Publications

inactivation of the rlud pseudouridine synthase has minimal effects on growth and ribosome function in wild-type escherichia coli and salmonella enterica.	the escherichia coli rlud gene encodes a pseudouridine synthase responsible for the pseudouridine (ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23s rrna. it has been reported that deletion of rlud in k-12 strains of e. coli is associated with extremely slow growth, increased readthrough of stop codons, and defects in 50s ribosomal subunit assembly and 30s-50s subunit association. suppressor mutations in the prfb and prfc genes encoding release factor 2 (rf2) and rf3 that res ...	2010	21037010
subunit dissociation and metal binding by escherichia coli apo-manganese superoxide dismutase.	metal binding by apo-manganese superoxide dismutase (apo-mnsod) is essential for functional maturation of the enzyme. previous studies have demonstrated that metal binding by apo-mnsod is conformationally gated, requiring protein reorganization for the metal to bind. we have now solved the x-ray crystal structure of apo-mnsod at 1.9å resolution. the organization of active site residues is independent of the presence of the metal cofactor, demonstrating that protein itself templates the unusual m ...	2010	21044611
subunit dissociation and metal binding by escherichia coli apo-manganese superoxide dismutase.	metal binding by apo-manganese superoxide dismutase (apo-mnsod) is essential for functional maturation of the enzyme. previous studies have demonstrated that metal binding by apo-mnsod is conformationally gated, requiring protein reorganization for the metal to bind. we have now solved the x-ray crystal structure of apo-mnsod at 1.9å resolution. the organization of active site residues is independent of the presence of the metal cofactor, demonstrating that protein itself templates the unusual m ...	2010	21044611
structure of dihydroorotase from bacillus anthracis at 2.6 å resolution.	dihydroorotase (ec 3.5.2.3) catalyzes the reversible cyclization of n-carbamoyl-l-aspartate to l-dihydroorotate in the third step of the pyrimidine-biosynthesis pathway in bacillus anthracis. a comparison is made between the structures of dihydroorotase from four different organisms, including b. anthracis dihydroorotase, and reveals substantial variations in the active site, dimer interface and overall tertiary structure. these differences demonstrate the utility of exploring multiple structure ...	2010	21045288
crystallization and preliminary x-ray diffraction analysis of human cytosolic seryl-trna synthetase.	human cytosolic seryl-trna synthetase (hsserrs) is responsible for the covalent attachment of serine to its cognate trna(ser). significant differences between the amino-acid sequences of eukaryotic, prokaryotic and archaebacterial serrss indicate that the domain composition of hsserrs differs from that of its eubacterial and archaebacterial analogues. as a consequence of an n-terminal insertion and a c-terminal extra-sequence, the binding mode of trna(ser) to hsserrs is expected to differ from t ...	2010	21045311
identification, cloning, and characterization of l-phenylserine dehydrogenase from pseudomonas syringae nk-15.	the gene encoding d-phenylserine dehydrogenase from pseudomonas syringae nk-15 was identified, and a 9,246-bp nucleotide sequence containing the gene was sequenced. six orfs were confirmed in the sequenced region, four of which were predicted to form an operon. a homology search of each orf predicted that orf3 encoded l-phenylserine dehydrogenase. hence, orf3 was cloned and overexpressed in escherichia coli cells and recombinant orf3 was purified to homogeneity and characterized. the purified or ...	2010	21048868
temporal regulation of gene expression of the thermus thermophilus bacteriophage p23-45.	regulation of gene expression during infection of the thermophilic bacterium thermus thermophilus hb8 with the bacteriophage p23-45 was investigated. macroarray analysis revealed host transcription shut-off and identified three temporal classes of phage genes; early, middle and late. primer extension experiments revealed that the 5' ends of p23-45 early transcripts are preceded by a common sequence motif that likely defines early viral promoters. t. thermophilus hb8 rna polymerase (rnap) recogni ...	2010	21050864
yaej is a novel ribosome-associated protein in escherichia coli that can hydrolyze peptidyl-trna on stalled ribosomes.	in bacteria, ribosomes often become stalled and are released by a trans-translation process mediated by transfer-messenger rna (tmrna). in the absence of tmrna, however, there is evidence that stalled ribosomes are released from non-stop mrnas. here, we show a novel ribosome rescue system mediated by a small basic protein, yaej, from escherichia coli, which is similar in sequence and structure to the catalytic domain 3 of polypeptide chain release factor (rf). in vitro translation experiments us ...	2010	21051357
