Publications

crystallization and avoiding the problem of hemihedral twinning in crystals of delta1-pyrroline-5-carboxylate dehydrogenase from thermus thermophilus.	delta1-pyrroline-5-carboxylate dehydrogenase from thermus thermophilus (ttp5cdh) has been crystallized in a citrate-bound form (ttp5cdh-cit). the crystals diffracted to well beyond 2 a resolution, but exhibited perfect or near-perfect hemihedral twinning. variation of crystallization conditions resulted in the growth of larger untwinned crystals or crystals with significantly reduced twin content, all with similar unit-cell parameters. the soaking of ttp5cdh-cit crystals in citrate-free solution ...	2005	16511109
a double mutation of escherichia coli2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase disrupts six hydrogen bonds with, yet fails to prevent binding of, an isoprenoid diphosphate.	the essential enzyme 2c-methyl-d-erythritol-2,4-cyclodiphosphate (mecp) synthase, found in most eubacteria and the apicomplexan parasites, participates in isoprenoid-precursor biosynthesis and is a validated target for the development of broad-spectrum antimicrobial drugs. the structure and mechanism of the enzyme have been elucidated and the recent exciting finding that the enzyme actually binds diphosphate-containing isoprenoids at the interface formed by the three subunits that constitute the ...	2005	16511114
structure of a class ii trmh trna-modifying enzyme from aquifex aeolicus.	biological rnas contain a variety of post-transcriptional modifications that facilitate their efficient function in the cellular environment. one of the two most common forms of modification is methylation of the 2'-hydroxyl group of the ribose sugar, which is performed by a number of s-adenosylmethionine (sam) dependent methyltransferases. in bacteria, many of these modifications in trna and rrna are carried out by the alpha/beta-knot superfamily of enzymes, whose sam-binding pocket is created ...	2005	16511140
cloning, purification and crystallization of thermus thermophilus proline dehydrogenase.	nature recycles l-proline by converting it to l-glutamate. this four-electron oxidation process is catalyzed by the two enzymes: proline dehydrogenase (prodh) and delta1-pyrroline-5-carboxylate dehydrogenase. this note reports the cloning, purification and crystallization of thermus thermophilus prodh, which is the prototype of a newly discovered superfamily of bacterial monofunctional prodhs. the results presented here include production of a monodisperse protein solution through use of the det ...	2005	16511143
structures of a putative rna 5-methyluridine methyltransferase, thermus thermophilus ttha1280, and its complex with s-adenosyl-l-homocysteine.	the thermus thermophilus hypothetical protein ttha1280 belongs to a family of predicted s-adenosyl-l-methionine (adomet) dependent rna methyltransferases (mtases) present in many bacterial and archaeal species. inspection of amino-acid sequence motifs common to class i rossmann-fold-like mtases suggested a specific role as an rna 5-methyluridine mtase. selenomethionine (semet) labelled and native versions of the protein were expressed, purified and crystallized. two crystal forms of the semet-la ...	2005	16511182
crystallization and preliminary x-ray crystallographic study of the wild type and two mutants of the cp1 hydrolytic domain from aquifex aeolicus leucyl-trna synthetase.	the editing or hydrolytic cp1 domain of leucyl-trna synthetase (leurs) hydrolyses several misactivated amino acids. the cp1 domain of aquifex aeolicus leurs was expressed, purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. crystals belong to space group p2(1)2(1)2(1), with unit-cell parameters a = 38.8, b = 98.4, c = 116.7 a. crystals diffract to beyond 1.8 a resolution and contain two monomers in the asymmetric unit. two cp1 mutants in w ...	2005	16511190
crystallization and preliminary x-ray analysis of cryptochrome 3 from arabidopsis thaliana.	cryptochromes are flavoproteins which serve as blue-light receptors in plants, animals, fungi and prokaryotes and belong to the same protein family as the catalytically active dna photolyases. cryptochrome 3 from the plant arabidopsis thaliana (cry3; 525 amino acids, 60.7 kda) is a representative of the novel crydash subfamily of uv-a/blue-light receptors and has been expressed as a mature fad-containing protein in escherichia coli without the signal sequence that directs the protein into plant ...	2005	16511200
structure of a conserved hypothetical protein, ttha0849 from thermus thermophilus hb8, at 2.4 a resolution: a putative member of the star-related lipid-transfer (start) domain superfamily.	the crystal structure of a conserved hypothetical protein, ttha0849 from thermus thermophilus hb8, has been determined at 2.4 a resolution as a part of a structural and functional genomics project on t. thermophilus hb8. the main-chain folding shows a compact alpha+beta motif, forming a hydrophobic cavity in the molecule. a structural similarity search reveals that it resembles those steroidogenic acute regulatory proteins that contain the lipid-transfer (start) domain, even though ttha0849 show ...	2005	16511226
purification, crystallization and preliminary x-ray crystallographic study of the l-fuculose-1-phosphate aldolase (fuca) from thermus thermophilus hb8.	fuculose phosphate aldolase catalyzes the reversible cleavage of l-fuculose-1-phosphate to dihydroxyacetone phosphate and l-lactaldehyde. the protein from thermus thermophilus hb8 is a biological tetramer with a subunit molecular weight of 21 591 da. purified fuca has been crystallized using sitting-drop vapour-diffusion and microbatch techniques at 293 k. the crystals belong to space group p4, with unit-cell parameters a = b = 100.94, c = 45.87 a. the presence of a dimer of the enzyme in the as ...	2005	16511238
accessibility of 18s rrna in human 40s subunits and 80s ribosomes at physiological magnesium ion concentrations--implications for the study of ribosome dynamics.	protein biosynthesis requires numerous conformational rearrangements within the ribosome. the structural core of the ribosome is composed of rna and is therefore dependent on counterions such as magnesium ions for function. many steps of translation can be compromised or inhibited if the concentration of mg(2+) is too low or too high. conditions previously used to probe the conformation of the mammalian ribosome in vitro used high mg(2+) concentrations that we find completely inhibit translation ...	2005	16314459
an assembly landscape for the 30s ribosomal subunit.	self-assembling macromolecular machines drive fundamental cellular processes, including transcription, messenger rna processing, translation, dna replication and cellular transport. the ribosome, which carries out protein synthesis, is one such machine, and the 30s subunit of the bacterial ribosome is the preeminent model system for biophysical analysis of large rna-protein complexes. our understanding of 30s assembly is incomplete, owing to the challenges of monitoring the association of many c ...	2005	16319883
compatible solutes of the hyperthermophile palaeococcus ferrophilus: osmoadaptation and thermoadaptation in the order thermococcales.	the effect of salinity and growth temperature on the accumulation of intracellular organic solutes was examined in the hyperthermophilic archaeon palaeococcus ferrophilus. the genus palaeococcus represents a deep-branching lineage of the order thermococcales, which diverged before thermococcus and pyrococcus. palaeococcus ferrophilus accumulated mannosylglycerate, glutamate, and aspartate as major compatible solutes. unlike members of the genera pyrococcus and thermococcus, palaeococcus ferrophi ...	2005	16332790
