Publications

characterization of rimo, a new member of the methylthiotransferase subclass of the radical sam superfamily.	rimo, encoded by the ylig gene in escherichia coli, has been recently identified in vivo as the enzyme responsible for the attachment of a methylthio group on the beta-carbon of asp88 of the small ribosomal protein s12 [anton, b. p., saleh, l., benner, j. s., raleigh, e. a., kasif, s., and roberts, r. j. (2008) proc. natl. acad. sci. u.s.a. 105, 1826-1831]. to date, it is the only enzyme known to catalyze methylthiolation of a protein substrate; the four other naturally occurring methylthio modi ...	2009	19736993
two-dimensional pulsed electron spin resonance characterization of 15n-labeled archaeal rieske-type ferredoxin.	two-dimensional electron spin-echo envelope modulation (eseem) analysis of the uniformly (15)n-labeled archaeal rieske-type [2fe-2s] ferredoxin (arf) from sulfolobus solfataricus p1 has been conducted in comparison with the previously characterized high-potential protein homologs. major differences among these proteins were found in the hyperfine sublevel correlation (hyscore) lineshapes and intensities of the signals in the (++) quadrant, which are contributed from weakly coupled (non-coordinat ...	2009	19804777
the cytochrome ba3 oxygen reductase from thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping.	the heme-copper oxygen reductases are redox-driven proton pumps that generate a proton motive force in both prokaryotes and mitochondria. these enzymes have been divided into 3 evolutionarily related groups: the a-, b- and c-families. most experimental work on proton-pumping mechanisms has been performed with members of the a-family. these enzymes require 2 proton input pathways (d- and k-channels) to transfer protons used for oxygen reduction chemistry and for proton pumping, with the d-channel ...	2009	19805275
structure of a trna-dependent kinase essential for selenocysteine decoding.	compared to bacteria, archaea and eukaryotes employ an additional enzyme for the biosynthesis of selenocysteine (sec), the 21(st) natural amino acid (aa). an essential rna-dependent kinase, o-phosphoseryl-trna(sec) kinase (pstk), converts seryl-trna(sec) to o-phosphoseryl-trna(sec), the immediate precursor of selenocysteinyl-trna(sec). the sequence of methanocaldococcus jannaschii pstk (mjpstk) suggests an n-terminal kinase domain (177 aa) followed by a presumed trna binding region (75 aa). the ...	2009	19805283
features of subunit nuom (nd4) in escherichia coli ndh-1: topology and implication of conserved glu144 for coupling site 1.	the bacterial h(+)-pumping nadh-quinone oxidoreductase (ndh-1) is an l-shaped membrane-bound enzymatic complex. escherichia coli ndh-1 is composed of 13 subunits (nuoa-n). nuom (nd4) subunit is one of the hydrophobic subunits that constitute the membrane arm of ndh-1 and was predicted to bear 14 helices. we attempted to clarify the membrane topology of nuom by the introduction of histidine tags into different positions by chromosomal site-directed mutagenesis. from the data, we propose a topolog ...	2009	19815558
structural insights into rna processing by the human risc-loading complex.	targeted gene silencing by rna interference (rnai) requires loading of a short guide rna (small interfering rna (sirna) or microrna (mirna)) onto an argonaute protein to form the functional center of an rna-induced silencing complex (risc). in humans, argonaute2 (ago2) assembles with the guide rna-generating enzyme dicer and the rna-binding protein trbp to form a risc-loading complex (rlc), which is necessary for efficient transfer of nascent sirnas and mirnas from dicer to ago2. here, using sin ...	2009	19820710
dual role of dna in regulating atp hydrolysis by the sopa partition protein.	in bacteria, mitotic stability of plasmids and many chromosomes depends on replicon-specific systems, which comprise a centromere, a centromere-binding protein and an atpase. dynamic self-assembly of the atpase appears to enable active partition of replicon copies into cell-halves, but for walker-box partition atpases the molecular mechanism is unknown. atpase activity appears to be essential for this process. dna and centromere-binding proteins are known to stimulate the atpase activity but mol ...	2009	19740757
in vitro metal uptake by recombinant human manganese superoxide dismutase.	metal uptake by the antioxidant defense metalloenzyme manganese superoxide dismutase (mnsod) is an essential step in the functional maturation of the protein that is just beginning to be investigated in detail. we have extended earlier in vitro studies on metal binding by the dimeric escherichia coli apo-mnsod to investigate the mechanism of metal uptake by tetrameric human and thermus thermophilus apo-mnsods. like the e. coli apo-mnsod, these proteins also bind metal ions in vitro in a thermall ...	2009	19755112
phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis.	mitochondria, the powerhouse of eukaryotic cells, have their own translation machinery that is solely responsible for synthesis of 13 mitochondrially encoded protein subunits of oxidative phosphorylation complexes. phosphorylation is a well-known post-translational modification in regulation of many processes in mammalian mitochondria including oxidative phosphorylation. however, there is still very limited knowledge on phosphorylation of mitochondrial ribosomal proteins and their role(s) in rib ...	2009	19702336
demonstration and characterization of the heterodimerization of znt5 and znt6 in the early secretory pathway.	the majority of cdf/znt zinc transporters form homo-oligomers. however, znt5, znt6, and their orthologues form hetero-oligomers in the early secretory pathway where they load zinc onto zinc-requiring enzymes and maintain secretory pathway functions. the details of this hetero-oligomerization remain to be elucidated, and much more is known about homo-oligomerization that occurs in other cdf/znt family proteins. here, we addressed this issue using co-immunoprecipitation experiments, mutagenesis, a ...	2009	19759014
mechanism of adp-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-adp-ribosylhydrolase drag.	adp-ribosylation is a ubiquitous regulatory posttranslational modification involved in numerous key processes such as dna repair, transcription, cell differentiation, apoptosis, and the pathogenic mechanism of certain bacterial toxins. despite the importance of this reversible process, very little is known about the structure and mechanism of the hydrolases that catalyze removal of the adp-ribose moiety. in the phototrophic bacterium rhodospirillum rubrum, dinitrogenase reductase-activating glyc ...	2009	19706507
structure of d-alanine-d-alanine ligase from thermus thermophilus hb8: cumulative conformational change and enzyme-ligand interactions.	d-alanine-d-alanine ligase (ddl) is one of the key enzymes in peptidoglycan biosynthesis and is an important target for drug discovery. the enzyme catalyzes the condensation of two d-ala molecules using atp to produce d-ala-d-ala, which is the terminal peptide of a peptidoglycan monomer. the structures of five forms of the enzyme from thermus thermophilus hb8 (ttddl) were determined: unliganded ttddl (2.3 a resolution), ttddl-adenylyl imidodiphosphate (2.6 a), ttddl-adp (2.2 a), ttddl-adp-d-ala ...	2009	19770507
crystal structures and biochemical analyses suggest a unique mechanism and role for human glycyl-trna synthetase in ap4a homeostasis.	aminoacyl-trna synthetases catalyze the attachment of amino acids to their cognate trnas for protein synthesis. however, the aminoacylation reaction can be diverted to produce diadenosine tetraphosphate (ap4a), a universal pleiotropic signaling molecule needed for cell regulation pathways. the only known mechanism for ap4a production by a trna synthetase is through the aminoacylation reaction intermediate aminoacyl-amp, thus making ap4a synthesis amino acid-dependent. here, we demonstrate a new ...	2009	19710017
