Publications

sequence analysis of four shigella boydii o-antigen loci: implication for escherichia coli and shigella relationships.	shigella strains are in reality clones of escherichia coli and are believed to have emerged relatively recently (g. m. pupo, r. lan, and p. r. reeves, proc. natl. acad. sci. usa 97:10567-10572, 2000). there are 33 o-antigen forms in these shigella clones, of which 12 are identical to o antigens of other e. coli strains. we sequenced o-antigen gene clusters from shigella boydii serotypes 4, 5, 6, and 9 and also studied the o53- and o79-antigen gene clusters of e. coli, encoding o antigens identic ...	2001	11598067
the organization of cytoplasmic ribosomal protein genes in the arabidopsis genome.	eukaryotic ribosomes are made of two components, four ribosomal rnas, and approximately 80 ribosomal proteins (r-proteins). the exact number of r-proteins and r-protein genes in higher plants is not known. the strong conservation in eukaryotic r-protein primary sequence allowed us to use the well-characterized rat (rattus norvegicus) r-protein set to identify orthologues on the five haploid chromosomes of arabidopsis. by use of the numerous expressed sequence tag (est) accessions and the complet ...	2001	11598216
influence of a sulfhydryl cross-link across the allosteric-site interface of e. coli phosphofructokinase.	to assess the role of quaternary stability on the properties of escherichia coli phosphofructokinase (pfk), a disulfide bond has been introduced across the subunit interface containing the allosteric binding sites in e. coli phosphofructokinase by changing n288 to cysteine. n288 is located in close proximity to the equivalent residue on an adjacent subunit. although sds-page of oxidized n288c indicates monomeric protein, blocking the six native cysteine residues with n-ethyl maleimide (nem) reve ...	2001	11604525
differential effects of replacing escherichia coli ribosomal protein l27 with its homologue from aquifex aeolicus.	the rpma gene, which encodes 50s ribosomal subunit protein l27, was cloned from the extreme thermophile aquifex aeolicus, and the protein was overexpressed and purified. comparison of the a. aeolicus protein with its homologue from escherichia coli by circular dichroism analysis and proton nuclear magnetic resonance spectroscopy showed that it readily adopts some structure in solution that is very stable, whereas the e. coli protein is unstructured under the same conditions. a mutant of e. coli ...	2001	11673426
clue to damage recognition by uvrb: residues in the beta-hairpin structure prevent binding to non-damaged dna.	uvrb, the ultimate damage-recognizing component of bacterial nucleotide excision repair, contains a flexible beta-hairpin rich in hydrophobic residues. we describe the properties of uvrb mutants in which these residues have been mutated. the results show that y101 and f108 in the tip of the hairpin are important for the strand-separating activity of uvrb, supporting the model that the beta-hairpin inserts between the two dna strands during the search for dna damage. residues y95 and y96 at the b ...	2001	11689453
structural and mutational studies of the recognition of the arginine trna-specific major identity element, a20, by arginyl-trna synthetase.	arginyl-trna synthetase (argrs) recognizes two major identity elements of trna(arg): a20, located at the outside corner of the l-shaped trna, and c35, the second letter of the anticodon. only a few exceptional organisms, such as the yeast saccharomyces cerevisiae, lack a20 in trna(arg). in the present study, we solved the crystal structure of a typical a20-recognizing argrs from thermus thermophilus at 2.3 a resolution. the structure of the t. thermophilus argrs was found to be similar to that o ...	2001	11698642
brucella abortus genes identified following constitutive growth and macrophage infection.	the chronicity of brucella abortus infection in humans and animals depends on the organism's ability to escape host defenses by gaining entry and surviving inside the macrophage. although no human vaccine exists for brucella, vaccine development in other bacteria has been based on deletions of selective nutritional as well as regulatory systems. our goal is to develop a vaccine for brucella. to further this aim, we have used a green fluorescent protein (gfp) reporter system to identify constitut ...	2001	11705955
nog2p, a putative gtpase associated with pre-60s subunits and required for late 60s maturation steps.	eukaryotic ribosome maturation depends on a set of well ordered processing steps. here we describe the functional characterization of yeast nog2p (ynr053cp), a highly conserved nuclear protein. nog2p contains a putative gtp-binding site, which is essential in vivo. kinetic and steady-state measurements of the levels of pre-rrnas in nog2p-depleted cells showed a defect in 5.8s and 25s maturation and a concomitant increase in the levels of both 27sb(s) and 7s(s) precursors. we found nog2p physical ...	2001	11707418
crystal structure of thermostable dna photolyase: pyrimidine-dimer recognition mechanism.	dna photolyase is a pyrimidine-dimer repair enzyme that uses visible light. photolyase generally contains two chromophore cofactors. one is a catalytic cofactor directly contributing to the repair of a pyrimidine-dimer. the other is a light-harvesting cofactor, which absorbs visible light and transfers energy to the catalytic cofactor. photolyases are classified according to their second cofactor into either a folate- or deazaflavin-type. the native structures of both types of photolyases have a ...	2001	11707580
the hunt for living gold. the search for organisms in extreme environments yields useful enzymes for industry.		2001	11713183
saturation mutagenesis of 5s rrna in saccharomyces cerevisiae.	rrnas are the central players in the reactions catalyzed by ribosomes, and the individual rrnas are actively involved in different ribosome functions. our previous demonstration that yeast 5s rrna mutants (called mof9) can impact translational reading frame maintenance showed an unexpected function for this ubiquitous biomolecule. at the time, however, the highly repetitive nature of the genes encoding rrnas precluded more detailed genetic and molecular analyses. a new genetic system allows all ...	2001	11713264
overexpression, purification and characterization of recj protein from thermus thermophilus hb8 and its core domain.	a recj homolog was cloned from the extremely thermophilic bacterium thermus themophilus hb8. it encodes a 527 amino acid protein that has 33% identity to escherichia coli recj protein and includes the characteristic motifs conserved among recj homologs. although t.thermophilus recj protein (ttrecj) was expressed as an inclusion body, it was purified in soluble form through denaturation with urea and subsequent refolding steps. limited proteolysis showed that ttrecj has a protease-resistant core ...	2001	11713311
importance of the conserved nucleotides around the trna-like structure of escherichia coli transfer-messenger rna for protein tagging.	a bacterial rna functioning as both trna and mrna, transfer-messenger rna (tmrna) rescues stalled ribosomes and clears the cell of incomplete polypeptides. for function, escherichia coli tmrna requires an elaborate interplay between a trna-like structure and an internal mrna domain that are connected by a 295 nt long compact secondary structure. the trna-like structure is surrounded by 16 unpaired nt, including 10 residues that are >95% conserved among the known 140 tmrna sequences. all these re ...	2001	11713316