the proficiency of a thermophilic chorismate mutase enzyme is solely through an entropic advantage in the enzyme reaction.	a study of the thermus thermophilus chorismate mutase (ttcm) is described by using quantum mechanics (self-consistent-charge density-functional tight binding)/molecular mechanics, umbrella sampling, and the weighted histogram analysis method. the computed free energies of activation for the reactions in water and ttcm are comparable to the experimental values. the free energies for formation of near attack conformer have been determined to be 8.06 and 0.05 kcal/mol in water and ttcm, respectivel ...	2005	16344484
crystallization of leucyl-trna synthetase complexed with trnaleu from the archaeon pyrococcus horikoshii.	all five trnaleu isoacceptors from the archaeon pyrococcus horikoshii have been transcribed in vitro and purified. the leucyl-trna synthetase (leurs) from p. horikoshii was overexpressed in escherichia coli and purified, and cocrystallizations with each of the trnaleu isoacceptors were attempted. cocrystals were obtained by the hanging-drop vapour-diffusion method, but only when the trnaleu isoacceptor with the anticodon caa was used. electrophoretic analyses revealed that the crystals contain b ...	2005	16508082
crystallization of leucyl-trna synthetase complexed with trnaleu from the archaeon pyrococcus horikoshii.	all five trnaleu isoacceptors from the archaeon pyrococcus horikoshii have been transcribed in vitro and purified. the leucyl-trna synthetase (leurs) from p. horikoshii was overexpressed in escherichia coli and purified, and cocrystallizations with each of the trnaleu isoacceptors were attempted. cocrystals were obtained by the hanging-drop vapour-diffusion method, but only when the trnaleu isoacceptor with the anticodon caa was used. electrophoretic analyses revealed that the crystals contain b ...	2005	16508082
purification, crystallization and preliminary crystallographic analysis of the vacuole-type atpase subunit e from pyrococcus horikoshii ot3.	the vacuole-type atpases in eukaryotic cells translocate protons across various biological membranes including the vacuolar membrane by consuming atp molecules. the e subunit of the multisubunit complex v-atpase from pyrococcus horikoshii ot3, which has a molecular weight of 22.88 kda, has been cloned, overexpressed in escherichia coli, purified and crystallized by the microbatch method using peg 4000 as a precipitant at 296 k. a data set to 1.85 a resolution with 98.8% completeness and an rmerg ...	2005	16508090
purification, crystallization and preliminary crystallographic analysis of the vacuole-type atpase subunit e from pyrococcus horikoshii ot3.	the vacuole-type atpases in eukaryotic cells translocate protons across various biological membranes including the vacuolar membrane by consuming atp molecules. the e subunit of the multisubunit complex v-atpase from pyrococcus horikoshii ot3, which has a molecular weight of 22.88 kda, has been cloned, overexpressed in escherichia coli, purified and crystallized by the microbatch method using peg 4000 as a precipitant at 296 k. a data set to 1.85 a resolution with 98.8% completeness and an rmerg ...	2005	16508090
enzyme adaptation to alkaline ph: atomic resolution (1.08 a) structure of phosphoserine aminotransferase from bacillus alcalophilus.	the crystal structure of the vitamin b(6)-dependent enzyme phosphoserine aminotransferase from the obligatory alkaliphile bacillus alcalophilus has been determined at 1.08 a resolution. the model was refined to an r-factor of 11.7% (r(free) = 13.9%). the enzyme displays a narrow ph optimum of enzymatic activity at ph 9.0. the final structure was compared to the previously reported structure of the mesophilic phosphoserine aminotransferase from escherichia coli and to that of phosphoserine aminot ...	2005	15608117
genetic determinant of intrinsic quinolone resistance in fusobacterium canifelinum.	fourteen fluoroquinolone-resistant fusobacterial strains, originating from cats or dogs, were characterized by sequencing of the 16s-23s and 16s rrna genes and dna-dna hybridization and were described as a new species, fusobacterium canifelinum. all of the strains are intrinsically resistant (mic, >4 g/ml) to levofloxacin and other fluoroquinolones. compared to the quinolone resistance-determining region (gyra) of the susceptible relative f. nucleatum, we found that ser79 was replaced with leuci ...	2005	15616329
staphylococcus aureus isdg and isdi, heme-degrading enzymes with structural similarity to monooxygenases.	heme-degrading enzymes are involved in human diseases ranging from stroke, cancer, and multiple sclerosis to infectious diseases such as malaria, diphtheria, and meningitis. all mammalian and microbial enzymes identified to date are members of the heme oxygenase superfamily and assume similar monomeric structures with an all alpha-helical fold. here we describe the crystal structures of isdg and isdi, two heme-degrading enzymes from staphylococcus aureus. the structures of both enzymes resemble ...	2005	15520015
staphylococcus aureus isdg and isdi, heme-degrading enzymes with structural similarity to monooxygenases.	heme-degrading enzymes are involved in human diseases ranging from stroke, cancer, and multiple sclerosis to infectious diseases such as malaria, diphtheria, and meningitis. all mammalian and microbial enzymes identified to date are members of the heme oxygenase superfamily and assume similar monomeric structures with an all alpha-helical fold. here we describe the crystal structures of isdg and isdi, two heme-degrading enzymes from staphylococcus aureus. the structures of both enzymes resemble ...	2005	15520015
x-ray crystal structure of ornithine acetyltransferase from the clavulanic acid biosynthesis gene cluster.	the orf6 gene from the clavulanic acid biosynthesis gene cluster encodes an oat (ornithine acetyltransferase). similar to other oats the enzyme has been shown to catalyse the reversible transfer of an acetyl group from n-acetylornithine to glutamate. oats are ntn (n-terminal nucleophile) enzymes, but are distinct from the better-characterized ntn hydrolase enzymes as they catalyse acetyl transfer rather than a hydrolysis reaction. in the present study, we describe the x-ray crystal structure of ...	2005	15352873
estimation of phylogeny using a general markov model.	the non-homogeneous model of nucleotide substitution proposed by barry and hartigan (stat sci, 2: 191-210) is the most general model of dna evolution assuming an independent and identical process at each site. we present a computational solution for this model, and use it to analyse two data sets, each violating one or more of the assumptions of stationarity, homogeneity, and reversibility. the log likelihood values returned by programs based on the f84 model (j mol evol, 29: 170-179), the gener ...	2005	19325854
estimation of phylogeny using a general markov model.	the non-homogeneous model of nucleotide substitution proposed by barry and hartigan (stat sci, 2: 191-210) is the most general model of dna evolution assuming an independent and identical process at each site. we present a computational solution for this model, and use it to analyse two data sets, each violating one or more of the assumptions of stationarity, homogeneity, and reversibility. the log likelihood values returned by programs based on the f84 model (j mol evol, 29: 170-179), the gener ...	2005	19325854