adenosine triphosphate stimulates aquifex aeolicus mutl endonuclease activity.	background: human pms2 (hpms2) homologues act to nick 5' and 3' to misincorporated nucleotides during mismatch repair in organisms that lack muth. mn(++) was previously found to stimulate the endonuclease activity of these homologues. atp was required for the nicking activity of hpms2 and ypms1, but was reported to inhibit bacterial mutl proteins from thermus thermophilus and aquifex aeolicus that displayed homology to hpms2. mutational analysis has identified the dqha(x)(2)e(x)(4)e motif presen ...	2009	19777055
mg(2+)-dependent gating of bacterial mgte channel underlies mg(2+) homeostasis.	the mgte family of mg(2+) transporters is ubiquitously distributed in all phylogenetic domains. recent crystal structures of the full-length mgte and of its cytosolic domain in the presence and absence of mg(2+) suggested a mg(2+)-homeostasis mechanism, in which the mgte cytosolic domain acts as a 'mg(2+) sensor' to regulate the gating of the ion-conducting pore in response to the intracellular mg(2+) concentration. however, complementary functional analyses to confirm the proposed model have be ...	2009	19798051
increased expression of the oxidative pentose phosphate pathway and gluconeogenesis in anaerobically growing xylose-utilizing saccharomyces cerevisiae.	fermentation of xylose to ethanol has been achieved in s. cerevisiae by genetic engineering. xylose utilization is however slow compared to glucose, and during anaerobic conditions addition of glucose has been necessary for cellular growth. in the current study, the xylose-utilizing strain tmb 3415 was employed to investigate differences between anaerobic utilization of glucose and xylose. this strain carried a xylose reductase (xyl1 k270r) engineered for increased nadh utilization and was capab ...	2009	19778438
identification of x-ding-cd4, a new member of human ding protein family that is secreted by hiv-1 resistant cd4(+) t cells and has anti-viral activity.	we reported previously the anti-viral activity named hrf (hiv-1 resistance factor) secreted by hiv-1 resistant cells. this work describes the identification of hrf from cell culture supernatant of hrf-producing cells (hrf(+) cells). employing the proteomics and cell based activity assay we recovered ten peptides sharing 80-93% sequence homology with other eukaryotic ding proteins; discrete amino acid characteristics found in our material suggested that hrf is a new member of ding proteins family ...	2009	19720052
interaction of the thermoplasma acidophilum a1a0-atp synthase peripheral stalk with the catalytic domain.	the peripheral stalk of the archaeal atp synthase (a1a0)-atp synthase is formed by the heterodimeric eh complex and is part of the stator domain, which counteracts the torque of rotational catalysis. here we used nuclear magnetic resonance spectroscopy to probe the interaction of the c-terminal domain of the eh heterodimer (e(ct1)h(ct)) with the n-terminal 23 residues of the b subunit (b(nt)). the data show a specific interaction of b(nt) peptide with 26 residues of the e(ct1)h(ct) domain, there ...	2009	19720061
promiscuous substrate recognition in folding and assembly activities of the trigger factor chaperone.	trigger factor (tf) is a molecular chaperone that binds to bacterial ribosomes where it contacts emerging nascent chains, but tf is also abundant free in the cytosol where its activity is less well characterized. in vitro studies show that tf promotes protein refolding. we find here that ribosome-free tf stably associates with and rescues from misfolding a large repertoire of full-length proteins. we identify over 170 members of this cytosolic escherichia coli tf substrate proteome, including ri ...	2009	19737520
crystal structure of ynje from escherichia coli, a sulfurtransferase with three rhodanese domains.	rhodaneses/sulfurtransferases are ubiquitous enzymes that catalyze the transfer of sulfane sulfur from a donor molecule to a thiophilic acceptor via an active site cysteine that is modified to a persulfide during the reaction. here, we present the first crystal structure of a triple-domain rhodanese-like protein, namely ynje from escherichia coli, in two states where its active site cysteine is either unmodified or present as a persulfide. compared to well-characterized tandem domain rhodaneses, ...	2009	19798741
multiple biochemical and morphological factors underlie the production of methylketones in tomato trichomes.	genetic analysis of interspecific populations derived from crosses between the wild tomato species solanum habrochaites f. sp. glabratum, which synthesizes and accumulates insecticidal methylketones (mk), mostly 2-undecanone and 2-tridecanone, in glandular trichomes, and cultivated tomato (solanum lycopersicum), which does not, demonstrated that several genetic loci contribute to mk metabolism in the wild species. a strong correlation was found between the shape of the glandular trichomes and th ...	2009	19801397
the structure of staphylococcus aureus phosphopantetheine adenylyltransferase in complex with 3'-phosphoadenosine 5'-phosphosulfate reveals a new ligand-binding mode.	bacterial phosphopantetheine adenylyltransferase (ppat) catalyzes the penultimate step in the coenzyme a (coa) biosynthetic pathway. it catalyzes the reversible transfer of an adenylyl group from atp to 4'-phosphopantetheine (ppant) to form dephospho-coa (dpcoa) and pyrophosphate. previous structural studies have revealed how several ligands are recognized by bacterial ppats. atp, adp, ppant and dpcoa bind to the same binding site in a highly similar manner, while coa binds to a partially overla ...	2009	19851003
inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic v1-atpase.	v-type atpases (v-atpases) are categorized as rotary atp synthase/atpase complexes. the v-atpases are distinct from f-atpases in terms of their rotation scheme, architecture and subunit composition. however, there is no detailed structural information on v-atpases despite the abundant biochemical and biophysical research. here, we report a crystallographic study of v1-atpase, from thermus thermophilus, which is a soluble component consisting of a, b, d and f subunits. the structure at 4.5 a reso ...	2009	19779483
ion-induced folding of a kink turn that departs from the conventional sequence.	kink turns (k-turns) are important structural motifs that create a sharp axial bend in rna. most conform to a consensus in which a three-nucleotide bulge is followed by consecutive ga and ag base pairs, and when these ga pairs are modified in vitro this generally leads to a failure to adopt the k-turn conformation. kt-23 in the 30s ribosomal subunit of thermus thermophilus is a rare exception in which the bulge-distal ag pair is replaced by a non-watson-crick a*u pair. in the context of the ...	2009	19783814
p38sj, a novel dingg protein protects neuronal cells from alcohol induced injury and death.	ethanol induces neuronal cell injury and death by dysregulating several signaling events that are controlled, in part, by activation of mapk/erk1/2 and/or inactivation of its corresponding phosphatase, pp1. recently, we have purified a novel protein of 38 kda in size, p38sj, from a callus culture of hypericum perforatum, which belongs to an emerging dingg family of proteins with phosphate binding activity. here, we show that treatment of neuronal cells with p38sj protects cells against injury in ...	2009	19739100