behavior of dna fibers stretched by precise meniscus motion control.	a modified dna combing method, which can precisely locate straightened dna fibers on a substrate, has been developed. precise motion control of a dna solution droplet on hydrophobic surfaces has allowed detailed analyses of dna straightening behavior. our method provides a technique for consistently straightening lambda phage dna on a trace of droplet motion, though the straightened dnas had several variations in their alignments. the dependence of the straightened dna frequency upon motion rate ...	2001	11713329
structure and dynamics of translation initiation factor aif-1a from the archaeon methanococcus jannaschii determined by nmr spectroscopy.	translation initiation factor 1a (aif-1a) from the archaeon methanococcus jannaschii was expressed in escherichia coli, purified, and characterized in terms of its structure and dynamics using multidimensional nmr methods. the protein was found to be a member of the ob-fold family of rna-associated proteins, containing a barrel of five beta-strands, a feature that is shared with the homologous eukaryotic translation initiation factor 1a (eif-1a), as well as the prokaryotic translation initiation ...	2001	11714910
h(2)o(2)-forming nadh oxidase with diaphorase (cytochrome) activity from archaeoglobus fulgidus.	an enzyme exhibiting nadh oxidase (diaphorase) activity was isolated from the hyperthermophilic sulfate-reducing anaerobe archaeoglobus fulgidus. n-terminal sequence of the protein indicates that it is coded for by open reading frame af0395 in the a. fulgidus genome. the gene af0395 was cloned and its product was purified from escherichia coli. like the native nadh oxidase (noxa2), the recombinant noxa2 (rnoxa2) has an apparent molecular mass of 47 kda, requires flavin adenine dinucleotide for a ...	2001	11717257
novel posttranslational activation of the lys2-encoded alpha-aminoadipate reductase for biosynthesis of lysine and site-directed mutational analysis of conserved amino acid residues in the activation domain of candida albicans.	the alpha-aminoadipate pathway for lysine biosynthesis is present only in fungi. the alpha-aminoadipate reductase (aar) of this pathway catalyzes the conversion of alpha-aminoadipic acid to alpha-aminoadipic-delta-semialdehyde by a complex mechanism involving two gene products, lys2p and lys5p. the lys2 and lys5 genes encode, respectively, a 155-kda inactive aar and a 30-kda phosphopantetheinyl transferase (pptase) which transfers a phosphopantetheinyl group from coenzyme a (coa) to lys2p for th ...	2001	11717270
adp-dependent phosphofructokinases in mesophilic and thermophilic methanogenic archaea.	phosphofructokinase (pfk) is a key enzyme of the glycolytic pathway in all domains of life. two related pfks, atp-dependent and pp(i)-dependent pfk, have been distinguished in bacteria and eucarya, as well as in some archaea. hyperthermophilic archaea of the order thermococcales, including pyrococcus and thermococcus spp., have recently been demonstrated to possess a unique adp-dependent pfk (adp-pfk) that appears to be phylogenetically distinct. here, we report the presence of adp-pfks in glyco ...	2001	11717273
different physiological roles of atp- and pp(i)-dependent phosphofructokinase isoenzymes in the methylotrophic actinomycete amycolatopsis methanolica.	cells of the actinomycete amycolatopsis methanolica grown on glucose possess only a single, exclusively pp(i)-dependent phosphofructokinase (pp(i)-pfk) (a. m. c. r. alves, g. j. w. euverink, h. j. hektor, j. van der vlag, w. vrijbloed, d.h.a. hondmann, j. visser, and l. dijkhuizen, j. bacteriol. 176:6827-6835, 1994). when this methylotrophic bacterium is grown on one-carbon (c(1)) compounds (e.g., methanol), an atp-dependent phosphofructokinase (atp-pfk) activity is specifically induced, complet ...	2001	11717283
complex i and its involvement in redox homeostasis and carbon and nitrogen metabolism in rhodobacter capsulatus.	a transposon mutant of rhodobacter capsulatus, strain mal7, that was incapable of photoautotrophic and chemoautotrophic growth and could not grow photoheterotrophically in the absence of an exogenous electron acceptor was isolated. the phenotype of strain mal7 suggested that the mutation was in some gene(s) not previously shown to be involved in co(2) fixation control. the site of transposition in strain mal7 was identified and shown to be in the gene nuof, which encodes one of the 14 subunits f ...	2001	11717288
cysteinyl-trna synthetase is not essential for viability of the archaeon methanococcus maripaludis.	the methanogenic archaea methanocaldococcus jannaschii and methanothermobacter thermautotrophicus contain a dual-specificity prolyl-trna synthetase (procysrs) that accurately forms both prolyl-trna (pro-trna) and cysteinyl-trna (cys-trna) suitable for in vivo translation. this intriguing enzyme may even perform its dual role in organisms that possess a canonical single-specificity cysteinyl-trna synthetase (cysrs), raising the question as to whether this latter aminoacyl-trna synthetase is indee ...	2001	11717392
recognizing the d-loop of transfer rnas.		2001	11717415
degradation of xylan to d-xylose by recombinant saccharomyces cerevisiae coexpressing the aspergillus niger beta-xylosidase (xlnd) and the trichoderma reesei xylanase ii (xyn2) genes.	the beta-xylosidase-encoding xlnd gene of aspergillus niger 90196 was amplified by the pcr technique from first-strand cdna synthesized on mrna isolated from the fungus. the nucleotide sequence of the cdna fragment was verified to contain a 2,412-bp open reading frame that encodes a 804-amino-acid propeptide. the 778-amino-acid mature protein, with a putative molecular mass of 85.1 kda, was fused in frame with the saccharomyces cerevisiae mating factor alpha1 signal peptide (mfalpha1(s)) to ensu ...	2001	11722900
deletion of the gre3 aldose reductase gene and its influence on xylose metabolism in recombinant strains of saccharomyces cerevisiae expressing the xyla and xks1 genes.	saccharomyces cerevisiae ferments hexoses efficiently but is unable to ferment xylose. when the bacterial enzyme xylose isomerase (xi) from thermus thermophilus was produced in s. cerevisiae, xylose utilization and ethanol formation were demonstrated. in addition, xylitol and acetate were formed. an unspecific aldose reductase (ar) capable of reducing xylose to xylitol has been identified in s. cerevisiae. the gre3 gene, encoding the ar enzyme, was deleted in s. cerevisiae cen.pk2-1c, yielding y ...	2001	11722921
v-shaped structure of glutamyl-trna reductase, the first enzyme of trna-dependent tetrapyrrole biosynthesis.	processes vital to life such as respiration and photosynthesis critically depend on the availability of tetrapyrroles including hemes and chlorophylls. trna-dependent catalysis generally is associated with protein biosynthesis. an exception is the reduction of glutamyl-trna to glutamate-1-semialdehyde by the enzyme glutamyl-trna reductase. this reaction is the indispensable initiating step of tetrapyrrole biosynthesis in plants and most prokaryotes. the crystal structure of glutamyl-trna reducta ...	2001	11726494