yaej is a novel ribosome-associated protein in escherichia coli that can hydrolyze peptidyl-trna on stalled ribosomes.	in bacteria, ribosomes often become stalled and are released by a trans-translation process mediated by transfer-messenger rna (tmrna). in the absence of tmrna, however, there is evidence that stalled ribosomes are released from non-stop mrnas. here, we show a novel ribosome rescue system mediated by a small basic protein, yaej, from escherichia coli, which is similar in sequence and structure to the catalytic domain 3 of polypeptide chain release factor (rf). in vitro translation experiments us ...	2010	21051357
characterization of cytochrome p450 monooxygenase cyp154h1 from the thermophilic soil bacterium thermobifida fusca.	cytochrome p450 monooxygenases are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. we have cloned the gene for a new cytochrome p450 monooxygenase, named cyp154h1, from the moderately thermophilic soil bacterium thermobifida fusca. the enzyme was overexpressed in escherichia coli at up to 14% of total soluble protein and purified to homogeneity in three steps. cyp154h1 activity was reconstituted using putidaredoxin reductase and putidare ...	2010	21057946
characterization of cytochrome p450 monooxygenase cyp154h1 from the thermophilic soil bacterium thermobifida fusca.	cytochrome p450 monooxygenases are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. we have cloned the gene for a new cytochrome p450 monooxygenase, named cyp154h1, from the moderately thermophilic soil bacterium thermobifida fusca. the enzyme was overexpressed in escherichia coli at up to 14% of total soluble protein and purified to homogeneity in three steps. cyp154h1 activity was reconstituted using putidaredoxin reductase and putidare ...	2010	21057946
packaging hiv virion components through dynamic equilibria of a human trna synthetase.	aminoacyl trna synthetases, components of the translation apparatus, have alternative functions outside of translation. the structural and mechanistic basis of these alternative functions is of great interest. as an example, reverse transcription of the hiv genome is primed by a human lysine-specific trna (trna(lys3)) that is packaged (into the virion) by the hiv gag protein with lysyl-trna synthetase (lysrs). not understood is the structural basis for simultaneous packaging of trna(lys3), lysrs ...	2010	21058683
the c-terminal domain of the mutl homolog from neisseria gonorrhoeae forms an inverted homodimer.	the mismatch repair (mmr) pathway serves to maintain the integrity of the genome by removing mispaired bases from the newly synthesized strand. in e. coli, muts, mutl and muth coordinate to discriminate the daughter strand through a mechanism involving lack of methylation on the new strand. this facilitates the creation of a nick by muth in the daughter strand to initiate mismatch repair. many bacteria and eukaryotes, including humans, do not possess a homolog of muth. although the exact strateg ...	2010	21060849
the mycobacterium tuberculosis drugome and its polypharmacological implications.	we report a computational approach that integrates structural bioinformatics, molecular modelling and systems biology to construct a drug-target network on a structural proteome-wide scale. the approach has been applied to the genome of mycobacterium tuberculosis (m.tb), the causative agent of one of today's most widely spread infectious diseases. the resulting drug-target interaction network for all structurally characterized approved drugs bound to putative m.tb receptors, we refer to as the ' ...	2010	21079673
a new hypothesis on the simultaneous direct and indirect proton pump mechanisms in nadh-quinone oxidoreductase (complex i).	recently, sazanov's group reported the x-ray structure of whole complex i [nature, 465, 441 (2010)], which presented a strong clue for a "piston-like" structure as a key element in an "indirect" proton pump. we have studied the nuol subunit which has a high sequence similarity to na(+)/h(+) antiporters, as do the nuom and n subunits. we constructed 27 site-directed nuol mutants. our data suggest that the h(+)/e(-) stoichiometry seems to have decreased from (4h(+)/2e(-)) in the wild-type to appro ...	2010	20816962