coupling atp utilization to protein remodeling by clpb, a hexameric aaa+ protein.	clpb and hsp104 are members of the aaa+ (atpases associated with various cellular activities) family of proteins and are molecular machines involved in thermotolerance. they are hexameric proteins containing 12 atp binding sites with two sites per protomer. clpb and hsp104 possess some innate protein remodeling activities; however, they require the collaboration of the dnak/hsp70 chaperone system to disaggregate and reactivate insoluble aggregated proteins. we investigated the mechanism by which ...	2009	19940245
h135a controls the redox activity of the sco copper center. kinetic and spectroscopic studies of the his135ala variant of bacillus subtilis sco.	sco-like proteins contain copper bound by two cysteines and a histidine residue. although their function is still incompletely understood, there is a clear involvement with the assembly of cytochrome oxidases that contain the cu(a) center in subunit 2, possibly mediating the transfer of copper into the cu(a) binuclear site. we are investigating the reaction chemistry of bsco, the homologue from bacillus subtilis. our studies have revealed that bsco behaves more like a redox protein than a metall ...	2009	19921776
communication between r481 and cu(b) in cytochrome bo(3) ubiquinol oxidase from escherichia coli.	the r481 residue of cytochrome bo(3) ubiquinol oxidase from e. coli is highly conserved in the heme-copper oxidase superfamily. it has been postulated to serve as part of a proton loading site that regulates proton translocation across the protein matrix of the enzyme. along these lines, proton pumping efficiency has been demonstrated to be abolished in many r481 mutants. however, r481q in bo(3) from e. coli has been shown to be fully functional, implying that the positive charge of the arginine ...	2009	19928831
the conserved lysine69 residue plays a catalytic role in mycobacterium tuberculosis shikimate dehydrogenase.	the shikimate pathway is an attractive target for the development of antitubercular agents because it is essential in mycobacterium tuberculosis, the causative agent of tuberculosis, but absent in humans. m. tuberculosis aroe-encoded shikimate dehydrogenase catalyzes the forth reaction in the shikimate pathway. structural and functional studies indicate that lysine69 may be involved in catalysis and/or substrate binding in m. tuberculosis shikimate dehydrogenase. investigation of the kinetic pro ...	2009	19917104
cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.	aspartokinase (ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ask network or from alternative pathways. ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. two subhomology divisions, ask(alpha) and ask(beta), have been recognize ...	2009	19946135
expression of reck and matrix metalloproteinase-2 in ameloblastoma.	ameloblastoma is a frequent odontogenic benign tumor characterized by local invasiveness, high risk of recurrence and occasional metastasis and malignant transformation. matrix metalloproteinase-2 (mmp-2) promotes tumor invasion and progression by destroying the extracellular matrix (ecm) and basement membrane. for this proteolytic activity, the endogenous inhibitor is reversion-inducing cysteine rich protein with kazal motifs (reck). the aim of this study was to characterize the relationship be ...	2009	19995435
posttranslational control of transcription factor fixk2, a key regulator for the bradyrhizobium japonicum-soybean symbiosis.	rhizobial fixk-like proteins play essential roles in activating genes for endosymbiotic life in legume root nodules, such as genes for micro-oxic respiration. in the facultative soybean symbiont, bradyrhizobium japonicum, the fixk(2) protein is the key player in a complex regulatory network. the fixk(2) gene itself is activated by the 2-component regulatory system fixlj in response to a moderate decrease of the oxygen tension, and the fixk(2) protein distributes and amplifies this response to th ...	2009	19955406
the crystal structure of apo-ftsh reveals domain movements necessary for substrate unfolding and translocation.	the hexameric membrane-spanning atp-dependent metalloprotease ftsh is universally conserved in eubacteria, mitochondria, and chloroplasts, where it fulfills key functions in quality control and signaling. as a member of the self-compartmentalizing atpases associated with various cellular activities (aaa+ proteases), ftsh converts the chemical energy stored in atp via conformational rearrangements into a mechanical force that is used for substrate unfolding and translocation into the proteolytic ...	2009	19955424
tissue inhibitor of metalloproteinase 1 expression associated with gene demethylation confers anoikis resistance in early phases of melanocyte malignant transformation.	although anoikis resistance has been considered a hallmark of malignant phenotype, the causal relation between neoplastic transformation and anchorage-independent growth remains undefined. we developed an experimental model of murine melanocyte malignant transformation, where a melanocyte lineage (melan-a) was submitted to sequential cycles of anchorage blockade, resulting in progressive morphologic alterations, and malignant transformation. throughout this process, cells corresponding to premal ...	2009	19956395
dissecting the role of critical residues and substrate preference of a fatty acyl-coa synthetase (fadd13) of mycobacterium tuberculosis.	newly emerging multi-drug resistant strains of mycobacterium tuberculosis (m.tb) severely limit the treatment options for tuberculosis (tb); hence, new antitubercular drugs are urgently needed. the myma operon is essential for the virulence and intracellular survival of m.tb and thus represents an attractive target for the development of new antitubercular drugs. this study is focused on the structure-function relationship of fatty acyl-coa synthetase (fadd13, rv3089) belonging to the myma opero ...	2009	20027301
the structural basis for mrna recognition and cleavage by the ribosome-dependent endonuclease rele.	translational control is widely used to adjust gene expression levels. during the stringent response in bacteria, mrna is degraded on the ribosome by the ribosome-dependent endonuclease, rele. the molecular basis for recognition of the ribosome and mrna by rele and the mechanism of cleavage are unknown. here, we present crystal structures of e. coli rele in isolation (2.5 a) and bound to programmed thermus thermophilus 70s ribosomes before (3.3 a) and after (3.6 a) cleavage. rele occupies the a ...	2009	20005802
structure of sure protein from aquifex aeolicus vf5 at 1.5 a resolution.	sure is a stationary-phase survival protein found in bacteria, eukaryotes and archaea that exhibits a divalent-metal-ion-dependent phosphatase activity and acts as a nucleotidase and polyphosphate phosphohydrolase. the structure of the sure protein from the hyperthermophile aquifex aeolicus has been solved at 1.5 a resolution using molecular replacement with one dimer in the asymmetric unit and refined to an r factor of 15.6%. the crystal packing reveals that two dimers assemble to form a tetram ...	2009	20054112
the chlamydial functional homolog of ksga confers kasugamycin sensitivity to chlamydia trachomatis and impacts bacterial fitness.	rrna adenine dimethyltransferases, represented by the escherichia coli ksga protein, are highly conserved phylogenetically and are generally not essential for growth. they are responsible for the post-transcriptional transfer of two methyl groups to two universally conserved adenosines located near the 3'end of the small subunit rrna and participate in ribosome maturation. all sequenced genomes of chlamydia reveal a ksga homolog in each species, including c. trachomatis. yet absence of a s-adeno ...	2009	20043826
horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein s4.	the universal ribosomal protein s4 is essential for the initiation of small subunit ribosomal assembly and translational accuracy. being part of the information processing machinery of the cell, the gene for s4 is generally thought of as being inherited vertically and has been used in concatenated gene phylogenies. here we report the evolution of ribosomal protein s4 in relation to a broad sharing of zinc/non-zinc forms of the gene and study the scope of horizontal gene transfer (hgt) of s4 duri ...	2009	19640295
a novel dimerization motif in the c-terminal domain of the thermus thermophilus dead box helicase hera confers substantial flexibility.	dead box helicases are involved in nearly all aspects of rna metabolism. they share a common helicase core, and may comprise additional domains that contribute to rna binding. the thermus thermophilus helicase hera is the first dimeric dead box helicase. crystal structures of hera fragments reveal a bipartite c-terminal domain with a novel dimerization motif and an rna-binding module. we provide a first glimpse on the additional rna-binding module outside the hera helicase core. the dimerization ...	2009	19050012
small molecule dnak modulators targeting the beta-domain.	the molecular chaperone dnak is essential for the survival of bacterial pathogens in the hostile environment of the host. hence, it is in principle a promising target for drug design but for which no current inhibitors are available apart from certain antimicrobial peptides. to this end, we have screened libraries of small molecules for their ability to interact with the substrate-binding domain of dnak. the most promising hit from the screen was synthesized and along with its analogs subjected ...	2009	19694756
structural characterization of a viral neil1 ortholog unliganded and bound to abasic site-containing dna.	endonuclease viii (nei) is a dna glycosylase of the base excision repair pathway that recognizes and excises oxidized pyrimidines. we determined the crystal structures of a neil1 ortholog from the giant mimivirus (mvnei1) unliganded and bound to dna containing tetrahydrofuran (thf), which is the first structure of any nei with an abasic site analog. the mvnei1 structures exhibit the same overall architecture as other enzymes of the fpg/nei family, which consists of two globular domains joined by ...	2009	19625256
the thermus thermophilus dead box helicase hera contains a modified rna recognition motif domain loosely connected to the helicase core.	dead box family helicases consist of a helicase core that is formed by two flexibly linked reca-like domains. the helicase activity can be regulated by n- or c-terminal extensions flanking the core. thermus thermophilus heat resistant rna-dependent atpase (hera) is the first dead box helicase that forms a dimer using a unique dimerization domain. in addition to the dimerization domain, hera contains a c-terminal rna binding domain (rbd) that shares sequence homology only to uncharacterized prote ...	2009	19710183
characterization of two seryl-trna synthetases in albomycin-producing streptomyces sp. strain atcc 700974.	the trojan horse antibiotic albomycin, produced by streptomyces sp. strain atcc 700974, contains a thioribosyl nucleoside moiety linked to a hydroxamate siderophore through a serine residue. the seryl nucleoside structure (sb-217452) is a potent inhibitor of seryl-trna synthetase (serrs) in the pathogenic bacterium staphylococcus aureus, with a 50% inhibitory concentration (ic(50)) of approximately 8 nm. in the albomycin-producing streptomyces sp., a bacterial serrs homolog (alb10) was found to ...	2009	19721072
a non-canonical dna structure enables homologous recombination in various genetic systems.	homologous recombination, which is critical to genetic diversity, depends on homologous pairing (hp). hp is the switch from parental to recombinant base pairs, which requires expansion of inter-base pair spaces. this expansion unavoidably causes untwisting of the parental double-stranded dna. reca/rad51-catalyzed atp-dependent hp is extensively stimulated in vitro by negative supercoils, which compensates for untwisting. however, in vivo, double-stranded dna is relaxed by bound proteins and thus ...	2009	19729448
identification of amino acids in the n-terminal domain of atypical methanogenic-type seryl-trna synthetase critical for trna recognition.	seryl-trna synthetase (serrs) from methanogenic archaeon methanosarcina barkeri, contains an idiosyncratic n-terminal domain, composed of an antiparallel beta-sheet capped by a helical bundle, connected to the catalytic core by a short linker peptide. it is very different from the coiled-coil trna binding domain in bacterial-type serrs. because the crystal structure of the methanogenic-type serrsxtrna complex has not been obtained, a docking model was produced, which indicated that highly conser ...	2009	19734148
structural insights into the mechanism of the allosteric transitions of mycobacterium tuberculosis camp receptor protein.	the camp receptor protein (crp) from mycobacterium tuberculosis is a camp-responsive global transcriptional regulator, responsible for the regulation of a multitude of diverse proteins. we have determined the crystal structures of the crp.camp and crp.n(6)-camp derivative-bound forms of the enzyme to 2.2- and 2.3 a-resolution, respectively, to investigate camp-mediated conformational and structural changes. the allosteric switch from the open, inactive conformation to the closed, active conforma ...	2009	19740754
functional specialization of transcription elongation factors.	elongation factors nusg and rfah evolved from a common ancestor and utilize the same binding site on rna polymerase (rnap) to modulate transcription. however, although nusg associates with rnap transcribing most escherichia coli genes, rfah regulates just a few operons containing ops, a dna sequence that mediates rfah recruitment. here, we describe the mechanism by which this specificity is maintained. we observe that rfah action is indeed restricted to those several operons that are devoid of n ...	2009	19096362
functional specialization of transcription elongation factors.	elongation factors nusg and rfah evolved from a common ancestor and utilize the same binding site on rna polymerase (rnap) to modulate transcription. however, although nusg associates with rnap transcribing most escherichia coli genes, rfah regulates just a few operons containing ops, a dna sequence that mediates rfah recruitment. here, we describe the mechanism by which this specificity is maintained. we observe that rfah action is indeed restricted to those several operons that are devoid of n ...	2009	19096362
a novel insertion mutation in streptomyces coelicolor ribosomal s12 protein results in paromomycin resistance and antibiotic overproduction.	we identified a novel paromomycin resistance-associated mutation in rpsl, caused by the insertion of a glycine residue at position 92, in streptomyces coelicolor ribosomal protein s12. this insertion mutation (gi92) resulted in a 20-fold increase in the paromomycin resistance level. in combination with another s12 mutation, k88e, the gi92 mutation markedly enhanced the production of the blue-colored polyketide antibiotic actinorhodin and the red-colored antibiotic undecylprodigiosin. the gene re ...	2009	19104019