mode of dna-protein interaction between the c-terminal domain of escherichia coli rna polymerase alpha subunit and t7d promoter up element.	the c-terminal domain (ctd) downstream from residue 235 of escherichia coli rna polymerase alpha subunit is involved in recognition of the promoter up element. here we have demonstrated, by dnase i and hydroxyl radical mapping, the presence of two up element subsites on the promoter d of phage t7, each located half and one-and-a-half helix turns, respectively, upstream from the promoter -35 element. this non-typical up element retained its alphactd-binding capability when transferred into the ge ...	2001	11812819
a protonated base pair participating in rrna tertiary structural interactions.	in the recently published x-ray crystallographic structure for the 50s subunit of haloarcula marismortui ribosomes, residue u2546 of the 23s rrna forms a non-watson-crick base pair with u2610. the corresponding residues in the secondary structure of the escherichia coli 23s molecule are u2511 and c2575, and it follows that the latter base (c2575) should be protonated in order to form a base pair that is isostructural with its counterpart in h.marismortui. this prediction was demonstrated experim ...	2001	11812838
nmr structure of a ribosomal rna hairpin containing a conserved cucaa pentaloop.	the structure of a 23 nt rna sequence, rggacccgggcucaaccugggucc, was elucidated using homonuclear nmr, distance geometry and restrained molecular dynamics. this rna is analogous to residues 612-628 of the escherichia coli 16s rrna. the structure of the rna reveals the presence of a pentaloop closed by a duplex stem in typical a-form conformation. the loop does not form a u-turn motif, as previously predicted. a non-planar a.c.a triple base interaction (hydrogen bonds a13 nh6-c10 o2 and c10 n3-a1 ...	2001	11812846
hepatitis c virus 3'x region interacts with human ribosomal proteins.	to identify proteins that can bind the 3' untranslated region (utr) of hepatitis c virus (hcv) we screened human cdna libraries using the saccharomyces cerevisiae three-hybrid system. screening with an rna sequence derived from the 3'-terminal 98 nucleotides (3'x region) of an infectious clone of hcv (h77c) yielded clones of human ribosomal proteins l22, l3, s3, and ml3, a mitochondrial homologue of l3. we performed preliminary characterization of the binding between the 3'x region and these pro ...	2001	11152508
development of a reverse transcription-pcr-dna enzyme immunoassay for detection of "norwalk-like" viruses and hepatitis a virus in stool and shellfish.	outbreaks of food- and waterborne gastroenteritis are being increasingly reported throughout the world. the analysis of environmental samples by newer diagnostic techniques such as reverse transcription-pcr (rt-pcr) amplification of nucleic acid has begun to identify human enteric viruses (predominantly "norwalk-like" viruses [nlvs]) as the cause of many of these outbreaks. to streamline nlv detection from environmental samples such as shellfish, we have developed an rt-pcr-oligoprobe amplificat ...	2001	11157239
the crystal structure of the ttcsaa protein: an export-related chaperone from thermus thermophilus.	the csaa protein was first characterized in bacillus subtilis as a molecular chaperone with export-related activities. here we report the 2.0 angstrom-resolution crystal structure of the thermus thermophilus csaa protein, designated ttcsaa. atomic structure and experiments in solution revealed a homodimer as the functional unit. the structure of the ttcsaa monomer is reminiscent of the well known oligonucleotide-binding fold, with the addition of extensions at the n- and c-termini that form an e ...	2001	11157762
structure of the emapii domain of human aminoacyl-trna synthetase complex reveals evolutionary dimer mimicry.	the emapii (endothelial monocyte-activating polypeptide ii) domain is a trna-binding domain associated with several aminoacyl-trna synthetases, which becomes an independent domain with inflammatory cytokine activity upon apoptotic cleavage from the p43 component of the multisynthetase complex. it comprises a domain that is highly homologous to bacterial trna-binding proteins (trbp), followed by an extra domain without homology to known proteins. trbps, which may represent ancient trna chaperones ...	2001	11157763
cloning of the soda gene from corynebacterium melassecola and role of superoxide dismutase in cellular viability.	the soda gene encoding the corynebacterium melassecola manganese-cofactored superoxide dismutase (sod) has been cloned in escherichia coli and sequenced. the gene is transcribed monocistronically; the predicted polypeptide is 200 amino acids long and associates in a homotetrameric, manganese-dependent form, able to complement an sod-deficient e. coli mutant. a second open reading frame, coding for a putative 217-amino-acid protein with high homology to peptide methionine sulfoxide reductases fro ...	2001	11157941
multiple regulatory mechanisms act on the 5' untranslated region of the s-layer gene from thermus thermophilus hb8.	the role of the 5' untranslated region (5'utr) of the s-layer gene from thermus thermophilus was analyzed through the isolation of delta 5'utr mutants. in these mutants the half-life of spla mrna was strongly reduced and slpa transcription was no longer subjected to growth phase-dependent repression. overproduction and detachment of the external envelopes of the mutants were observed in stationary phase.	2001	11157968
role of the tat ransport system in nitrous oxide reductase translocation and cytochrome cd1 biosynthesis in pseudomonas stutzeri.	by transforming n2o to n2, the multicopper enzyme nitrous oxide reductase provides a periplasmic electron sink for a respiratory chain that is part of denitrification. the signal sequence of the enzyme carries the heptameric twin-arginine consensus motif characteristic of the tat pathway. we have identified tat genes of pseudomonas stutzeri and functionally analyzed the unlinked tatc and tate loci. a tatc mutant retained n2o reductase in the cytoplasm in the unprocessed form and lacking the meta ...	2001	11160097
new host-vector system for thermus spp. based on the malate dehydrogenase gene.	a thermus thermophilus hb27 strain was constructed in which the malate dehydrogenase (mdh) gene was deleted. the deltamdh colonies are recognized by a small-colony phenotype. wild-type phenotype is restored by transformation with thermus plasmids or integration vector containing an intact mdh gene. the wild-type phenotype provides a positive selection tool for the introduction of plasmid dna into thermus spp., and because mdh levels can be readily quantified, this host-vector system is a conveni ...	2001	11160114
kh domain: one motif, two folds.	the k homology (kh) module is a widespread rna-binding motif that has been detected by sequence similarity searches in such proteins as heterogeneous nuclear ribonucleoprotein k (hnrnp k) and ribosomal protein s3. analysis of spatial structures of kh domains in hnrnp k and s3 reveals that they are topologically dissimilar and thus belong to different protein folds. thus kh motif proteins provide a rare example of protein domains that share significant sequence similarity in the motif regions but ...	2001	11160884