size matters: a view of selenocysteine incorporation from the ribosome.	this review focuses on the known factors required for selenocysteine (sec) incorporation in eukaryotes and highlights recent findings that have compelled us to propose a new model for the mechanism of sec incorporation. in light of this data we also review the controversial aspects of the previous model specifically regarding the proposed interaction between sbp2 and eefsec. in addition, the relevance of two recently discovered factors in the recoding of sec are reviewed. the role of the ribosom ...	2005	16416259
size matters: a view of selenocysteine incorporation from the ribosome.	this review focuses on the known factors required for selenocysteine (sec) incorporation in eukaryotes and highlights recent findings that have compelled us to propose a new model for the mechanism of sec incorporation. in light of this data we also review the controversial aspects of the previous model specifically regarding the proposed interaction between sbp2 and eefsec. in addition, the relevance of two recently discovered factors in the recoding of sec are reviewed. the role of the ribosom ...	2005	16416259
the structural biology center 19id undulator beamline: facility specifications and protein crystallographic results.	the 19id undulator beamline of the structure biology center has been designed and built to take full advantage of the high flux, brilliance and quality of x-ray beams delivered by the advanced photon source. the beamline optics are capable of delivering monochromatic x-rays with photon energies from 3.5 to 20 kev (3.5-0.6 a wavelength) with fluxes up to 8-18 x 10(12) photons s(-1) (depending on photon energy) onto cryogenically cooled crystal samples. the size of the beam (full width at half-max ...	2005	16371706
the structural biology center 19id undulator beamline: facility specifications and protein crystallographic results.	the 19id undulator beamline of the structure biology center has been designed and built to take full advantage of the high flux, brilliance and quality of x-ray beams delivered by the advanced photon source. the beamline optics are capable of delivering monochromatic x-rays with photon energies from 3.5 to 20 kev (3.5-0.6 a wavelength) with fluxes up to 8-18 x 10(12) photons s(-1) (depending on photon energy) onto cryogenically cooled crystal samples. the size of the beam (full width at half-max ...	2005	16371706
the fidelity of translation initiation: reciprocal activities of eif1, if3 and ycih.	eukaryotic initiation factor eif1 and the functional c-terminal domain of prokaryotic initiation factor if3 maintain the fidelity of initiation codon selection in eukaryotes and prokaryotes, respectively, and bind to the same regions of small ribosomal subunits, between the platform and initiator trna. here we report that these nonhomologous factors can bind to the same regions of heterologous subunits and perform their functions in heterologous systems in a reciprocal manner, discriminating aga ...	2005	16362046
the fidelity of translation initiation: reciprocal activities of eif1, if3 and ycih.	eukaryotic initiation factor eif1 and the functional c-terminal domain of prokaryotic initiation factor if3 maintain the fidelity of initiation codon selection in eukaryotes and prokaryotes, respectively, and bind to the same regions of small ribosomal subunits, between the platform and initiator trna. here we report that these nonhomologous factors can bind to the same regions of heterologous subunits and perform their functions in heterologous systems in a reciprocal manner, discriminating aga ...	2005	16362046
the membrane protein data bank.	the membrane protein data bank (mpdb) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. data originates from the protein data bank and other databases, and from the literature. structures are based on x-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. the mpdb is searchable online by protein characteristic, structure determination method, crystallization ...	2005	16314922
the membrane protein data bank.	the membrane protein data bank (mpdb) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. data originates from the protein data bank and other databases, and from the literature. structures are based on x-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. the mpdb is searchable online by protein characteristic, structure determination method, crystallization ...	2005	16314922
multiplexed tandem pcr: gene profiling from small amounts of rna using sybr green detection.	multiplexed tandem pcr (mt-pcr) is a process for highly multiplexed gene expression profiling. in the first step, multiple primer pairs are added to the rna to be analysed together with reverse transcriptase and taq dna polymerase. following reverse transcription, the multiplexed amplicons are simultaneously amplified for a small number of cycles so as to avoid competition between amplicons. the reaction product is then diluted and analysed in multiple individual pcrs using primers nested inside ...	2005	16314310
miniseed3 (mini3), a wrky family gene, and haiku2 (iku2), a leucine-rich repeat (lrr) kinase gene, are regulators of seed size in arabidopsis.	we have identified mutant alleles of two sporophytically acting genes, haiku2 (iku2) and miniseed3 (mini3). homozygotes of these alleles produce a small seed phenotype associated with reduced growth and early cellularization of the endosperm. this phenotype is similar to that described for another seed size gene, iku1. mini3 encodes wrky10, a wrky class transcription factor. mini3 promoter::gus fusions show the gene is expressed in pollen and in the developing endosperm from the two nuclei stage ...	2005	16293693
a mutation in the anticodon of a single trnaala is sufficient to confer auxin resistance in arabidopsis.	auxin-resistant mutants have been useful for dissecting the mechanisms that underlie auxin-mediated biological processes. here we report the isolation and molecular characterization of a novel auxin-resistant mutant in arabidopsis (arabidopsis thaliana). like known mutated aux/iaa transcription factors, the mutant described here displayed dominant resistance to exogenously supplied auxins (sirtinol, 2,4-dichlorophenoxyacetic acid, indole-3-acetic acid) and a host of pleiotropic phenotypes, inclu ...	2005	16244142
a colorimetric method for point mutation detection using high-fidelity dna ligase.	the present study reported proof-of-principle for a genotyping assay approach that can detect single nucleotide polymorphisms (snps) through the gold nanoparticle assembly and the ligase reaction. by incorporating the high-fidelity dna ligase (tth dna ligase) into the allele-specific ligation-based gold nanoparticle assembly, this assay provided a convenient yet powerful colorimetric detection that enabled a straightforward single-base discrimination without the need of precise temperature contr ...	2005	16257979
single-molecule forster resonance energy transfer study of protein dynamics under denaturing conditions.	proteins are highly complex systems, exhibiting a substantial degree of structural variability in their folded state. in the presence of denaturants, the heterogeneity is greatly enhanced, and fluctuations among vast numbers of folded and unfolded conformations occur via many different pathways. here, we have studied the structure and dynamics of the small enzyme ribonuclease hi (rnase h) in the presence of the chemical denaturant guanidinium chloride (gdmcl) using single-molecule fluorescence m ...	2005	16221762