a novel insertion mutation in streptomyces coelicolor ribosomal s12 protein results in paromomycin resistance and antibiotic overproduction.	we identified a novel paromomycin resistance-associated mutation in rpsl, caused by the insertion of a glycine residue at position 92, in streptomyces coelicolor ribosomal protein s12. this insertion mutation (gi92) resulted in a 20-fold increase in the paromomycin resistance level. in combination with another s12 mutation, k88e, the gi92 mutation markedly enhanced the production of the blue-colored polyketide antibiotic actinorhodin and the red-colored antibiotic undecylprodigiosin. the gene re ...	2009	19104019
epr evidence of cyanide binding to the mn(mg) center of cytochrome c oxidase: support for cu(a)-mg involvement in proton pumping.	we examined the anion binding behavior of the mg(mn) site in cytochrome c oxidase to test a possible role of this center in proton pumping. rhodobacter sphaeroides grown in a mn(ii)-rich medium replaces the intrinsic mg(ii) ion with an epr-detectable mn(ii) ion without change in activity. due to its close proximity and a shared ligand, oxidized cu(a) is spin-coupled to the mn(ii) ion, affecting the epr spectrum. an examination of both bovine and r.s. oxidase crystal structures reveals a hydrogen ...	2009	19108635
a signal relay between ribosomal protein s12 and elongation factor ef-tu during decoding of mrna.	codon recognition by aminoacyl-trna on the ribosome triggers a process leading to gtp hydrolysis by elongation factor tu (ef-tu) and release of aminoacyl-trna into the a site of the ribosome. the nature of this signal is largely unknown. here, we present genetic evidence that a specific set of direct interactions between ribosomal protein s12 and aminoacyl-trna, together with contacts between s12 and 16s rrna, provide a pathway for the signaling of codon recognition to ef-tu. three novel amino a ...	2009	19095621
the crystal structure of galacto-n-biose/lacto-n-biose i phosphorylase: a large deformation of a tim barrel scaffold.	galacto-n-biose/lacto-n-biose i phosphorylase (glnbp) from bifidobacterium longum, a key enzyme for intestinal growth, phosphorolyses galacto-n-biose and lacto-n-biose i with anomeric inversion. glnbp homologues are often found in human pathogenic and commensal bacteria, and their substrate specificities potentially define the nutritional acquisition ability of these microbes in their habitat. we report the crystal structures of glnbp in five different ligand-binding forms. this is the first thr ...	2009	19124470
architectural underpinnings of the genetic code for glutamine.	structure-based mutational analysis was used to probe the architecture of the glutamine binding pocket in escherichia coli glutaminyl-trna synthetase (glnrs). crystallographic studies of several different glnrs complexes in a lattice that supports catalytic activity have shown that the glutamine amide group makes only ambiguous hydrogen-bonding interactions with a tyrosine hydroxyl and bound water molecule, rather than the highly specific hydrogen-bonding and electrostatic interactions made by t ...	2009	19128026
combined microspectrophotometric and crystallographic examination of chemically reduced and x-ray radiation-reduced forms of cytochrome ba3 oxidase from thermus thermophilus: structure of the reduced form of the enzyme.	three paths for obtaining crystals of reduced (ii-e4q/i-k258r) cytochrome ba(3) are described, and the structures of these are reported at approximately 2.8-3.0 a resolution. microspectrophotometry of single crystals of thermus ba(3) oxidase at 100 k was used to show that crystals of the oxidized enzyme are reduced in an intense x-ray (beam line 7-1 at the stanford synchrotron radiation laboratory), being nearly complete in 1 min. the previously reported structures of ba(3) (protein data bank en ...	2009	19140675
a conserved active site tyrosine residue of proline dehydrogenase helps enforce the preference for proline over hydroxyproline as the substrate.	proline dehydrogenase (prodh) catalyzes the oxidation of l-proline to delta-1-pyrroline-5-carboxylate. prodhs exhibit a pronounced preference for proline over hydroxyproline (trans-4-hydroxy-l-proline) as the substrate, but the basis for specificity is unknown. the goal of this study, therefore, is to gain insight into the structural determinants of substrate specificity of this class of enzyme, with a focus on understanding how prodhs discriminate between the two closely related molecules, prol ...	2009	19140736
coarse-grained modeling of large rna molecules with knowledge-based potentials and structural filters.	understanding the function of complex rna molecules depends critically on understanding their structure. however, creating three-dimensional (3d) structural models of rna remains a significant challenge. we present a protocol (the nucleic acid simulation tool [nast]) for rna modeling that uses an rna-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate plausible 3d structures. we demonstrate nast's capabilities by using only secondary structure and tertiar ...	2009	19144906
genetic and structural analysis of base substitutions in the central pseudoknot of thermus thermophilus 16s ribosomal rna.	characterization of base substitutions in rrnas has provided important insights into the mechanism of protein synthesis. knowledge of the structural effects of such alterations is limited, and could be greatly expanded with the development of a genetic system based on an organism amenable to both genetics and structural biology. here, we describe the genetic analysis of base substitutions in 16s ribosomal rna of the extreme thermophile thermus thermophilus, and an analysis of the conformational ...	2009	19144908
electronic structure of the ground and excited states of the cu(a) site by nmr spectroscopy.	the electronic properties of thermus thermophilus cu(a) in the oxidized form were studied by (1)h and (13)c nmr spectroscopy. all of the (1)h and (13)c resonances from cysteine and imidazole ligands were observed and assigned in a sequence-specific fashion. the detection of net electron spin density on a peptide moiety is attributed to the presence of a h-bond to a coordinating sulfur atom. this hydrogen bond is conserved in all natural cu(a) variants and plays an important role for maintaining ...	2009	19146411
mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at trna wobble positions.	the wobble modification in trnas, 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)u), is required for the proper decoding of nnr codons in eukaryotes. the 2-thio group confers conformational rigidity of mcm(5)s(2)u by largely fixing the c3'-endo ribose puckering, ensuring stable and accurate codon-anticodon pairing. we have identified five genes in saccharomyces cerevisiae, yil008w (urm1), yhr111w (uba4), yor251c (tum1), ynl119w (ncs2) and ygl211w (ncs6), that are required for 2-thiolation of m ...	2009	19151091
constant c10 ring stoichiometry in the escherichia coli atp synthase analyzed by cross-linking.	the subunit c stoichiometry of escherichia coli atp synthase was studied by intermolecular cross-linking via oxidation of bi-cysteine-substituted subunit c (ca21c/cm65c). independent of the carbon source used for growth and independent of the presence of other fof1 subunits, an equal pattern of cross-link formation stopping at the formation of decamers was obtained.	2009	19181809
mitochondrial dna damage in iron overload.	chronic iron overload has slow and insidious effects on heart, liver, and other organs. because iron-driven oxidation of most biologic materials (such as lipids and proteins) is readily repaired, this slow progression of organ damage implies some kind of biological "memory." we hypothesized that cumulative iron-catalyzed oxidant damage to mtdna might occur in iron overload, perhaps explaining the often lethal cardiac dysfunction. real time pcr was used to examine the "intactness" of mttdna in cu ...	2009	19095657