characterization of rnase p from thermotoga maritima.	the protein subunit of rnase p from a thermophilic bacterium, thermotoga maritima, was overexpressed in and purified from escherichia coli. the cloned protein was reconstituted with the rna subunit transcribed in vitro. the temperature optimum of the holoenzyme is near 50 degrees c, with no enzymatic activity at 65 degrees c or above. this finding is in sharp contrast to the optimal growth temperature of t.maritima, which is near 80 degrees c. however, in heterologous reconstitution experiments ...	2001	11160919
crystal structure of the holliday junction migration motor protein ruvb from thermus thermophilus hb8.	we report here the crystal structure of the ruvb motor protein from thermus thermophilus hb8, which drives branch migration of the holliday junction during homologous recombination. ruvb has a crescent-like architecture consisting of three consecutive domains, the first two of which are involved in atp binding and hydrolysis. dna is likely to interact with a large basic cleft, which encompasses the atp-binding pocket and domain boundaries, whereas the junction-recognition protein ruva may bind a ...	2001	11171970
connection between poly-beta-hydroxybutyrate biosynthesis and growth on c(1) and c(2) compounds in the methylotroph methylobacterium extorquens am1.	several dna regions containing genes involved in poly-beta-hydroxybutyrate (phb) biosynthesis and degradation and also in fatty acid degradation were identified from genomic sequence data and have been characterized in the serine cycle facultative methylotroph methylobacterium extorquens am1. genes involved in phb biosynthesis include those encoding beta-ketothiolase (phaa), nadph-linked acetoacetyl coenzyme a (acetyl-coa) reductase (phab), and phb synthase (phac). phaa and phab are closely link ...	2001	11208803
experimental evolution of enzyme temperature activity profile: selection in vivo and characterization of low-temperature-adapted mutants of pyrococcus furiosus ornithine carbamoyltransferase.	we have obtained mutants of pyrococcus furiosus ornithine carbamoyltransferase active at low temperatures by selecting for complementation of an appropriate yeast mutant after in vivo mutagenesis. the mutants were double ones, still complementing at 15 degrees c, a temperature already in the psychrophilic range. their kinetic analysis is reported.	2001	11208811
occurrence of transsulfuration in synthesis of l-homocysteine in an extremely thermophilic bacterium, thermus thermophilus hb8.	a cell extract of an extremely thermophilic bacterium, thermus thermophilus hb8, cultured in a synthetic medium catalyzed cystathionine gamma-synthesis with o-acetyl-l-homoserine and l-cysteine as substrates but not beta-synthesis with dl-homocysteine and l-serine (or o-acetyl-l-serine). the amounts of synthesized enzymes metabolizing sulfur-containing amino acids were estimated by determining their catalytic activities in cell extracts. the syntheses of cystathionine beta-lyase (ec 4.4.1.8) and ...	2001	11222609
crystal structure of the lrp-like transcriptional regulator from the archaeon pyrococcus furiosus.	the lrpa protein from the hyperthermophilic archaeon pyrococcus furiosus belongs to the lrp/asnc family of transcriptional regulatory proteins, of which the escherichia coli leucine-responsive regulatory protein is the archetype. its crystal structure has been determined at 2.9 a resolution and is the first for a member of the lrp/asnc family, as well as one of the first for a transcriptional regulator from a hyperthermophile. the structure consists of an n-terminal domain containing a helix-tur ...	2001	11230123
genome of the extremely radiation-resistant bacterium deinococcus radiodurans viewed from the perspective of comparative genomics.	the bacterium deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, uv radiation, oxidizing agents, and electrophilic mutagens. d. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. these characte ...	2001	11238985
crystal structure of hiv-1 reverse transcriptase in complex with a polypurine tract rna:dna.	we have determined the 3.0 a resolution structure of wild-type hiv-1 reverse transcriptase in complex with an rna:dna oligonucleotide whose sequence includes a purine-rich segment from the hiv-1 genome called the polypurine tract (ppt). the ppt is resistant to ribonuclease h (rnase h) cleavage and is used as a primer for second dna strand synthesis. the 'rnase h primer grip', consisting of amino acids that interact with the dna primer strand, may contribute to rnase h catalysis and cleavage spec ...	2001	11250910
recombinant thermus aquaticus rna polymerase, a new tool for structure-based analysis of transcription.	the three-dimensional structure of dna-dependent rna polymerase (rnap) from thermophilic thermus aquaticus has recently been determined at 3.3 a resolution. currently, very little is known about t. aquaticus transcription and no genetic system to study t. aquaticus rnap genes is available. to overcome these limitations, we cloned and overexpressed t. aquaticus rnap genes in escherichia coli. overproduced t. aquaticus rnap subunits assembled into functional rnap in vitro and in vivo when coexpres ...	2001	11114902
rubrerythrin and rubredoxin oxidoreductase in desulfovibrio vulgaris: a novel oxidative stress protection system.	evidence is presented for an alternative to the superoxide dismutase (sod)-catalase oxidative stress defense system in desulfovibrio vulgaris (strain hildenborough). this alternative system consists of the nonheme iron proteins, rubrerythrin (rbr) and rubredoxin oxidoreductase (rbo), the product of the rbo gene (also called desulfoferrodoxin). a deltarbo strain of d. vulgaris was found to be more sensitive to internal superoxide exposure than was the wild type. unlike rbo, expression of plasmid- ...	2001	11114906
characterization and evolution of anthranilate 1,2-dioxygenase from acinetobacter sp. strain adp1.	the two-component anthranilate 1,2-dioxygenase of the bacterium acinetobacter sp. strain adp1 was expressed in escherichia coli and purified to homogeneity. this enzyme converts anthranilate (2-aminobenzoate) to catechol with insertion of both atoms of o(2) and consumption of one nadh. the terminal oxygenase component formed an alpha(3)beta(3) hexamer of 54- and 19-kda subunits. biochemical analyses demonstrated one rieske-type [2fe-2s] center and one mononuclear nonheme iron center in each larg ...	2001	11114907
initiation factor 2 of myxococcus xanthus, a large version of prokaryotic translation initiation factor 2.	we have isolated the structural gene for translation initiation factor if2 (infb) from the myxobacterium myxococcus xanthus. the gene (3.22 kb) encodes a 1,070-residue protein showing extensive homology within its g domain and c terminus to the equivalent regions of if2 from escherichia coli. the protein cross-reacts with antibodies raised against e. coli if2 and was able to complement an e. coli infb mutant. the m. xanthus protein is the largest if2 known to date. this is essentially due to a l ...	2001	11114918
vima gene downstream of reca is involved in virulence modulation in porphyromonas gingivalis w83.	a 0.9-kb open reading frame encoding a unique 32-kda protein was identified downstream of the reca gene of porphyromonas gingivalis. reverse transcription-pcr and northern blot analysis showed that both the reca gene and this open reading frame are part of the same transcriptional unit. this cloned fragment was insertionally inactivated using the ermf-ermam antibiotic resistance cassette to create a defective mutant by allelic exchange. when plated on brucella blood agar, the mutant strain, desi ...	2001	11119521