bacteria, yeast, worms, and flies: exploiting simple model organisms to investigate human mitochondrial diseases.	the extensive conservation of mitochondrial structure, composition, and function across evolution offers a unique opportunity to expand our understanding of human mitochondrial biology and disease. by investigating the biology of much simpler model organisms, it is often possible to answer questions that are unreachable at the clinical level. here, we review the relative utility of four different model organisms, namely the bacterium escherichia coli, the yeast saccharomyces cerevisiae, the nema ...	2010	20818735
crystallization and preliminary x-ray crystallographic study of genx, a lysyl-trna synthetase paralogue from escherichia coli, in complex with translation elongation factor p.	genx, a lysyl-trna synthetase paralogue from escherichia coli, was overexpressed in e. coli, purified by three chromatographic steps and cocrystallized with a lysyl adenylate analogue (lysams) by the hanging-drop vapour-diffusion method using peg 4000 as a precipitant. the genx-lysams crystals belonged to the triclinic space group p1, with unit-cell parameters a=54.80, b=69.15, c=94.08 a, alpha=95.47, beta=106.51, gamma=90.46 degrees, and diffracted to 1.9 a resolution. furthermore, genx was coc ...	2010	20823541
the membrane subunit nuol(nd5) is involved in the indirect proton pumping mechanism of escherichia coli complex i.	complex i pumps protons across the membrane by using downhill redox energy. here, to investigate the proton pumping mechanism by complex i, we focused on the largest transmembrane subunit nuol (escherichia coli nd5 homolog). nuol/nd5 is believed to have h(+) translocation site(s), because of a high sequence similarity to multi-subunit na(+)/h(+) antiporters. we mutated thirteen highly conserved residues between nuol/nd5 and mrpa of na(+)/h(+) antiporters in the chromosomal nuol gene. the dnadh o ...	2010	20826797
sequence- and structure-specific rna processing by a crispr endonuclease.	many bacteria and archaea contain clustered regularly interspaced short palindromic repeats (crisprs) that confer resistance to invasive genetic elements. central to this immune system is the production of crispr-derived rnas (crrnas) after transcription of the crispr locus. here, we identify the endoribonuclease (csy4) responsible for crispr transcript (pre-crrna) processing in pseudomonas aeruginosa. a 1.8 angstrom crystal structure of csy4 bound to its cognate rna reveals that csy4 makes sequ ...	2010	20829488
molecular modeling study for interaction between bacillus subtilis obg and nucleotides.	the bacterial obg proteins (spo0b-associated gtp-binding protein) belong to the subfamily of p-loop gtpase proteins that contain two equally and highly conserved domains, a c-terminal gtp binding domain and an n-terminal glycine-rich domain which is referred as the "obg fold" and now it is considered as one of the new targets for antibacterial drug. when the obg protein is associated with gtp, it becomes activated, because conformation of obg fold changes due to the structural changes of gtpase ...	2010	20830302
structural and biochemical studies of a fluoroacetyl-coa-specific thioesterase reveal a molecular basis for fluorine selectivity.	we have initiated a broad-based program aimed at understanding the molecular basis of fluorine specificity in enzymatic systems, and in this context, we report crystallographic and biochemical studies on a fluoroacetyl-coenzyme a (coa) specific thioesterase (flk) from streptomyces cattleya. our data establish that flk is competent to protect its host from fluoroacetate toxicity in vivo and demonstrate a 10(6)-fold discrimination between fluoroacetyl-coa (k(cat)/k(m) = 5 × 10⁷ m⁻¹ s⁻¹) and acetyl ...	2010	20836570
inhibition of osteoclast bone resorption by disrupting vacuolar h+-atpase a3-b2 subunit interaction.	vacuolar h(+)-atpases (v-atpases) are highly expressed in ruffled borders of bone-resorbing osteoclasts, where they play a crucial role in skeletal remodeling. to discover protein-protein interactions with the a subunit in mammalian v-atpases, a gal4 activation domain fusion library was constructed from an in vitro osteoclast model, receptor activator of nf-κb ligand-differentiated raw 264.7 cells. this library was screened with a bait construct consisting of a gal4 binding domain fused to the n ...	2010	20837476
small-molecule antioxidant proteome-shields in deinococcus radiodurans.	for deinococcus radiodurans and other bacteria which are extremely resistant to ionizing radiation, ultraviolet radiation, and desiccation, a mechanistic link exists between resistance, manganese accumulation, and protein protection. we show that ultrafiltered, protein-free preparations of d. radiodurans cell extracts prevent protein oxidation at massive doses of ionizing radiation. in contrast, ultrafiltrates from ionizing radiation-sensitive bacteria were not protective. the d. radiodurans ult ...	2010	20838443