amyloid formation of a protein in the absence of initial unfolding and destabilization of the native state.	in 5% (v/v) trifluoroethanol, ph 5.5, 25 degrees c one of the acylphosphatases from drosophila melanogaster (acpdro2) forms fibrillar aggregates that bind thioflavin t and congo red and have an extensive beta-sheet structure, as revealed by circular dichroism. atomic force microscopy indicates that the fibrils and their constituent protofilaments have diameters compatible with those of natural amyloid fibrils. spectroscopic and biochemical investigation, carried out using near- and far-uv circul ...	2005	16169977
deacylated trna is released from the e site upon a site occupation but before gtp is hydrolyzed by ef-tu.	the presence or absence of deacylated trna at the e site sharply influences the activation energy required for binding of a ternary complex to the ribosomal a site indicating the different conformations that the e-trna imparts on the ribosome. here we address two questions: (i) whether or not peptidyltransferase--the essential catalytic activity of the large ribosomal subunit--also depends on the occupancy state of the e site and (ii) at what stage the e-trna is released during an elongation cyc ...	2005	16166657
protein content of minimal and ancestral ribosome.	minimal genome approaches seek to define the smallest gene complement compatible with modern-type cellular life on earth. a consensus of computational and experimental approaches indicates that a minimal genome is close to 300 protein-coding genes, if a rich medium is provided for cell growth. i relate ribosomal gene content in completely sequenced genomes to ribosomal subunit structure and approximate the protein components of the putative minimal ribosome and the ribosome of the last universal ...	2005	16043494
the genomics of disulfide bonding and protein stabilization in thermophiles.	thermophilic organisms flourish in varied high-temperature environmental niches that are deadly to other organisms. recently, genomic evidence has implicated a critical role for disulfide bonds in the structural stabilization of intracellular proteins from certain of these organisms, contrary to the conventional view that structural disulfide bonds are exclusively extracellular. here both computational and structural data are presented to explore the occurrence of disulfide bonds as a protein-st ...	2005	16111437
profunc: a server for predicting protein function from 3d structure.	profunc (http://www.ebi.ac.uk/thornton-srv/databases/profunc) is a web server for predicting the likely function of proteins whose 3d structure is known but whose function is not. users submit the coordinates of their structure to the server in pdb format. profunc makes use of both existing and novel methods to analyse the protein's sequence and structure identifying functional motifs or close relationships to functionally characterized proteins. a summary of the analyses provides an at-a-glance ...	2005	15980588
popscomp: an automated interaction analysis of biomolecular complexes.	large-scale analysis of biomolecular complexes reveals the functional network within the cell. computational methods are required to extract the essential information from the available data. the popscomp server is designed to calculate the interaction surface between all components of a given complex structure consisting of proteins, dna or rna molecules. the server returns matrices and graphs of surface area burial that can be used to automatically annotate components and residues that are inv ...	2005	15980485
identification of novel restriction endonuclease-like fold families among hypothetical proteins.	restriction endonucleases and other nucleic acid cleaving enzymes form a large and extremely diverse superfamily that display little sequence similarity despite retaining a common core fold responsible for cleavage. the lack of significant sequence similarity between protein families makes homology inference a challenging task and hinders new family identification with traditional sequence-based approaches. using the consensus fold recognition method meta-basic that combines sequence profiles wi ...	2005	15972856
mapping the interaction of smpb with ribosomes by footprinting of ribosomal rna.	in trans-translation transfer messenger rna (tmrna) and small protein b (smpb) rescue ribosomes stalled on truncated or in other ways problematic mrnas. smpb promotes the binding of tmrna to the ribosome but there is uncertainty about the number of participating smpb molecules as well as their ribosomal location. here, the interaction of smpb with ribosomal subunits and ribosomes was studied by isolation of smpb containing complexes followed by chemical modification of ribosomal rna with dimethy ...	2005	15972795
5s rrna: structure and function from head to toe.	5s rrna is uniquely positioned so as to link together all of the functional centers of the ribosome. previous studies have supported the hypothesis that 5s rrna acts as a physical transducer of information, facilitating communication between the different functional centers and coordinating of the multiple events catalyzed by the ribosome. here, we present a synthesis of both structural and genetic information to construct a more detailed picture of how 5s rrna may act to transmit and coordinate ...	2005	18074004
the cryptochromes.	cryptochromes are photoreceptors that regulate entrainment by light of the circadian clock in plants and animals. they also act as integral parts of the central circadian oscillator in animal brains and as receptors controlling photomorphogenesis in response to blue or ultraviolet (uv-a) light in plants. cryptochromes are probably the evolutionary descendents of dna photolyases, which are light-activated dna-repair enzymes, and are classified into three groups -- plant cryptochromes, animal cryp ...	2005	15892880
diagnostic application of padlock probes--multiplex detection of plant pathogens using universal microarrays.	padlock probes (plps) are long oligonucleotides, whose ends are complementary to adjacent target sequences. upon hybridization to the target, the two ends are brought into contact, allowing plp circularization by ligation. plps provide extremely specific target recognition, which is followed by universal amplification and microarray detection. since target recognition is separated from downstream processing, plps enable the development of flexible and extendable diagnostic systems, targeting div ...	2005	15860767
recurrent structural rna motifs, isostericity matrices and sequence alignments.	the occurrences of two recurrent motifs in ribosomal rna sequences, the kink-turn and the c-loop, are examined in crystal structures and systematically compared with sequence alignments of rrnas from the three kingdoms of life in order to identify the range of the structural and sequence variations. isostericity matrices are used to analyze structurally the sequence variations of the characteristic non-watson-crick base pairs for each motif. we show that isostericity matrices for non-watson-cric ...	2005	15860776