molecular ecology of tetracycline resistance: development and validation of primers for detection of tetracycline resistance genes encoding ribosomal protection proteins.	phylogenetic analysis of tetracycline resistance genes encoding the ribosomal protection proteins (rpps) revealed the monophyletic origin of these genes. the most deeply branching class, exemplified by tet and otra, consisted of genes from the antibiotic-producing organisms streptomyces rimosus and streptomyces lividans. with a high degree of confidence, the corresponding genes of the other seven classes (tet m, tet s, tet o, tet w, tet q, tet t, and tetb p) formed phylogenetically distinct sepa ...	2001	11133424
ihfa gene of the bacterium myxococcus xanthus and its role in activation of carotenoid genes by blue light.	myxococcus xanthus responds to blue light by producing carotenoids. several regulatory genes are known that participate in the light action mechanism, which leads to the transcriptional activation of the carotenoid genes. we had already reported the isolation of a carotenoid-less, tn5-induced strain (mr508), whose mutant site was unlinked to the indicated regulatory genes. here, we show that omegamr508::tn5 affects all known light-inducible promoters in different ways. it blocks the activation o ...	2001	11133949
gene cluster of rhodothermus marinus high-potential iron-sulfur protein: oxygen oxidoreductase, a caa(3)-type oxidase belonging to the superfamily of heme-copper oxidases.	the respiratory chain of the thermohalophilic bacterium rhodothermus marinus contains an oxygen reductase, which uses hipip (high potential iron-sulfur protein) as an electron donor. the structural genes encoding the four subunits of this hipip:oxygen oxidoreductase were cloned and sequenced. the genes for subunits ii, i, iii, and iv (named rcoxa to rcoxd) are found in this order and seemed to be organized in an operon of at least five genes with a terminator structure a few nucleotides downstre ...	2001	11133964
identification of the outer membrane porin of thermus thermophilus hb8: the channel-forming complex has an unusually high molecular mass and an extremely large single-channel conductance.	the outer membrane of the thermophilic bacterium thermus thermophilus was isolated using sucrose step gradient centrifugation. its detergent extracts contained an ion-permeable channel with an extremely high single-channel conductance of 20 ns in 1 m kcl. the channel protein was purified by preparative sodium dodecyl sulfate (sds)-polyacylamide gel electrophoresis. it has a high molecular mass of 185 kda, and its channel-forming ability resists boiling in sds for 10 min.	2001	11133980
a subunit of human nuclear rnase p has atpase activity.	human nuclear rnase p purified from hela cells has atpase activity. this activity is associated with one of the protein subunits of the enzyme, rpp20. thus, human nuclear rnase p, which contains several proteins and one essential rna, has at least one other enzymatic activity in addition to cleavage of phosphoester bonds in rna. the amino acid sequence of rpp20 has a signature motif found in an atpase-containing subunit of a family of protein complexes (abc transporters) that mediate a variety o ...	2001	11149958
distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal rna.	the relative substitution rate of each nucleotide site in bacterial small subunit rrna, large subunit rrna and 5s rrna was calculated from sequence alignments for each molecule. two-dimensional and three-dimensional variability maps of the rrnas were obtained by plotting the substitution rates on secondary structure models and on the tertiary structure of the rrnas available from x-ray diffraction results. this showed that the substitution rates are generally low near the centre of the ribosome, ...	2001	11812832
aaa proteins: in search of a common molecular basis. international meeting on cellular functions of aaa proteins.		2001	11713188
gene cassette pcr: sequence-independent recovery of entire genes from environmental dna.	the vast majority of bacteria in the environment have yet to be cultured. consequently, a major proportion of both genetic diversity within known gene families and an unknown number of novel gene families reside in these uncultured organisms. isolation of these genes is limited by lack of sequence information. where such sequence data exist, pcr directed at conserved sequence motifs recovers only partial genes. here we outline a strategy for recovering complete open reading frames from environme ...	2001	11679351
electrostatics of nanosystems: application to microtubules and the ribosome.	evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. foremost among the models used to elucidate the electrostatic potential is the poisson-boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. here we present the application of numerical methods to enable the trivially parallel solution of the poisson-boltzmann eq ...	2001	11517324
functional relevance of the disulfide-linked complex of the n-terminal pdz domain of inad with norpa.	in drosophila, phototransduction is mediated by g(q)-activation of phospholipase c and is a well studied model system for understanding the kinetics of signal initiation, propagation and termination controlled by g proteins. the proper intracellular targeting and spatial arrangement of most proteins involved in fly phototransduction require the multi-domain scaffolding protein inad, composed almost entirely of five pdz domains, which independently bind various proteins including norpa, the relev ...	2001	11500369
survey and summary: the applications of universal dna base analogues.	a universal base analogue forms 'base pairs' with each of the natural dna/rna bases with little discrimination between them. a number of such analogues have been prepared and their applications as biochemical tools investigated. most of these analogues are non-hydrogen bonding, hydrophobic, aromatic 'bases' which stabilise duplex dna by stacking interactions. this review of the literature of universal bases (to 2000) details the analogues investigated, and their uses and limitations are discusse ...	2001	11410649
enhancing the catalytic repertoire of nucleic acids: a systematic study of linker length and rigidity.	the incorporation of potentially catalytic groups in dna is of interest for the in vitro selection of novel deoxyribozymes. a series of 10 c5-modified analogues of 2'-deoxyuridine triphosphate have been synthesised that possess side chains of differing flexibility and bearing a primary amino or imidazole functionality. for each series of nucleotide analogues differing degrees of flexibility of the c5 side chain was achieved through the use of alkynyl, alkenyl and alkyl moieties. the imidazole fu ...	2001	11266559
chloroplast ribosomal protein s7 of chlamydomonas binds to chloroplast mrna leader sequences and may be involved in translation initiation.	certain mutations isolated in the 5' untranslated region (5'utr) of the chloroplast rps7 gene in chlamydomonas reduce expression of reporter genes. second site suppressors in this 5'utr sequence restore reporter expression. 5'utr sequences with the original mutations fail to bind a 20-kd protein, one of five proteins that bind to leaders of several chloroplast genes. however, 5'utrs from suppressed mutants restore binding to this protein but do not bind a 47-kd protein present on the wild type a ...	2001	11158540
