Publications

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
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
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