independent binding sites of small protein b onto transfer-messenger rna during trans-translation.	stalled bacterial ribosomes are freed by transfer-messenger rna (tmrna). with the help of small protein b (smpb), protein synthesis restarts and tmrna adds a tag to the stalled protein for destruction. the conformation of a 347 nt long tmrna from a thermophile and its interactions with smpb were monitored using structural probes. the rna is highly folded, including the reading frame, with <30% of unpaired residues. footprints between smpb and tmrna are in the elbow of the trna domain, in some ps ...	2005	15860775
atp-sensitive k+ channel channel/enzyme multimer: metabolic gating in the heart.	cardiac atp-sensitive k(+) (k(atp)) channels, gated by cellular metabolism, are formed by association of the inwardly rectifying potassium channel kir6.2, the potassium conducting subunit, and sur2a, the atp-binding cassette protein that serves as the regulatory subunit. kir6.2 is the principal site of atp-induced channel inhibition, while sur2a regulates k(+) flux through adenine nucleotide binding and catalysis. the atpase-driven conformations within the regulatory sur2a subunit of the k(atp) ...	2005	15910874
the application of cluster analysis in the intercomparison of loop structures in rna.	we have developed a computational approach for the comparison and classification of rna loop structures. hairpin or interior loops identified in atomic resolution rna structures were intercompared by conformational matching. the root-mean-square deviation (rmsd) values between all pairs of rna fragments of interest, even if from different molecules, are calculated. subsequently, cluster analysis is performed on the resulting matrix of rmsd distances using the unweighted pair group method with ar ...	2005	15769871
towards understanding the molecular basis of bacterial dna segregation.	bacteria ensure the fidelity of genetic inheritance by the coordinated control of chromosome segregation and cell division. here, we review the molecules and mechanisms that govern the correct subcellular positioning and rapid separation of newly replicated chromosomes and plasmids towards the cell poles and, significantly, the emergence of mitotic-like machineries capable of segregating plasmid dna. we further describe surprising similarities between proteins involved in dna partitioning (para/ ...	2005	15897178
graphical representation of ribosomal rna probe accessibility data using arb software package.	taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. a frequently applied technology, fluorescence in situ hybridization (fish), besides single cell identification, allows the localization and functional studies of the microbial community composition. careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridiza ...	2005	15777482
another biological effect of tosylphenylalanylchloromethane (tpck): it prevents p47phox phosphorylation and translocation upon neutrophil stimulation.	tpck (tosylphenylalanylchloromethane), first discovered as a serine protease inhibitor, has been described to affect in diverse systems a number of physiological events probably unrelated to its antiprotease effect, such as proliferation, apoptosis and tumour formation. in the present study, we focus on its inhibition of the neutrophil respiratory burst, an important element of non-specific immunological defence. the superoxide anion-producing enzyme, nadph oxidase, is quiescent in resting cells ...	2005	15498025
hsp70 chaperones: cellular functions and molecular mechanism.	hsp70 proteins are central components of the cellular network of molecular chaperones and folding catalysts. they assist a large variety of protein folding processes in the cell by transient association of their substrate binding domain with short hydrophobic peptide segments within their substrate proteins. the substrate binding and release cycle is driven by the switching of hsp70 between the low-affinity atp bound state and the high-affinity adp bound state. thus, atp binding and hydrolysis a ...	2005	15770419
protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins.	recent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. our ability to test and refine these relationships has been limited, however, by a variety of difficulties associated with the comparison of folding and unfolding rates, thermodynamics, and structure across diverse sets of proteins. these difficulties include the wide, potentially confounding range of experimental conditions and methods employed to date and the di ...	2005	15689503
initiation of protein synthesis in bacteria.	valuable information on translation initiation is available from biochemical data and recently solved structures. we present a detailed description of current knowledge about the structure, function, and interactions of the individual components involved in bacterial translation initiation. the first section describes the ribosomal features relevant to the initiation process. subsequent sections describe the structure, function, and interactions of the mrna, the initiator trna, and the initiatio ...	2005	15755955
evolutionary profiles from the qr factorization of multiple sequence alignments.	we present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. the method, based on the multidimensional qr factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of ...	2005	15741270
homology-extended sequence alignment.	we present a profile-profile multiple alignment strategy that uses database searching to collect homologues for each sequence in a given set, in order to enrich their available evolutionary information for the alignment. for each of the alignment sequences, the putative homologous sequences that score above a pre-defined threshold are incorporated into a position-specific pre-alignment profile. the enriched position-specific profile is used for standard progressive alignment, thereby more accura ...	2005	15699183
nadp-malate dehydrogenase from unicellular green alga chlamydomonas reinhardtii. a first step toward redox regulation?	the determinants of the thioredoxin (trx)-dependent redox regulation of the chloroplastic nadp-malate dehydrogenase (nadp-mdh) from the eukaryotic green alga chlamydomonas reinhardtii have been investigated using site-directed mutagenesis. the results indicate that a single c-terminal disulfide is responsible for this regulation. the redox midpoint potential of this disulfide is less negative than that of the higher plant enzyme. the regulation is of an all-or-nothing type, lacking the fine-tuni ...	2005	15579663
ribosomal protein l1 recognizes the same specific structural motif in its target sites on the autoregulatory mrna and 23s rrna.	the rna-binding ability of ribosomal protein l1 is of profound interest since the protein has a dual function as a ribosomal protein binding rrna and as a translational repressor binding its mrna. here, we report the crystal structure of ribosomal protein l1 in complex with a specific fragment of its mrna and compare it with the structure of l1 in complex with a specific fragment of 23s rrna determined earlier. in both complexes, a strongly conserved rna structural motif is involved in l1 bindin ...	2005	15659579
a vibrational spectral maker for probing the hydrogen-bonding status of protonated asp and glu residues.	hydrogen bonding is a fundamental element in protein structure and function. breaking a single hydrogen bond may impair the stability of a protein. we report an infrared vibrational spectral marker for probing the hydrogen-bond number for buried, protonated asp or glu residues in proteins. ab initio computational studies were performed on hydrogen-bonding interactions of a cooh group with a variety of side-chain model compounds of polar and charged amino acids in vacuum using density function th ...	2005	15653739
