. all the streptococcus pneumoniae strains harbored typical lyta alleles, whereas nonpneumococcal isolates belonging to the mitis group always carried atypical alleles. a sequence alignment show ...	2006	16597847
molecular characterization of subject-specific oral microflora during initial colonization of enamel.	the initial microbial colonization of tooth surfaces is a repeatable and selective process, with certain bacterial species predominating in the nascent biofilm. characterization of the initial microflora is the first step in understanding interactions among community members that shape ensuing biofilm development. using molecular methods and a retrievable enamel chip model, we characterized the microbial diversity of early dental biofilms in three subjects. a total of 531 16s rrna gene sequences ...	2006	16597990
a phylogenomic profile of globins.	globins occur in all three kingdoms of life: they can be classified into single-domain globins and chimeric globins. the latter comprise the flavohemoglobins with a c-terminal fad-binding domain and the gene-regulating globin coupled sensors, with variable c-terminal domains. the single-domain globins encompass sequences related to chimeric globins and "truncated" hemoglobins with a 2-over-2 instead of the canonical 3-over-3 alpha-helical fold.	2006	16600051
crystal structure of bacillus subtilis trmb, the trna (m7g46) methyltransferase.	the structure of bacillus subtilis trmb (bstrmb), the trna (m7g46) methyltransferase, was determined at a resolution of 2.1 a. this is the first structure of a member of the trmb family to be determined by x-ray crystallography. it reveals a unique variant of the rossmann-fold methyltransferase (rfm) structure, with the n-terminal helix folded on the opposite site of the catalytic domain. the architecture of the active site and a computational docking model of bstrmb in complex with the methyl g ...	2006	16600901
melanocyte transformation associated with substrate adhesion impediment.	exclude experimental models of malignant transformation employ chemical and physical carcinogens or genetic manipulations to study tumor progression. in this work, different melanoma cell lines were established after submitting a nontumorigenic melanocyte lineage (melan-a) to sequential cycles of forced anchorage impediment. the great majority of these cells underwent anoikis when maintained in suspension. after one deadhesion cycle, phenotypic alterations were noticeable in the few surviving ce ...	2006	16611417
small protein b interacts with the large and the small subunits of a stalled ribosome during trans-translation.	during trans-translation, stalled bacterial ribosomes are rescued by small protein b (smpb) and by transfer-messenger rna (tmrna). stalled ribosomes switch translation from the defective messages to a short internal reading frame on tmrna that tags the nascent peptide chain for degradation and recycles the ribosomes. we present evidences that smpb binds the large and small ribosomal subunits in vivo and in vitro. the binding between smpb and the ribosomal subunits is very tight, with a dissociat ...	2006	16611927
the domain of the bacillus subtilis dead-box helicase yxin that is responsible for specific binding of 23s rrna has an rna recognition motif fold.	the yxin protein of bacillus subtilis is a member of the dbpa subfamily of prokaryotic dead-box rna helicases. like dbpa, it binds with high affinity and specificity to segments of 23s ribosomal rna as short as 32 nucleotides (nt) that include hairpin 92. several experiments have shown that the 76-residue carboxy-terminal domain of yxin is responsible for the high-affinity rna binding. the domain has been crystallized and its structure has been solved to 1.7 angstroms resolution. the structure r ...	2006	16611943
comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms.	six diverse prokaryotic and five eukaryotic genomes were compared to deduce whether the protein synthesis termination signal has common determinants within and across both kingdoms. four of the six prokaryotic and all of the eukaryotic genomes investigated demonstrated a similar pattern of nucleotide bias both 5' and 3' of the stop codon. a preferred core signal of 4 nt was evident, encompassing the stop codon and the following nucleotide. codons decoded by hyper-modified trnas were over-represe ...	2006	16614446
proteins surrounding hairpin iiie of the hepatitis c virus internal ribosome entry site on the human 40s ribosomal subunit.	binding of the internal ribosome entry site (ires) of the hepatitis c virus (hcv) rna to the eif-free 40s ribosomal subunit is the first step of initiation of translation of the viral rna. hairpins iiid and iiie comprising 253-302 nt of the ires are known to be essential for binding to the 40s subunit. here we have examined the molecular environment of the hcv ires in its binary complex with the human 40s ribosomal subunit. for this purpose, two rna derivatives were used that bore a photoactivat ...	2006	16614452