structural and kinetic characterization of 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolase, a protocatechuate degradation enzyme evolutionarily convergent with the hpai and dmpg pyruvate aldolases.	4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate (hmg/cha) aldolase from pseudomonas putida f1 catalyzes the last step of the bacterial protocatechuate 4,5-cleavage pathway. the preferred substrates of the enzyme are 2-keto-4-hydroxy acids with a 4-carboxylate substitution. the enzyme also exhibits oxaloacetate decarboxylation and pyruvate α-proton exchange activity. sodium oxalate is a competitive inhibitor of the aldolase reaction. the ph dependence of k(cat)/k(m) and k(cat) ...	2010	20843800
bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria.	the catalytic domain of the f-atpase in mitochondria protrudes into the matrix of the organelle, and is attached to the membrane domain by central and peripheral stalks. energy for the synthesis of atp from adp and phosphate is provided by the transmembrane proton-motive-force across the inner membrane, generated by respiration. the proton-motive force is coupled mechanically to atp synthesis by the rotation at about 100 times per second of the central stalk and an attached ring of c-subunits in ...	2010	20847295
cadaverine covalently linked to peptidoglycan is required for interaction between the peptidoglycan and the periplasm-exposed s-layer-homologous domain of major outer membrane protein mep45 in selenomonas ruminantium.	the peptidoglycan of selenomonas ruminantium is covalently bound to cadaverine (pg-cadaverine), which likely plays a significant role in maintaining the integrity of the cell surface structure. the outer membrane of this bacterium contains a 45-kda major protein (mep45) that is a putative peptidoglycan-associated protein. in this report, we determined the nucleotide sequence of the mep45 gene and investigated the relationship between pg-cadaverine, mep45, and the cell surface structure. amino ac ...	2010	20851903
structural basis for 16s ribosomal rna cleavage by the cytotoxic domain of colicin e3.	the toxin colicin e3 targets the 30s subunit of bacterial ribosomes and cleaves a phosphodiester bond in the decoding center. we present the crystal structure of the 70s ribosome in complex with the cytotoxic domain of colicin e3 (e3-rrnase). the structure reveals how the rrnase domain of colicin binds to the a site of the decoding center in the 70s ribosome and cleaves the 16s ribosomal rna (rrna) between a1493 and g1494. the cleavage mechanism involves the concerted action of conserved residue ...	2010	20852642
lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes.	the structure of the protein-translocating channel secyeβ from pyrococcus furiosus at 3.1-å resolution suggests a mechanism for chaperoning transmembrane regions of a protein substrate during its lateral delivery into the lipid bilayer. cytoplasmic segments of secy orient the c-terminal α-helical region of another molecule, suggesting a general binding mode and a promiscuous guiding surface capable of accommodating diverse nascent chains at the exit of the ribosomal tunnel. to accommodate this p ...	2010	20855604
complete structural model of escherichia coli rna polymerase from a hybrid approach.	the escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. nevertheless, a molecular understanding of the details of e. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on e. coli rna polymerase (rnap). we use a combination of approaches, including high-resolution x-ray crystallography, ab i ...	2010	20856905
role of hsp70 atpase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with nefs.	catalysis of adp-atp exchange by nucleotide exchange factors (nefs) is central to the activity of hsp70 molecular chaperones. yet, the mechanism of interaction of this family of chaperones with nefs is not well understood in the context of the sequence evolution and structural dynamics of hsp70 atpase domains. we studied the interactions of hsp70 atpase domains with four different nefs on the basis of the evolutionary trace and co-evolution of the atpase domain sequence, combined with elastic ne ...	2010	20862304
comparative genomics of gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential.	gardnerella vaginalis is described as a common vaginal bacterial species whose presence correlates strongly with bacterial vaginosis (bv). here we report the genome sequencing and comparative analyses of three strains of g. vaginalis. strains 317 (atcc 14019) and 594 (atcc 14018) were isolated from the vaginal tracts of women with symptomatic bv, while strain 409-05 was isolated from a healthy, asymptomatic individual with a nugent score of 9.	2010	20865041