aminoacyl-trna synthetases database.	aminoacyl-trna synthetases (aarss) are at the center of the question of the origin of life. they constitute a family of enzymes integrating the two levels of cellular organization: nucleic acids and proteins. aarss arose early in evolution and are believed to be a group of ancient proteins. they are responsible for attaching amino acid residues to their cognate trna molecules, which is the first step in the protein synthesis. the role they play in a living cell is essential for the precise decip ...	2001	11125115
molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils.	microorganisms that use nitrate as an alternative terminal electron acceptor play an important role in the global nitrogen cycle. the diversity of the nitrate-reducing community in soil and the influence of the maize roots on the structure of this community were studied. the narg gene encoding the membrane bound nitrate reductase was selected as a functional marker for the nitrate-reducing community. the use of narg is of special interest because the phylogeny of the narg gene closely reflects t ...	2002	12450836
the ribosome filter hypothesis.	a variety of posttranscriptional mechanisms affects the processing, subcellular localization, and translation of messenger rnas (mrnas). translational control appears to occur primarily at the initiation rather than the elongation stage. it has been suggested that translation is mediated largely by means of a cap-binding/scanning mechanism. on the basis of recent findings, we propose here that differential binding of particular mrnas to eukaryotic 40s ribosomal subunits before translation may al ...	2002	12221294
the non-watson-crick base pairs and their associated isostericity matrices.	rna molecules exhibit complex structures in which a large fraction of the bases engage in non-watson-crick base pairing, forming motifs that mediate long-range rna-rna interactions and create binding sites for proteins and small molecule ligands. the rapidly growing number of three-dimensional rna structures at atomic resolution requires that databases contain the annotation of such base pairs. an unambiguous and descriptive nomenclature was proposed recently in which rna base pairs were classif ...	2002	12177293
linamarase expression in cassava cultivars with roots of low- and high-cyanide content.	this paper reports the expression and localization of linamarase in roots of two cassava (manihot esculenta crantz) cultivars of low and high cyanide. two different patterns of linamarase activity were observed. in the low-cyanide type, young leaves displayed very high enzyme activity during the early plant growing stage (3 months), whereas in root peel, the activity increased progressively to reach a peak in 11-month-old plants. conversely, in the high-cyanide cultivar (hcv), root peel linamara ...	2002	12177481
bruce: a program for the detection of transfer-messenger rna genes in nucleotide sequences.	a computer program, bruce, was developed for the identification of transfer-messenger rna (tmrna) genes. the program employs heuristic algorithms to search for a trna(ala)-like secondary structure surrounding a short sequence encoding the tag peptide. in the 57 completely sequenced bacterial genomes where tmrna genes have been reported previously, bruce identified all with no false positives. in addition, bruce found 99 of the 100 tmrnas identified previously in other bacteria, red chloroplasts ...	2002	12140330
the time course of changes in mrna levels in tree shrew sclera during induced myopia and recovery.	in tree shrews, visual form deprivation produces increased axial elongation of the deprived eye and a myopic shift in refractive state. a change in scleral extensibility (creep rate) is closely associated with the change in axial elongation rate. these effects may be due to scleral tissue remodeling produced by a change in scleral gene expression. in this study, the authors investigated the time course of changes in scleral mrna levels for selected proteins during the development of form depriva ...	2002	12091398
parameter optimized surfaces (pops): analysis of key interactions and conformational changes in the ribosome.	we present a new method for the calculation of solvent accessible surface areas at the atomic and residue levels, which we call parameter optimized surfaces (pops-a and pops-r ). atomic and residue areas (the latter simulated with a single sphere centered at the c(alpha)s atom for amino acids and at the p atom for nucleotides) have been optimized versus accurate all-atoms methods. we concentrated on an analytical formula for the approximation of solvent accessibilities. the formula is simple, ea ...	2002	12087181
trilogy: discovery of sequence-structure patterns across diverse proteins.	we describe a new computer program, trilogy, for the automated discovery of sequence-structure patterns in proteins. trilogy implements a pattern discovery algorithm that begins with an exhaustive analysis of flexible three-residue patterns; a subset of these patterns are selected as seeds for an extension process in which longer patterns are identified. a key feature of the method is explicit treatment of both the sequence and structure components of these motifs: each trilogy pattern is a pair ...	2002	12084910
integration of dna ligation and rolling circle amplification for the homogeneous, end-point detection of single nucleotide polymorphisms.	association studies using common sequence variants or single nucleotide polymorphisms (snps) may provide a powerful approach to dissect the genetic inheritance of common complex traits. such studies necessitate the development of cost-effective, high throughput technologies for scoring snps. the method described in this paper for the co-detection of both alleles of a snp in a single homogeneous reaction combines the specificity of a high fidelity dna ligation step with the power of rolling circl ...	2002	12060698
tracing the evolution of rna structure in ribosomes.	the elucidation of ribosomal structure has shown that the function of ribosomes is fundamentally confined to dynamic interactions established between the rna components of the ribosomal ensemble. these findings now enable a detailed analysis of the evolution of ribosomal rna (rrna) structure. the origin and diversification of rrna was studied here using phylogenetic tools directly at the structural level. a rooted universal tree was reconstructed from the combined secondary structures of large ( ...	2002	12034847
high affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands.	we have isolated 2'-fluoro-substituted rna aptamers that bind to streptavidin (sa) with an affinity around 7 +/- 1.8 nm, comparable with that of recently described peptide aptamers. binding to sa was not prevented by prior saturation with biotin, enabling nucleic acid aptamers to form useful ternary complexes. mutagenesis, secondary structure analysis, ribonuclease footprinting and deletion analysis provided evidence for the essential structural features of sa-binding aptamers. in order to provi ...	2002	12000850