characterization of two novel alpha-glucosidases from bifidobacterium breve ucc2003.	two alpha-glucosidase-encoding genes (agl1 and agl2) from bifidobacterium breve ucc2003 were identified and characterized. based on their similarity to characterized carbohydrate hydrolases, the agl1 and agl2 enzymes are both assigned to a subgroup of the glycosyl hydrolase family 13, the alpha-1,6-glucosidases (ec 3.2.1.10). recombinant agl1 and agl2 into which a his(12) sequence was incorporated (agl1(his) and agl2(his), respectively) exhibited hydrolytic activity towards panose, isomaltose, i ...	2009	19114534
characterization of two novel alpha-glucosidases from bifidobacterium breve ucc2003.	two alpha-glucosidase-encoding genes (agl1 and agl2) from bifidobacterium breve ucc2003 were identified and characterized. based on their similarity to characterized carbohydrate hydrolases, the agl1 and agl2 enzymes are both assigned to a subgroup of the glycosyl hydrolase family 13, the alpha-1,6-glucosidases (ec 3.2.1.10). recombinant agl1 and agl2 into which a his(12) sequence was incorporated (agl1(his) and agl2(his), respectively) exhibited hydrolytic activity towards panose, isomaltose, i ...	2009	19114534
dihydroorotase from the hyperthermophile aquifex aeolicus is activated by stoichiometric association with aspartate transcarbamoylase and forms a one-pot reactor for pyrimidine biosynthesis.	in prokaryotes, the first three enzymes in pyrimidine biosynthesis, carbamoyl phosphate synthetase (cps), aspartate transcarbamoylase (atc), and dihydroorotase (dho), are commonly expressed separately and either function independently (escherichia coli) or associate into multifunctional complexes (aquifex aeolicus). in mammals the enzymes are expressed as a single polypeptide chain (cad) in the order cps-dho-atc and associate into a hexamer. this study presents the three-dimensional structure of ...	2009	19128030
ribosome hijacking: a role for small protein b during trans-translation.	tight recognition of codon-anticodon pairings by the ribosome ensures the accuracy and fidelity of protein synthesis. in eubacteria, translational surveillance and ribosome rescue are performed by the 'tmrna-smpb' system (transfer messenger rna-small protein b). remarkably, entry and accommodation of aminoacylated-tmrna into stalled ribosomes occur without a codon-anticodon interaction but in the presence of smpb. here, we show that within a stalled ribosome, smpb interacts with the three univer ...	2009	19132006
cloning, expression, crystallization and preliminary x-ray crystallographic analysis of glutamyl-trna synthetase (xoo1504) from xanthomonas oryzae pv. oryzae.	the gltx gene from xanthomonas oryzae pv. oryzae (xoo1504) encodes glutamyl-trna synthetase (glurs), one of the most important enzymes involved in bacterial blight (bb), which causes huge production losses of rice worldwide. glurs is a class i-type aminoacyl-trna synthetase (aars) that is primarily responsible for the glutamylation of trna(glu). it plays an essential role in protein synthesis, as well as the regulation of cells, in all organisms. as it represents an important target for the deve ...	2009	19153456
identification of a new endogenous metabolite and the characterization of its protein interactions through an immobilization approach.	the emerging field of global mass-based metabolomics provides a platform for discovering unknown metabolites and their specific biochemical pathways. we report the identification of a new endogenous metabolite, n(4)-(n-acetylaminopropyl)spermidine and the use of a novel proteomics based method for the investigation of its protein interaction using metabolite immobilization on agarose beads. the metabolite was isolated from the organism pyrococcus furiosus, and structurally characterized through ...	2009	19055353
differential effects of mitochondrial complex i inhibitors on production of reactive oxygen species.	we have investigated the production of reactive oxygen species (ros) by complex i in isolated open bovine heart submitochondrial membrane fragments during forward electron transfer in presence of nadh, by means of the probe 2',7'-dichlorodihydrofluorescein diacetate. ros production by complex i is strictly related to its inhibited state. our results indicate that different complex i inhibitors can be grouped into two classes: class a inhibitors (rotenone, piericidin a and rolliniastatin 1 and 2) ...	2009	19059197
differential effects of mitochondrial complex i inhibitors on production of reactive oxygen species.	we have investigated the production of reactive oxygen species (ros) by complex i in isolated open bovine heart submitochondrial membrane fragments during forward electron transfer in presence of nadh, by means of the probe 2',7'-dichlorodihydrofluorescein diacetate. ros production by complex i is strictly related to its inhibited state. our results indicate that different complex i inhibitors can be grouped into two classes: class a inhibitors (rotenone, piericidin a and rolliniastatin 1 and 2) ...	2009	19059197
superoxide dismutase from the eukaryotic thermophile alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.	prokaryotic thermophiles supply stable human protein homologs for structural biology; yet, eukaryotic thermophiles would provide more similar macromolecules plus those missing in microbes. alvinella pompejana is a deep-sea hydrothermal-vent worm that has been found in temperatures averaging as high as 68 degrees c, with spikes up to 84 degrees c. here, we used cu,zn superoxide dismutase (sod) to test if this eukaryotic thermophile can provide insights into macromolecular mechanisms and stability ...	2009	19063897
superoxide dismutase from the eukaryotic thermophile alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.	prokaryotic thermophiles supply stable human protein homologs for structural biology; yet, eukaryotic thermophiles would provide more similar macromolecules plus those missing in microbes. alvinella pompejana is a deep-sea hydrothermal-vent worm that has been found in temperatures averaging as high as 68 degrees c, with spikes up to 84 degrees c. here, we used cu,zn superoxide dismutase (sod) to test if this eukaryotic thermophile can provide insights into macromolecular mechanisms and stability ...	2009	19063897
structure and non-essential function of glycerol kinase in plasmodium falciparum blood stages.	malaria pathology is caused by multiplication of asexual parasites within erythrocytes, whereas mosquito transmission of malaria is mediated by sexual precursor cells (gametocytes). microarray analysis identified glycerol kinase (gk) as the second most highly upregulated gene in plasmodium falciparum gametocytes with no expression detectable in asexual blood stage parasites. phosphorylation of glycerol by gk is the rate-limiting step in glycerol utilization. deletion of this gene from p. falcipa ...	2009	19040641
rrna suppressor of a eukaryotic translation initiation factor 5b/initiation factor 2 mutant reveals a binding site for translational gtpases on the small ribosomal subunit.	the translational gtpases promote initiation, elongation, and termination of protein synthesis by interacting with the ribosome. mutations that impair gtp hydrolysis by eukaryotic translation initiation factor 5b/initiation factor 2 (eif5b/if2) impair yeast cell growth due to failure to dissociate from the ribosome following subunit joining. a mutation in helix h5 of the 18s rrna in the 40s ribosomal subunit and intragenic mutations in domain ii of eif5b suppress the toxic effects associated wit ...	2009	19029250