site-specific labeling of the ribosome for single-molecule spectroscopy.	single-molecule fluorescence spectroscopy can reveal mechanistic and kinetic details that may not be observed in static structural and bulk biochemical studies of protein synthesis. one approach requires site-specific and stable attachment of fluorophores to the components of translation machinery. fluorescent tagging of the ribosome is a prerequisite for the observation of dynamic changes in ribosomal conformation during translation using fluorescence methods. modifications of the ribosomal par ...	2005	15647501
comparative analysis of eubacterial dna polymerase iii alpha subunits.	dna polymerase iii is one of the five eubacterial dna polymerases that is responsible for the replication of dna duplex. among the ten subunits of the dna polymerase iii core enzyme, the alpha subunit catalyzes the reaction for polymerizing both dna strands. in this study, we extracted genomic sequences of the alpha subunit from 159 sequenced eubacterial genomes, and carried out sequence-based phylogenetic and structural analyses. we found that all eubacterial genomes have one or more alpha subu ...	2006	17531796
comparative analysis of eubacterial dna polymerase iii alpha subunits.	dna polymerase iii is one of the five eubacterial dna polymerases that is responsible for the replication of dna duplex. among the ten subunits of the dna polymerase iii core enzyme, the alpha subunit catalyzes the reaction for polymerizing both dna strands. in this study, we extracted genomic sequences of the alpha subunit from 159 sequenced eubacterial genomes, and carried out sequence-based phylogenetic and structural analyses. we found that all eubacterial genomes have one or more alpha subu ...	2006	17531796
mechanism of trna-dependent editing in translational quality control.	protein synthesis requires the pairing of amino acids with trnas catalyzed by the aminoacyl-trna synthetases. the synthetases are highly specific, but errors in amino acid selection are occasionally made, opening the door to inaccurate translation of the genetic code. the fidelity of protein synthesis is maintained by the editing activities of synthetases, which remove noncognate amino acids from trnas before they are delivered to the ribosome. although editing has been described in numerous syn ...	2006	17185419
mechanism of trna-dependent editing in translational quality control.	protein synthesis requires the pairing of amino acids with trnas catalyzed by the aminoacyl-trna synthetases. the synthetases are highly specific, but errors in amino acid selection are occasionally made, opening the door to inaccurate translation of the genetic code. the fidelity of protein synthesis is maintained by the editing activities of synthetases, which remove noncognate amino acids from trnas before they are delivered to the ribosome. although editing has been described in numerous syn ...	2006	17185419
a structural model reveals energy transduction in dynein.	intracellular active transport is driven by atp-hydrolyzing motor proteins that move along cytoskeletal filaments. in particular, the microtubule-associated dynein motor is involved in the transport of organelles and vesicles, the maintenance of the golgi, and mitosis. however, unlike kinesin and myosin, the mechanism by which dynein converts chemical energy into mechanical force remains largely a mystery, due primarily to the lack of a high-resolution molecular structure. using homology modelin ...	2006	17121997
characteristics of the nuclear (18s, 5.8s, 28s and 5s) and mitochondrial (12s and 16s) rrna genes of apis mellifera (insecta: hymenoptera): structure, organization, and retrotransposable elements.	as an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18s, 5.8s, 28s and 5s) and mitochondrial (12s and 16s) ribosomal rna (rrna)-encoding gene sequences (rdna) and related internally and externally transcribed spacer regions of apis mellifera (insecta: hymenoptera: apocrita). additionally, we predict secondary structures for the mature rrna molecules based on comparative sequence analyses with other arthropod taxa and reference to re ...	2006	17069639
diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-i release factor that potentially recognizes atypical mrna signals other than normal stop codons.	while all codons that specify amino acids are universally recognized by trna molecules, codons signaling termination of translation are recognized by proteins known as class-i release factors (rf). in most eukaryotes and archaea a single rf accomplishes termination at all three stop codons. in most bacteria, there are two rfs with overlapping specificity, rf1 recognizes ua(a/g) and rf2 recognizes u(a/g)a.	2006	16970810
the structure and function of frataxin.	frataxin, a highly conserved protein found in prokaryotes and eukaryotes, is required for efficient regulation of cellular iron homeostasis. humans with a frataxin deficiency have the cardio- and neurodegenerative disorder friedreich's ataxia, commonly resulting from a gaa trinucleotide repeat expansion in the frataxin gene. while frataxin's specific function remains a point of controversy, the general consensus is that the protein assists in controlling cellular iron homeostasis by directly bin ...	2006	16911956
structural basis for topoisomerase vi inhibition by the anti-hsp90 drug radicicol.	members of the ghl atpase superfamily, including type ii topoisomerases, hsp90-class chaperones, and mutl, all share a common ghkl-type atp-binding fold and act as nucleotide-controlled 'molecular clamps'. these enzymes' atp-binding sites have proven to be rich drug targets, and certain inhibitors of type ii topoisomerases and hsp90 bind to this region and competitively inhibit these enzymes. recently, it was found that radicicol, a drug known to block hsp90 function, also inhibits the archaeal ...	2006	16920739
a new paradigm: manganese superoxide dismutase influences the production of h2o2 in cells and thereby their biological state.	the principal source of hydrogen peroxide in mitochondria is thought to be from the dismutation of superoxide via the enzyme manganese superoxide dismutase (mnsod). however, the nature of the effect of sod on the cellular production of h(2)o(2) is not widely appreciated. the current paradigm is that the presence of sod results in a lower level of h(2)o(2) because it would prevent the non-enzymatic reactions of superoxide that form h(2)o(2). the goal of this work was to: a) demonstrate that sod c ...	2006	17015180
evidence for existence of "mesotogas," members of the order thermotogales adapted to low-temperature environments.	all cultivated isolates of the bacterial order thermotogales are either thermophiles or hyperthermophiles, but thermotogales 16s rrna gene sequences have been detected in many mesophilic anaerobic and microaerophilic environments, particularly within communities involved in the remediation of pollutants. here we provide metagenomic evidence for the existence of thermotogales lineages, which we informally call "mesotoga," that are adapted to growth at lower temperatures. two fosmid clones contain ...	2006	16820506