the accessory subunit of dna polymerase gamma is essential for mitochondrial dna maintenance and development in drosophila melanogaster.	dna polymerase gamma, pol gamma, is the key replicative enzyme in animal mitochondria. the drosophila enzyme is a heterodimer comprising catalytic and accessory subunits of 125 kda and 35 kda, respectively. both subunits have been cloned and characterized in a variety of model systems, and genetic mutants of the catalytic subunit were first identified in drosophila, as chemically induced mutations that disrupt larval behavior (tamas). mutations in the gene encoding the accessory subunit have not ...	2002	11917141
5s ribosomal rna database.	ribosomal 5s rna (5s rrna) is an integral component of the large ribosomal subunit in all known organisms with the exception only of mitochondrial ribosomes of fungi and animals. it is thought to enhance protein synthesis by stabilization of a ribosome structure. this paper presents the updated database of 5s rrna and their genes (5s rdna). its short characteristics are presented in the introduction. the database contains 2280 primary structures of 5s rrna and 5s rrna genes. these include 536 eu ...	2002	11752286
the european database on small subunit ribosomal rna.	the european database on ssu rrna can be consulted via the world wideweb at http://rrna.uia.ac.be/ssu/ and compiles all complete or nearly complete small subunit ribosomal rna sequences. sequences are provided in aligned format. the alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. additional information such as literature references, taxonomy, secondary structure models and nucleotide variability maps, is also av ...	2002	11752288
mmdb: entrez's 3d-structure database.	three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. the goal of entrez's 3d-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. to this end entrez's search engine provides three powerful features. (i) sequence and structure neighbors; one may select all sequences similar to one of ...	2002	11752307
molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium thermus thermophilus strain hb27.	thermus thermophilus hb27, an extremely thermophilic bacterium, exhibits high competence for natural transformation. to identify genes of the natural transformation machinery of t. thermophilus hb27, we performed homology searches in the partially completed t. thermophilus genomic sequence for conserved competence genes. these analyses resulted in the detection of 28 open reading frames (orfs) exhibiting significant similarities to known competence proteins of gram-negative and gram-positive bac ...	2002	11823215
corynebacterium glutamicum utilizes both transsulfuration and direct sulfhydrylation pathways for methionine biosynthesis.	a direct sulfhydrylation pathway for methionine biosynthesis in corynebacterium glutamicum was found. the pathway was catalyzed by mety encoding o-acetylhomoserine sulfhydrylase. the gene mety, located immediately upstream of meta, was found to encode a protein of 437 amino acids with a deduced molecular mass of 46,751 da. in accordance with dna and protein sequence data, the introduction of mety into c. glutamicum resulted in the accumulation of a 47-kda protein in the cells and a 30-fold incre ...	2002	11844756
structural analysis of an escherichia coli endonuclease viii covalent reaction intermediate.	endonuclease viii (nei) of escherichia coli is a dna repair enzyme that excises oxidized pyrimidines from dna. nei shares with formamidopyrimidine-dna glycosylase (fpg) sequence homology and a similar mechanism of action: the latter involves removal of the damaged base followed by two sequential beta-elimination steps. however, nei differs significantly from fpg in substrate specificity. we determined the structure of nei covalently crosslinked to a 13mer oligodeoxynucleotide duplex at 1.25 a re ...	2002	11847126
identification of a mycobacterium tuberculosis putative classical nitroreductase gene whose expression is coregulated with that of the acr aene within macrophages, in standing versus shaking cultures, and under low oxygen conditions.	tuberculosis remains a leading killer worldwide, and new approaches for its treatment and prevention are urgently needed. this effort will benefit greatly from a better understanding of gene regulation in mycobacterium tuberculosis, particularly with respect to this pathogen's response to its host environment. we examined the behavior of two promoters from the divergently transcribed m. tuberculosis genes acr/hspx/rv2031c (alpha-crystallin homolog) and rv2032/acg (acr-coregulated gene) by using ...	2002	11854240
trna-like recognition of group i introns by a tyrosyl-trna synthetase.	the neurospora crassa mitochondrial tyrosyl-trna synthetase (cyt-18 protein) functions in splicing group i introns by promoting the formation of the catalytically active rna structure. previous work suggested that cyt-18 recognizes a conserved trna-like structure of the group i intron catalytic core. here, directed hydroxyl-radical cleavage assays show that the nucleotide-binding fold and c-terminal domains of cyt-18 interact with the expected group i intron cognates of the aminoacyl-acceptor st ...	2002	11854463
polypeptide release at sense and noncognate stop codons by localized charge-exchange alterations in translational release factors.	the mechanism of stop codon recognition during translation has long been a puzzle. only recently has it been established that a tripeptide in the bacterial release factors (rfs) 1 and 2 serves as the "anticodon" in deciphering stop codons in mrna. however, the molecular basis of the accuracy of stop codon recognition is unknown. although specific tripeptides in the rfs are primarily responsible for selective reading of cognate stop codons, charge-flip variant rf proteins, altered at conserved gl ...	2002	11854484
identification and comparative analysis of the chloroplast alpha-subunit gene of dna-dependent rna polymerase from seven euglena species.	when the sequence of the euglena gracilis chloroplast genome was reported in 1993 the alpha-subunit gene (rpoa) of rna polymerase appeared to be missing, based on a comparison of all putative reading frames to the then known rpoa loci. since there has been a large increase in known rpoa sequences, the question of a euglena chloroplast rpoa gene was re-examined. a previously described unknown reading frame of 161 codons was found to be part of an rpoa gene split by a single group iii intron. this ...	2002	11861918
analysis of the aaa sensor-2 motif in the c-terminal atpase domain of hsp104 with a site-specific fluorescent probe of nucleotide binding.	hsp104 from saccharomyces cerevisiae is a hexameric protein with two aaa atpase domains (n- and c-terminal nucleotide-binding domains nbd1 and nbd2, respectively) per monomer. our previous analysis of the hsp104 atp hydrolysis cycle revealed that nbd1 and nbd2 have very different catalytic properties, but each shows positive cooperativity in hydrolysis. there is also communication between the two domains, in that atp hydrolysis at nbd1 depends on the nucleotide that is bound to nbd2. here, we ex ...	2002	11867765
transfer rna-dependent amino acid biosynthesis: an essential route to asparagine formation.	biochemical experiments and genomic sequence analysis showed that deinococcus radiodurans and thermus thermophilus do not possess asparagine synthetase (encoded by asna or asnb), the enzyme forming asparagine from aspartate. instead these organisms derive asparagine from asparaginyl-trna, which is made from aspartate in the trna-dependent transamidation pathway [becker, h. d. & kern, d. (1998) proc. natl. acad. sci. usa 95, 12832-12837; and curnow, a. w., tumbula, d. l., pelaschier, j. t., min, ...	2002	11880622