rrna suppressor of a eukaryotic translation initiation factor 5b/initiation factor 2 mutant reveals a binding site for translational gtpases on the small ribosomal subunit.	the translational gtpases promote initiation, elongation, and termination of protein synthesis by interacting with the ribosome. mutations that impair gtp hydrolysis by eukaryotic translation initiation factor 5b/initiation factor 2 (eif5b/if2) impair yeast cell growth due to failure to dissociate from the ribosome following subunit joining. a mutation in helix h5 of the 18s rrna in the 40s ribosomal subunit and intragenic mutations in domain ii of eif5b suppress the toxic effects associated wit ...	2009	19029250
function and ribosomal localization of aif6, a translational regulator shared by archaea and eukarya.	the translation factor if6 is shared by the archaea and the eukarya, but is not found in bacteria. the properties of eukaryal if6 (eif6) have been extensively studied, but remain somewhat elusive. eif6 behaves as a ribosome-anti-association factor and is involved in mirna-mediated gene silencing; however, it also seems to participate in ribosome synthesis and export. here we have determined the function and ribosomal localization of the archaeal (sulfolobus solfataricus) if6 homologue (aif6). we ...	2009	19036786
function and ribosomal localization of aif6, a translational regulator shared by archaea and eukarya.	the translation factor if6 is shared by the archaea and the eukarya, but is not found in bacteria. the properties of eukaryal if6 (eif6) have been extensively studied, but remain somewhat elusive. eif6 behaves as a ribosome-anti-association factor and is involved in mirna-mediated gene silencing; however, it also seems to participate in ribosome synthesis and export. here we have determined the function and ribosomal localization of the archaeal (sulfolobus solfataricus) if6 homologue (aif6). we ...	2009	19036786
minor changes largely restore catalytic activity of archaeal rnase p rna from methanothermobacter thermoautotrophicus.	the increased protein proportion of archaeal and eukaryal ribonuclease (rnase) p holoenzymes parallels a vast decrease in the catalytic activity of their rna subunits (p rnas) alone. we show that a few mutations toward the bacterial p rna consensus substantially activate the catalytic (c-) domain of archaeal p rna from methanothermobacter, in the absence and presence of the bacterial rnase p protein. large increases in ribozyme activity required the cooperative effect of at least two structural ...	2009	19036794
minor changes largely restore catalytic activity of archaeal rnase p rna from methanothermobacter thermoautotrophicus.	the increased protein proportion of archaeal and eukaryal ribonuclease (rnase) p holoenzymes parallels a vast decrease in the catalytic activity of their rna subunits (p rnas) alone. we show that a few mutations toward the bacterial p rna consensus substantially activate the catalytic (c-) domain of archaeal p rna from methanothermobacter, in the absence and presence of the bacterial rnase p protein. large increases in ribozyme activity required the cooperative effect of at least two structural ...	2009	19036794
unfolding thermodynamics of the delta-domain in the prohead i subunit of phage hk97: determination by factor analysis of raman spectra.	an early step in the morphogenesis of the double-stranded dna (dsdna) bacteriophage hk97 is the assembly of a precursor shell (prohead i) from 420 copies of a 384-residue subunit (gp5). although formation of prohead i requires direct participation of gp5 residues 2-103 (delta-domain), this domain is eliminated by viral protease prior to subsequent shell maturation and dna packaging. the prohead i delta-domain is thought to resemble a phage scaffolding protein, by virtue of its highly alpha-helic ...	2009	18983851
contributions of the two accessory subunits, rnaseh2b and rnaseh2c, to the activity and properties of the human rnase h2 complex.	eukaryotic rnase h2 is a heterotrimeric enzyme. here, we show that the biochemical composition and stoichiometry of the human rnase h2 complex is consistent with the properties previously deduced from genetic studies. the catalytic subunit of eukaryotic rnase h2, rnaseh2a, is well conserved and similar to the monomeric prokaryotic rnase hii. in contrast, the rnaseh2b and rnaseh2c subunits from human and saccharomyces cerevisiae share very little homology, although they both form soluble b/c comp ...	2009	19015152
unfolding thermodynamics of the delta-domain in the prohead i subunit of phage hk97: determination by factor analysis of raman spectra.	an early step in the morphogenesis of the double-stranded dna (dsdna) bacteriophage hk97 is the assembly of a precursor shell (prohead i) from 420 copies of a 384-residue subunit (gp5). although formation of prohead i requires direct participation of gp5 residues 2-103 (delta-domain), this domain is eliminated by viral protease prior to subsequent shell maturation and dna packaging. the prohead i delta-domain is thought to resemble a phage scaffolding protein, by virtue of its highly alpha-helic ...	2009	18983851
contributions of the two accessory subunits, rnaseh2b and rnaseh2c, to the activity and properties of the human rnase h2 complex.	eukaryotic rnase h2 is a heterotrimeric enzyme. here, we show that the biochemical composition and stoichiometry of the human rnase h2 complex is consistent with the properties previously deduced from genetic studies. the catalytic subunit of eukaryotic rnase h2, rnaseh2a, is well conserved and similar to the monomeric prokaryotic rnase hii. in contrast, the rnaseh2b and rnaseh2c subunits from human and saccharomyces cerevisiae share very little homology, although they both form soluble b/c comp ...	2009	19015152
transcription inactivation through local refolding of the rna polymerase structure.	structural studies of antibiotics not only provide a shortcut to medicine allowing for rational structure-based drug design, but may also capture snapshots of dynamic intermediates that become 'frozen' after inhibitor binding. myxopyronin inhibits bacterial rna polymerase (rnap) by an unknown mechanism. here we report the structure of dmyx--a desmethyl derivative of myxopyronin b--complexed with a thermus thermophilus rnap holoenzyme. the antibiotic binds to a pocket deep inside the rnap clamp h ...	2009	18946472
glucose- and glucokinase-controlled mal gene expression in escherichia coli.	malt is the central transcriptional activator of all mal genes in escherichia coli. its activity is controlled by the inducer maltotriose. it can be inhibited by the interaction with certain proteins, and its expression can be controlled. we report here a novel aspect of mal gene regulation: the effect of cytoplasmic glucose and glucokinase (glk) on the activity and the expression of malt. amylomaltase (malq) is essential for the metabolism of maltose. it forms maltodextrins and glucose from mal ...	2009	19028900
structural and biochemical studies of tigar (tp53-induced glycolysis and apoptosis regulator).	activation of the p53 tumor suppressor by cellular stress leads to variable responses ranging from growth inhibition to apoptosis. tigar is a novel p53-inducible gene that inhibits glycolysis by reducing cellular levels of fructose-2,6-bisphosphate, an activator of glycolysis and inhibitor of gluconeogenesis. here we describe structural and biochemical studies of tigar from danio rerio. the overall structure forms a histidine phosphatase fold with a phosphate molecule coordinated to the catalyti ...	2009	19015259