functional conformations of the l11-ribosomal rna complex revealed by correlative analysis of cryo-em and molecular dynamics simulations.	the interaction between the gtpase-associated center (gac) and the aminoacyl-trna.ef-tu.gtp ternary complex is of crucial importance in the dynamic process of decoding and trna accommodation. the gac includes protein l11 and helices 43-44 of 23s rrna (referred to as l11-rrna complex). in this study, a method of fitting based on a systematic comparison between cryo-electron microscopy (cryo-em) density maps and structures obtained by molecular dynamics simulations has been developed. this method ...	2006	16682558
the building blocks and motifs of rna architecture.	rna motifs can be defined broadly as recurrent structural elements containing multiple intramolecular rna-rna interactions, as observed in atomic-resolution rna structures. they constitute the modular building blocks of rna architecture, which is organized hierarchically. recent work has focused on analyzing rna backbone conformations to identify, define and search for new instances of recurrent motifs in x-ray structures. one current view asserts that recurrent rna strand segments with characte ...	2006	16713707
activation of superoxide dismutases: putting the metal to the pedal.	superoxide dismutases (sod) are important anti-oxidant enzymes that guard against superoxide toxicity. various sod enzymes have been characterized that employ either a copper, manganese, iron or nickel co-factor to carry out the disproportionation of superoxide. this review focuses on the copper and manganese forms, with particular emphasis on how the metal is inserted in vivo into the active site of sod. copper and manganese sods diverge greatly in sequence and also in the metal insertion proce ...	2006	16828895
evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal rna using arb software package.	availability of high-resolution rna crystal structures for the 30s and 50s ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal rna (rrna) for evaluating sequence alignments of rrna genes. furthermore, the secondary and tertiary structural features of rrna are highly useful and successfully employed in designing rrna targeted oligonucleotide probes intended for in situ hybridization ...	2006	16672074
dynamic protein domains: identification, interdependence, and stability.	existing methods of domain identification in proteins usually provide no information about the degree of domain independence and stability. however, this information is vital for many areas of protein research. the recently developed hierarchical clustering of correlation patterns (hccp) technique provides machine-based domain identification in a computationally simple and physically consistent way. here we present the modification of this technique, which not only allows determination of the mo ...	2006	16632509
nuclear photosynthetic gene expression is synergistically modulated by rates of protein synthesis in chloroplasts and mitochondria.	arabidopsis thaliana mutants prors1-1 and -2 were identified on the basis of a decrease in effective photosystem ii quantum yield. mutations were localized to the 5'-untranslated region of the nuclear gene prolyl-trna synthetase1 (prors1), which acts in both plastids and mitochondria. in prors1-1 and -2, prors1 expression is reduced, along with protein synthesis in both organelles. prors1 null alleles (prors1-3 and -4) result in embryo sac and embryo development arrest. in mutants with the leaky ...	2006	16517761
ribose 2'-hydroxyl groups in the 5' strand of the acceptor arm of p-site trna are not essential for ef-g catalyzed translocation.	the coupled movement of trna-mrna complex through the ribosome is a fundamental step during the protein elongation process. we demonstrate that the ribosome will translocate a p-site-bound trna(met) with a break in the phosphodiester backbone between positions 17 and 18 in the d-loop. crystallographic data showed that the acceptor arms of p- and e-site trna interact extensively with the ribosomal large subunit. therefore, we used this fragmented p-site-bound trna(met) to investigate the contribu ...	2006	16489185
exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds.	as tertiary structure is currently available only for a fraction of known protein families, it is important to assess what parts of sequence space have been structurally characterized. we consider protein domains whose structure can be predicted by sequence similarity to proteins with solved structure and address the following questions. do these domains represent an unbiased random sample of all sequence families? do targets solved by structural genomic initiatives (sgi) provide such a sample? ...	2006	16549009
a putative rna-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic rnai, and hypothetical mechanisms of action.	all archaeal and many bacterial genomes contain clustered regularly interspaced short palindrome repeats (crispr) and variable arrays of the crispr-associated (cas) genes that have been previously implicated in a novel form of dna repair on the basis of comparative analysis of their protein product sequences. however, the proximity of crispr and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis.	2006	16545108
nucleotide exchange via local protein unfolding--structure of rab8 in complex with mss4.	rab gtpases function as essential regulators of vesicle transport in eukaryotic cells. mss4 was shown to stimulate nucleotide exchange on rab proteins associated with the exocytic pathway and to have nucleotide-free-rab chaperone activity. a detailed kinetic analysis of mss4 interaction with rab8 showed that mss4 is a relatively slow exchange factor that forms a long-lived nucleotide-free complex with rabgtpase. in contrast to other characterized exchange factor-gtpase complexes, mss4:rab8 compl ...	2006	16541104
methionine oxidation of monomeric lambda repressor: the denatured state ensemble under nondenaturing conditions.	although poorly understood, the properties of the denatured state ensemble are critical to the thermodynamics and the kinetics of protein folding. the most relevant conformations to cellular protein folding are the ones populated under physiological conditions. to avoid the problem of low expression that is seen with unstable variants, we used methionine oxidation to destabilize monomeric lambda repressor and predominantly populate the denatured state under nondenaturing buffer conditions. the d ...	2006	16452618
defining the primary route for lutein synthesis in plants: the role of arabidopsis carotenoid beta-ring hydroxylase cyp97a3.	lutein, a dihydroxy derivative of alpha-carotene (beta,epsilon-carotene), is the most abundant carotenoid in photosynthetic plant tissues where it plays important roles in light-harvesting complex-ii structure and function. the synthesis of lutein from lycopene requires at least four distinct enzymatic reactions: beta- and epsilon-ring cyclizations and hydroxylation of each ring at the c-3 position. three carotenoid hydroxylases have already been identified in arabidopsis, two nonheme diiron bet ...	2006	16492736
nucleic acid visualization with ucsf chimera.	with the increase in the number of large, 3d, high-resolution nucleic acid structures, particularly of the 30s and 50s ribosomal subunits and the intact bacterial ribosome, advancements in the visualization of nucleic acid structural features are essential. large molecular structures are complicated and detailed, and one goal of visualization software is to allow the user to simplify the display of some features and accent others. we describe an extension to the ucsf chimera molecular visualizat ...	2006	16478715