filamentous phage active on the gram-positive bacterium propionibacterium freudenreichii.	we present the first description of a single-stranded dna filamentous phage able to replicate in a gram-positive bacterium. phage b5 infects propionibacterium freudenreichii and has a genome consisting of 5,806 bases coding for 10 putative open reading frames. the organization of the genome is very similar to the organization of the genomes of filamentous phages active on gram-negative bacteria. the putative coat protein exhibits homology with the coat proteins of phages ph75 and pf3 active on t ...	2002	11889111
the trna specificity of thermus thermophilus ef-tu.	by introducing a gac anticodon, 21 different escherichia coli trnas were misacylated with either phenylalanine or valine and assayed for their affinity to thermus thermophilus elongation factor tu (ef-tu)*gtp by using a ribonuclease protection assay. the presence of a common esterified amino acid permits the thermodynamic contribution of each trna body to the overall affinity to be evaluated. the e. coli elongator trnas exhibit a wide range of binding affinities that varied from -11.7 kcal/mol f ...	2002	11891293
mutations in the 16s rrna genes of helicobacter pylori mediate resistance to tetracycline.	low-cost and rescue treatments for helicobacter pylori infections involve combinations of several drugs including tetracycline. resistance to tetracycline has recently emerged in h. pylori. the 16s rrna gene sequences of two tetracycline-resistant clinical isolates (mic = 64 microg/ml) were determined and compared to the consensus h. pylori 16s rrna sequence. one isolate had four nucleotide substitutions, and the other had four substitutions and two deletions. natural transformation with the 16s ...	2002	11914344
reduced oxidative pentose phosphate pathway flux in recombinant xylose-utilizing saccharomyces cerevisiae strains improves the ethanol yield from xylose.	in recombinant, xylose-fermenting saccharomyces cerevisiae, about 30% of the consumed xylose is converted to xylitol. xylitol production results from a cofactor imbalance, since xylose reductase uses both nadph and nadh, while xylitol dehydrogenase uses only nad(+). in this study we increased the ethanol yield and decreased the xylitol yield by lowering the flux through the nadph-producing pentose phosphate pathway. the pentose phosphate pathway was blocked either by disruption of the gnd1 gene, ...	2002	11916674
use of fe(iii) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of geothermobacterium ferrireducens gen. nov., sp. nov.	it has recently been recognized that the ability to use fe(iii) as a terminal electron acceptor is a highly conserved characteristic in hyperthermophilic microorganisms. this suggests that it may be possible to recover as-yet-uncultured hyperthermophiles in pure culture if fe(iii) is used as an electron acceptor. as part of a study of the microbial diversity of the obsidian pool area in yellowstone national park, wyo., hot sediment samples were used as the inoculum for enrichment cultures in med ...	2002	11916691
efficient trans-cleavage by the schistosoma mansoni smalpha1 hammerhead ribozyme in the extreme thermophile thermus thermophilus.	the catalytic hammerhead structure has been found in association with repetitive dna from several animals, including salamanders, crickets and schistosomes, and functions to process in cis the long multimer transcripts into monomer rna in vivo. the cellular role of these repetitive elements and their transcripts is unknown. moreover, none of these natural hammerheads have been shown to trans-cleave a host mrna in vivo. we analyzed the cis- and trans-cleavage properties of the hammerhead ribozyme ...	2002	11917021
tspgwi, a thermophilic class-iis restriction endonuclease from thermus sp., recognizes novel asymmetric sequence 5'-acgga(n11/9)-3'.	a novel prototype class-iis restriction endonuclease, tspgwi, was isolated from the thermophilic bacterium thermus sp. gw. the recognition sequence and cleavage positions have been established: tspgwi recognizes the non-palindromic 5-bp sequence 5'-acgga-3' and cleaves the dna 11 and 9 nt downstream in the top and bottom strand, respectively. in addition, an accompanying endonuclease, tspgwii, an isoschizomer of pst i, was found in thermus sp. gw cells.	2002	11917039
the large subunit of initiation factor aif2 is a close structural homologue of elongation factors.	the heterotrimeric factor e/aif2 plays a central role in eukaryotic/archaeal initiation of translation. by delivering the initiator methionyl-trna to the ribosome, e/aif2 ensures specificity of initiation codon selection. the three subunits of aif2 from the hyperthermophilic archaeon pyrococcus abyssi could be overproduced in escherichia coli. the beta and gamma subunits each contain a tightly bound zinc. the large gamma subunit is shown to form the structural core for trimer assembly. the cryst ...	2002	11927566
the solution structure of ribosomal protein l18 from thermus thermophilus reveals a conserved rna-binding fold.	we have determined the solution structure of ribosomal protein l18 from thermus thermophilus. l18 is a 12.5 kda protein of the large subunit of the ribosome and binds to both 5 s and 23 s rrna. in the uncomplexed state l18 folds to a mixed alpha/beta globular structure with a long disordered n-terminal region. we compared our high-resolution structure with rna-complexed l18 from haloarcula marismortui and t. thermophilus to examine rna-induced as well as species-dependent structural differences. ...	2002	11964156
stability and interactions of the amino-terminal domain of clpb from escherichia coli.	clpb is a member of a multichaperone system in escherichia coli (with dnak, dnaj, and grpe) that reactivates aggregated proteins. the sequence of clpb contains two atp-binding regions that are enclosed between the n- and c-terminal extensions. whereas it has been found that the n-terminal region of clpb is essential for the chaperone activity, the structure of this region is not known, and its biochemical properties have not been studied. we expressed and purified the n-terminal fragment of clpb ...	2002	11967375
the crystal structure of exonuclease recj bound to mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity.	recj, a 5' to 3' exonuclease specific for single-stranded dna, functions in dna repair and recombination systems. we determined the crystal structure of recj bound to mn(2+) ion essential for its activity. recj has a novel fold in which two domains are interconnected by a long helix, forming a central groove. mn(2+) is located on the wall of the groove and is coordinated by conserved residues characteristic of a family of phosphoesterases that includes recj proteins. the groove is composed of re ...	2002	11972066
modulation of trnaala identity by inorganic pyrophosphatase.	a highly sensitive assay of trna aminoacylation was developed that directly measures the fraction of aminoacylated trna by following amino acid attachment to the 3'-(32)p-labeled trna. when applied to escherichia coli alanyl-trna synthetase, the assay allowed accurate measurement of aminoacylation of the most deleterious mutants of trna(ala). the effect of trna(ala) identity mutations on both aminoacylation efficiency (k(cat)/k(m)) and steady-state level of aminoacyl-trna was evaluated in the ab ...	2002	11983895