recr-mediated modulation of recf dimer specificity for single- and double-stranded dna.	recf pathway proteins play an important role in the restart of stalled replication and dna repair in prokaryotes. following dna damage, recf, recr, and reco initiate homologous recombination (hr) by loading of the reca recombinase on single-stranded (ss) dna, protected by ssdna-binding protein. the specific role of recf in this process is not well understood. previous studies have proposed that recf directs the recor complex to boundaries of damaged dna regions by recognizing single-stranded/dou ...	2009	19017635
biochemical and structural properties of mouse kynurenine aminotransferase iii.	kynurenine aminotransferase iii (kat iii) has been considered to be involved in the production of mammalian brain kynurenic acid (kyna), which plays an important role in protecting neurons from overstimulation by excitatory neurotransmitters. the enzyme was identified based on its high sequence identity with mammalian kat i, but its activity toward kynurenine and its structural characteristics have not been established. in this study, the biochemical and structural properties of mouse kat iii (m ...	2009	19029248
biochemical and structural properties of mouse kynurenine aminotransferase iii.	kynurenine aminotransferase iii (kat iii) has been considered to be involved in the production of mammalian brain kynurenic acid (kyna), which plays an important role in protecting neurons from overstimulation by excitatory neurotransmitters. the enzyme was identified based on its high sequence identity with mammalian kat i, but its activity toward kynurenine and its structural characteristics have not been established. in this study, the biochemical and structural properties of mouse kat iii (m ...	2009	19029248
structure and function of hiv-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition.	the rapid replication of hiv-1 and the errors made during viral replication cause the virus to evolve rapidly in patients, making the problems of vaccine development and drug therapy particularly challenging. in the absence of an effective vaccine, drugs are the only useful treatment. anti-hiv drugs work; so far drug therapy has saved more than three million years of life. unfortunately, hiv-1 develops resistance to all of the available drugs. although a number of useful anti-hiv drugs have been ...	2009	19022262
the mycobacterium tuberculosis mep (2c-methyl-d-erythritol 4-phosphate) pathway as a new drug target.	tuberculosis (tb) is still a major public health problem, compounded by the human immunodeficiency virus (hiv)-tb co-infection and recent emergence of multidrug-resistant (mdr) and extensively drug resistant (xdr)-tb. novel anti-tb drugs are urgently required. in this context, the 2c-methyl-d-erythritol 4-phosphate (mep) pathway of mycobacterium tuberculosis has drawn attention; it is one of several pathways vital for m. tuberculosis viability and the human host lacks homologous enzymes. thus, t ...	2009	18793870
novel escherichia coli rf1 mutants with decreased translation termination activity and increased sensitivity to the cytotoxic effect of the bacterial toxins kid and rele.	novel mutations in prfa, the gene for the polypeptide release factor rf1 of escherichia coli, were isolated using a positive genetic screen based on the pard (kis, kid) toxin-antitoxin system. this original approach allowed the direct selection of mutants with altered translational termination efficiency at uag codons. the isolated prfa mutants displayed a approximately 10-fold decrease in uag termination efficiency with no significant changes in rf1 stability in vivo. all three mutations, g121s ...	2009	19019162
glucose- and glucokinase-controlled mal gene expression in escherichia coli.	malt is the central transcriptional activator of all mal genes in escherichia coli. its activity is controlled by the inducer maltotriose. it can be inhibited by the interaction with certain proteins, and its expression can be controlled. we report here a novel aspect of mal gene regulation: the effect of cytoplasmic glucose and glucokinase (glk) on the activity and the expression of malt. amylomaltase (malq) is essential for the metabolism of maltose. it forms maltodextrins and glucose from mal ...	2009	19028900
structure and function of hiv-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition.	the rapid replication of hiv-1 and the errors made during viral replication cause the virus to evolve rapidly in patients, making the problems of vaccine development and drug therapy particularly challenging. in the absence of an effective vaccine, drugs are the only useful treatment. anti-hiv drugs work; so far drug therapy has saved more than three million years of life. unfortunately, hiv-1 develops resistance to all of the available drugs. although a number of useful anti-hiv drugs have been ...	2009	19022262
phylogenetic analysis of rubella virus strains from an outbreak in madrid, spain, from 2004 to 2005.	an outbreak of rubella affected 460 individuals in 2004 and 2005 in the community of madrid, spain. most of the patients were nonvaccinated latin american immigrants or spanish males. this study presents the first data on rubella virus genotypes in spain. forty selected clinical samples (2 urine, 5 serum, 3 blood, 2 saliva, and 28 pharyngeal exudate samples) from 40 cases were collected. the 739-nucleotide sequence recommended by the world health organization obtained from viral rna in these sam ...	2009	19020066
phylogenetic analysis of rubella virus strains from an outbreak in madrid, spain, from 2004 to 2005.	an outbreak of rubella affected 460 individuals in 2004 and 2005 in the community of madrid, spain. most of the patients were nonvaccinated latin american immigrants or spanish males. this study presents the first data on rubella virus genotypes in spain. forty selected clinical samples (2 urine, 5 serum, 3 blood, 2 saliva, and 28 pharyngeal exudate samples) from 40 cases were collected. the 739-nucleotide sequence recommended by the world health organization obtained from viral rna in these sam ...	2009	19020066
structure of putative 4-amino-4-deoxychorismate lyase from thermus thermophilus hb8.	the pyridoxal 5'-phosphate-dependent enzyme 4-amino-4-deoxychorismate lyase converts 4-amino-4-deoxychorismate to p-aminobenzoate and pyruvate in one of the crucial steps in the folate-biosynthesis pathway. the primary structure of the hypothetical protein ttha0621 from thermus thermophilus hb8 suggests that ttha0621 is a putative 4-amino-4-deoxychorismate lyase. here, the crystal structure of ttha0621 is reported at 1.93 a resolution. the asymmetric unit contained four ncs molecules related by ...	2009	20054118
the mycobacterium tuberculosis mep (2c-methyl-d-erythritol 4-phosphate) pathway as a new drug target.	tuberculosis (tb) is still a major public health problem, compounded by the human immunodeficiency virus (hiv)-tb co-infection and recent emergence of multidrug-resistant (mdr) and extensively drug resistant (xdr)-tb. novel anti-tb drugs are urgently required. in this context, the 2c-methyl-d-erythritol 4-phosphate (mep) pathway of mycobacterium tuberculosis has drawn attention; it is one of several pathways vital for m. tuberculosis viability and the human host lacks homologous enzymes. thus, t ...	2009	18793870
escherichia coli tmrna lacking pseudoknot 1 tags truncated proteins in vivo and in vitro.	transfer-messenger rna (tmrna) and protein smpb facilitate trans-translation, a quality-control process that tags truncated proteins with short peptides recognized by a number of proteases and recycles ribosomes stalled at the 3' end of mrna templates lacking stop codons. the tmrna molecule is a hybrid of trna- and mrna-like domains that are usually connected by four pseudoknots (pk1-pk4). replacement of pk1 with a single-stranded rna yields pk1l, a mutant tmrna that tags truncated proteins very ...	2009	19001120