the post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5a (eif5a).	the eukaryotic translation initiation factor 5a (eif5a) is the only cellular protein that contains the unique polyamine-derived amino acid, hypusine [nepsilon-(4-amino-2-hydroxybutyl)lysine]. hypusine is formed in eif5a by a novel post-translational modification reaction that involves two enzymatic steps. in the first step, deoxyhypusine synthase catalyzes the cleavage of the polyamine spermidine and transfer of its 4-aminobutyl moiety to the epsilon-amino group of one specific lysine residue of ...	2006	16452303
structural biology of rna silencing and its functional implications.	we outline structure-function contributions from our laboratories on protein-rna recognition events that monitor sirna length, 5 -phosphate and 2-nucleotide 3 overhangs, as well as the architecture of argonaute, its externally bound sirna complex, and argonaute-based models involving guide-strand-mediated mrna binding, cleavage, and release.	2006	17381284
conserved quantitative stability/flexibility relationships (qsfr) in an orthologous rnase h pair.	many reports qualitatively describe conserved stability and flexibility profiles across protein families, but biophysical modeling schemes have not been available to robustly quantify both. here we investigate an orthologous rnase h pair by using a minimal distance constraint model (dcm). the dcm is an all atom microscopic model [jacobs and dallakyan, biophys j 2005;88(2):903-915] that accurately reproduces heat capacity measurements [livesay et al., febs lett 2004;576(3):468-476], and is unique ...	2006	16287093
a structural model for the large subunit of the mammalian mitochondrial ribosome.	protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. evolutionary changes in protein and rna sequences can affect the 3d organization of structural features in ribosomes in different species. the most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. the rna component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. ...	2006	16510155
specific functional interactions of nucleotides at key -3 and +4 positions flanking the initiation codon with components of the mammalian 48s translation initiation complex.	eukaryotic initiation factor (eif) 1 maintains the fidelity of initiation codon selection and enables mammalian 43s preinitiation complexes to discriminate against aug codons with a context that deviates from the optimum sequence gcc(a/g)ccaugg, in which the purines at (-)3 and (+)4 positions are most important. we hypothesize that eif1 acts by antagonizing conformational changes that occur in ribosomal complexes upon codon-anticodon base-pairing during 48s initiation complex formation, and that ...	2006	16510876
identification of a histidine-tyrosine cross-link in the active site of the cbb3-type cytochrome c oxidase from rhodobacter sphaeroides.	the heme-copper oxidases constitute a superfamily of terminal dioxygen-reducing enzymes located in the inner mitochondrial or in the bacterial cell membrane. the presence of a mechanistically important covalent bond between a histidine ligand of the copper ion (cu(b)) in the active site and a generally conserved tyrosine residue nearby has been shown to exist in the canonical cytochrome c oxidases. however, according to sequence alignment studies, this critical tyrosine is missing from the subfa ...	2006	17060620
crystallization, preliminary crystallographic analysis and phasing of the thiosulfate-binding protein soxy from chlorobium limicola f. thiosulfatophilum.	the 22 kda soxyz protein complex from the green sulfur bacterium chlorobium limicola f. thiosulfatophilum is a central player in the sulfur-oxidizing (sox) enzyme system of the organism by activating thiosulfate for oxidation by soxxa and soxb. it has been proposed that soxyz exists as a heterodimer or heterotetramer, but the properties and role of the individual components of the complex thus far remain unknown. here, the heterologous expression, purification, and the crystallization of stable ...	2006	17077486
overexpression, crystallization and preliminary x-ray crystallographic analysis of phosphopantetheine adenylyltransferase from enterococcus faecalis.	phosphopantetheine adenylyltransferase, an essential enzyme in the coenzyme a biosynthetic pathway, catalyzes the reversible transfer of an adenylyl group from atp to 4'-phosphopantetheine, yielding 3'-dephospho-coa and pyrophosphate. enterococcus faecalis ppat has been overexpressed in escherichia coli as a fusion with a c-terminal purification tag and crystallized at 297 k using a reservoir solution consisting of 0.1 m sodium hepes ph 7.5, 0.8 m sodium dihydrogen phosphate and 0.8 m potassium ...	2006	17077496
the methanothermobacter thermautotrophicus exoiii homologue mth212 is a dna uridine endonuclease.	the genome of methanothermobacter thermautotrophicus, as a hitherto unique case, is apparently devoid of genes coding for general uracil dna glycosylases, the universal mediators of base excision repair following hydrolytic deamination of dna cytosine residues. we have now identified protein mth212, a member of the exoiii family of nucleases, as a possible initiator of dna uracil repair in this organism. this enzyme, in addition to bearing all the enzymological hallmarks of an exoiii homologue, ...	2006	17012282
an evolutionary 'intermediate state' of mitochondrial translation systems found in trichinella species of parasitic nematodes: co-evolution of trna and ef-tu.	ef-tu delivers aminoacyl-trnas to ribosomes in the translation system. however, unusual truncations found in some animal mitochondrial trnas seem to prevent recognition by a canonical ef-tu. we showed previously that the chromadorean nematode has two distinct ef-tus, one of which (ef-tu1) binds only to t-armless aminoacyl-trnas and the other (ef-tu2) binds to d-armless ser-trnas. neither of the ef-tus can bind to canonical cloverleaf trnas. in this study, by analyzing the translation system of e ...	2006	17012285
preparation, crystallization and preliminary x-ray analysis of protein ytlp from bacillus subtilis.	bacillus subtilis ytlp is a protein that is predicted to belong to the bacterial and archael 2'-5' rna-ligase family. it contains 183 residues and two copies of the hxtx sequence motif conserved among proteins belonging to this family. in order to determine the structure of ytlp and to compare it with the paralogue yjcg and identified 2'-5' rna ligases, the gene ytlp was amplified from b. subtilis genomic dna and cloned into expression vector pet-21a. the soluble protein was produced in escheric ...	2006	17012785
cloning, purification and preliminary crystallographic analysis of a putative pyridoxal kinase from bacillus subtilis.	pyridoxal kinases (pdxk) are able to catalyse the phosphorylation of three vitamin b(6) precursors, pyridoxal, pyridoxine and pyridoxamine, to their 5'-phosphates and play an important role in the vitamin b(6) salvage pathway. recently, the thid gene of bacillus subtilis was found to encode an enzyme which has the activity expected of a pyridoxal kinase despite its previous assignment as an hmpp kinase owing to higher sequence similarity. as such, this enzyme would appear to represent a new clas ...	2006	17012797