structure and mechanism of orf36, an amino sugar oxidizing enzyme in everninomicin biosynthesis .	everninomicin is a highly modified octasaccharide that belongs to the orthosomycin family of antibiotics and possesses potent gram-positive antibiotic activity, including broad-spectrum efficacy against multidrug resistant enterococci and staphylococcus aureus. among its distinctive structural features is a nitro sugar, l-evernitrose, analogues of which decorate a variety of natural products. recently, we identified a nitrososynthase enzyme encoded by orf36 from micromonospora carbonacea var. af ...	2010	20866105
the roles of several residues of escherichia coli dna photolyase in the highly efficient photo-repair of cyclobutane pyrimidine dimers.	escherichia coli dna photolyase is an enzyme that repairs the major kind of uv-induced lesions, cyclobutane pyrimidine dimer (cpd) in dna utilizing 350-450 nm light as energy source. the enzyme has very high photo-repair efficiency (the quantum yield of the reaction is ~0.85), which is significantly greater than many model compounds that mimic photolyase. this suggests that some residues of the protein play important roles in the photo-repair of cpd. in this paper, we have focused on several res ...	2010	20871655
histidine 197 in release factor 1 is essential for a site binding and peptide release.	class i peptide release factors 1 and 2 (rf1 and rf2, respectively) recognize the stop codons in the ribosomal decoding center and catalyze peptidyl-trna hydrolysis. high-fidelity stop codon recognition by these release factors is essential for accurate peptide synthesis and ribosome recycling. x-ray crystal structures of rf1 and rf2 bound to the ribosome have identified residues in the mrna-protein interface that appear to be critical for stop codon recognition. especially interesting is a cons ...	2010	20873815
hmp binding protein thiy and hmp-p synthase thi5 are structural homologues.	the atp-binding cassette transporter system thixyz transports n-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (famp), a thiamin salvage pathway intermediate, into cells. famp is then converted to 4-amino-5-(hydroxymethyl)-2-methylpyrimidine (hmp) and recycled into the thiamin biosynthetic pathway. thiy is the periplasmic substrate binding protein of the thixyz system and delivers the substrate famp to the transmembrane domain. we report the crystal structure of bacillus halodurans thiy with ...	2010	20873853
revisiting the structures of several antibiotics bound to the bacterial ribosome.	the increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental pr ...	2010	20876130
evolution and multiplicity of arginine decarboxylases in polyamine biosynthesis and essential role in bacillus subtilis biofilm formation.	arginine decarboxylases (adcs; ec 4.1.1.19) from four different protein fold families are important for polyamine biosynthesis in bacteria, archaea, and plants. biosynthetic alanine racemase fold (ar-fold) adc is widespread in bacteria and plants. we report the discovery and characterization of an ancestral form of the ar-fold adc in the bacterial chloroflexi and bacteroidetes phyla. the ancestral ar-fold adc lacks a large insertion found in escherichia coli and plant ar-fold adc and is more sim ...	2010	20876533
crystal structure analysis of bacillus subtilis ferredoxin-nadp(+) oxidoreductase and the structural basis for its substrate selectivity.	bacillus subtilis yumc encodes a novel type of ferredoxin-nadp+ oxidoreductase (fnr) with a primary sequence and oligomeric conformation distinct from those of previously known fnrs. in this study, the crystal structure of b. subtilis fnr (bsfnr) complexed with nadp+ has been determined. bsfnr features two distinct binding domains for fad and nadph in accordance with its structural similarity to escherichia coli nadph-thioredoxin reductase (tdr) and tdr-like protein from thermus thermophilus hb8 ...	2010	20878669
binding and cleavage of crispr rna by cas6.	the crispr-cas system provides many prokaryotes with acquired resistance to viruses and other mobile genetic elements. the core components of this defense system are small, host-encoded prokaryotic silencing (psi)rnas and cas (crispr-associated) proteins. invader-derived sequences within the psirnas guide cas effector proteins to recognize and silence invader nucleic acids. critical for crispr-cas defense is processing of the psirnas from the primary transcripts of the host crispr (clustered reg ...	2010	20884784
iron-sulfur world in aerobic and hyperthermoacidophilic archaea sulfolobus.	the general importance of the fe-s cluster prosthetic groups in biology is primarily attributable to specific features of iron and sulfur chemistry, and the assembly and interplay of the fe-s cluster core with the surrounding protein is the key to in-depth understanding of the underlying mechanisms. in the aerobic and thermoacidophilic archaea, zinc-containing ferredoxin is abundant in the cytoplasm, functioning as a key electron carrier, and many fe-s enzymes are produced to participate in the ...	2010	20885930
hemin binds to human cytoplasmic arginyl-trna synthetase and inhibits its catalytic activity.	the free form of human cytoplasmic arginyl-trna synthetase (hcargrs) is hypothesized to participate in ubiquitin-dependent protein degradation by offering arginyl-trna(arg) to arginyl-trna transferase (ate1). we investigated the effect of hemin on hcargrs based on the fact that hemin regulates several critical proteins in the "n-end rule" protein degradation pathway. extensive biochemical evidence has established that hemin could bind to both forms of hcargrs in vitro. based on the spectral chan ...	2010	20923763
cleavage of model substrates by archaeal rnase p: role of protein cofactors in cleavage-site selection.	rnase p is a catalytic ribonucleoprotein primarily involved in trna biogenesis. archaeal rnase p comprises a catalytic rnase p rna (rpr) and at least four protein cofactors (rpps), which function as two binary complexes (pop5•rpp30 and rpp21• rpp29). exploiting the ability to assemble a functional pyrococcus furiosus (pfu) rnase p in vitro, we examined the role of rpps in influencing substrate recognition by the rpr. we first demonstrate that pfu rpr, like its bacterial and eukaryal counterparts ...	2010	20935047
cleavage of model substrates by archaeal rnase p: role of protein cofactors in cleavage-site selection.	rnase p is a catalytic ribonucleoprotein primarily involved in trna biogenesis. archaeal rnase p comprises a catalytic rnase p rna (rpr) and at least four protein cofactors (rpps), which function as two binary complexes (pop5•rpp30 and rpp21• rpp29). exploiting the ability to assemble a functional pyrococcus furiosus (pfu) rnase p in vitro, we examined the role of rpps in influencing substrate recognition by the rpr. we first demonstrate that pfu rpr, like its bacterial and eukaryal counterparts ...	2010	20935047
antisense tools for functional studies of human argonaute proteins.	the argonaute proteins play essential roles in development and cellular metabolism in many organisms, including plants, flies, worms, and mammals. whereas in organisms such as caenorhabditis elegans and arabidopsis thaliana, creation of argonaute mutant strains allowed the study of their biological functions, in mammals the application of this approach is limited by its difficulty and in the specific case of ago2 gene, by the lethality of such mutation. hence, in human cells, functional studies ...	2010	20935067
crl binds to domain 2 of σ(s) and confers a competitive advantage on a natural rpos mutant of salmonella enterica serovar typhi.	the rpos sigma factor (σ(s)) is the master regulator of the bacterial response to a variety of stresses. mutants in rpos arise in bacterial populations in the absence of stress, probably as a consequence of a subtle balance between self-preservation and nutritional competence. we characterized here one natural rpos mutant of salmonella enterica serovar typhi (ty19). we show that the rpos allele of ty19 (rpos(ty19)) led to the synthesis of a σ(s)(ty19) protein carrying a single glycine-to-valine ...	2010	20935100
archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in trna modification revealed by comparative genomic analysis.	the recent discovery of protein modification by samps, ubiquitin-like (ubl) proteins from the archaeon haloferax volcanii, prompted a comprehensive comparative-genomic analysis of archaeal ubl protein genes and the genes for enzymes thought to be functionally associated with ubl proteins. this analysis showed that most archaea encode members of two major groups of ubl proteins with the β-grasp fold, the this and moad families, and indicated that the this family genes are rarely linked to genes f ...	2010	20936112
visualizing the transfer-messenger rna as the ribosome resumes translation.	bacterial ribosomes stalled by truncated mrnas are rescued by transfer-messenger rna (tmrna), a dual-function molecule that contains a trna-like domain (tld) and an internal open reading frame (orf). occupying the empty a site with its tld, the tmrna enters the ribosome with the help of elongation factor tu and a protein factor called small protein b (smpb), and switches the translation to its own orf. in this study, using cryo-electron microscopy, we obtained the first structure of an in vivo-f ...	2010	20940705
the structure of kpn03535 (gi\|152972051), a novel putative lipoprotein from klebsiella pneumoniae, reveals an ob-fold.	kpn03535 (gi\|152972051) is a putative lipoprotein of unknown function that is secreted by klebsiella pneumoniae mgh 78578. the crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the ob-fold and structurally similar to the bacterial cpx-pathway protein nlpe, single-stranded dna-binding (ssb) proteins and toxins. k. pneumoniae mgh 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pat ...	2010	20944219
the structure of kpn03535 (gi\|152972051), a novel putative lipoprotein from klebsiella pneumoniae, reveals an ob-fold.	kpn03535 (gi\|152972051) is a putative lipoprotein of unknown function that is secreted by klebsiella pneumoniae mgh 78578. the crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the ob-fold and structurally similar to the bacterial cpx-pathway protein nlpe, single-stranded dna-binding (ssb) proteins and toxins. k. pneumoniae mgh 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pat ...	2010	20944219
biochemical characterization of individual components of the allochromatium vinosum dsrmkjop transmembrane complex aids understanding of complex function in vivo.	the dsrmkjop transmembrane complex has a most important function in dissimilatory sulfur metabolism and consists of cytoplasmic, periplasmic, and membrane integral proteins carrying fes centers and b- and c-type cytochromes as cofactors. in this study, the complex was isolated from the purple sulfur bacterium allochromatium vinosum and individual components were characterized as recombinant proteins. the two integral membrane proteins dsrm and dsrp were successfully produced in escherichia coli ...	2010	20952577
tmrna-smpb: a journey to the centre of the bacterial ribosome.	ribosomes mediate protein synthesis by decoding the information carried by messenger rnas (mrnas) and catalysing peptide bond formation between amino acids. when bacterial ribosomes stall on incomplete messages, the trans-translation quality control mechanism is activated by the transfer-messenger rna bound to small protein b (tmrna-smpb ribonucleoprotein complex). trans-translation liberates the stalled ribosomes and triggers degradation of the incomplete proteins. here, we present the cryo-ele ...	2010	20953161
structure of the mycobacterium tuberculosis d-alanine:d-alanine ligase, a target of the antituberculosis drug d-cycloserine.	d-alanine:d-alanine ligase (ec 6.3.2.4; ddl) catalyzes the atp-driven ligation of two d-alanine (d-ala) molecules to form the d-alanyl:d-alanine dipeptide. this molecule is a key building block in peptidoglycan biosynthesis, making ddl an attractive target for drug development. d-cycloserine (dcs), an analog of d-ala and a prototype ddl inhibitor, has shown promise for the treatment of tuberculosis. here, we report the crystal structure of mycobacterium tuberculosis ddl at a resolution of 2.1 å. ...	2010	20956591
structure of the mycobacterium tuberculosis d-alanine:d-alanine ligase, a target of the antituberculosis drug d-cycloserine.	d-alanine:d-alanine ligase (ec 6.3.2.4; ddl) catalyzes the atp-driven ligation of two d-alanine (d-ala) molecules to form the d-alanyl:d-alanine dipeptide. this molecule is a key building block in peptidoglycan biosynthesis, making ddl an attractive target for drug development. d-cycloserine (dcs), an analog of d-ala and a prototype ddl inhibitor, has shown promise for the treatment of tuberculosis. here, we report the crystal structure of mycobacterium tuberculosis ddl at a resolution of 2.1 å. ...	2010	20956591
modification of 16s ribosomal rna by the ksga methyltransferase restructures the 30s subunit to optimize ribosome function.	all organisms incorporate post-transcriptional modifications into ribosomal rna, influencing ribosome assembly and function in ways that are poorly understood. the most highly conserved modification is the dimethylation of two adenosines near the 3' end of the small subunit rrna. lack of these methylations due to deficiency in the ksga methyltransferase stimulates translational errors during both the initiation and elongation phases of protein synthesis and confers resistance to the antibiotic k ...	2010	20962038
new functional sulfide oxidase-oxygen reductase supercomplex in the membrane of the hyperthermophilic bacterium aquifex aeolicus.	aquifex aeolicus, a hyperthermophilic and microaerophilic bacterium, obtains energy for growth from inorganic compounds alone. it was previously proposed that one of the respiratory pathways in this organism consists of the electron transfer from hydrogen sulfide (h(2)s) to molecular oxygen. h(2)s is oxidized by the sulfide quinone reductase, a membrane-bound flavoenzyme, which reduces the quinone pool. we have purified and characterized a novel membrane-bound multienzyme supercomplex that bring ...	2010	20971847
omnipotent role of archaeal elongation factor 1 alpha (ef1α in translational elongation and termination, and quality control of protein synthesis.	the molecular mechanisms of translation termination and mrna surveillance in archaea remain unclear. in eukaryotes, erf3 and hbs1, which are homologous to the trna carrier gtpase ef1α, respectively bind erf1 and pelota to decipher stop codons or to facilitate mrna surveillance. however, genome-wide searches of archaea have failed to detect any orthologs to both gtpases. here, we report the crystal structure of arf1 from an archaeon, aeropyrum pernix, and present strong evidence that the authenti ...	2010	20974926
genomic adaptation of prokaryotic organisms at high temperature.	one of the central issues of evolutionary genomics is to find out the adaptive strategies of microorganisms to stabilize nucleic acid molecules under high temperature. thermal adaptation hypothesis gives a link between g+c content and growth temperature if there is a considerable variation of guanine and cytosine content between species. however, there has been a long-standing debate regarding the correlations between genomic gc content and optimal growth temperature (topt). we urged that adapta ...	2010	20975899
error-prone translesion dna synthesis by escherichia coli dna polymerase iv (dinb) on templates containing 1,2-dihydro-2-oxoadenine.	escherichia coli dna polymerase iv (pol iv) is involved in bypass replication of damaged bases in dna. reactive oxygen species (ros) are generated continuously during normal metabolism and as a result of exogenous stress such as ionizing radiation. ros induce various kinds of base damage in dna. it is important to examine whether pol iv is able to bypass oxidatively damaged bases. in this study, recombinant pol iv was incubated with oligonucleotides containing thymine glycol (dtg), 5-formyluraci ...	2010	20976264
production of cell-cell signalling molecules by bacteria isolated from human chronic wounds.	to (i) identify chronic wound bacteria and to test their ability to produce acyl-homoserine-lactones (ahls) and autoinducer-2 (ai-2) cell-cell signalling molecules and (ii) determine whether chronic wound debridement samples might contain these molecules.	2010	19840177
production of cell-cell signalling molecules by bacteria isolated from human chronic wounds.	to (i) identify chronic wound bacteria and to test their ability to produce acyl-homoserine-lactones (ahls) and autoinducer-2 (ai-2) cell-cell signalling molecules and (ii) determine whether chronic wound debridement samples might contain these molecules.	2010	19840177
direct evidence for nitrogen ligation to the high stability semiquinone intermediate in escherichia coli nitrate reductase a.	the membrane-bound heterotrimeric nitrate reductase a (narghi) catalyzes the oxidation of quinols in the cytoplasmic membrane of escherichia coli and reduces nitrate to nitrite in the cytoplasm. the enzyme strongly stabilizes a menasemiquinone intermediate at a quinol oxidation site (q(d)) located in the vicinity of the distal heme b(d). here molecular details of the interaction between the semiquinone radical and the protein environment have been provided using advanced multifrequency pulsed ep ...	2010	19892705
direct evidence for nitrogen ligation to the high stability semiquinone intermediate in escherichia coli nitrate reductase a.	the membrane-bound heterotrimeric nitrate reductase a (narghi) catalyzes the oxidation of quinols in the cytoplasmic membrane of escherichia coli and reduces nitrate to nitrite in the cytoplasm. the enzyme strongly stabilizes a menasemiquinone intermediate at a quinol oxidation site (q(d)) located in the vicinity of the distal heme b(d). here molecular details of the interaction between the semiquinone radical and the protein environment have been provided using advanced multifrequency pulsed ep ...	2010	19892705
molecular evolution of multisubunit rna polymerases: structural analysis.	comprehensive multiple sequence alignments of the multisubunit dna-dependent rna polymerase (rnap) large subunits, including the bacterial beta and beta' subunits and their homologs from archaebacterial rnaps, eukaryotic rnaps i-iii, nuclear-cytoplasmic large double-stranded dna virus rnaps, and plant plastid rnaps, were created [lane, w. j. and darst, s. a. (2009). molecular evolution of multisubunit rna polymerases: sequence analysis. in press]. the alignments were used to delineate sequence r ...	2010	19895816
molecular evolution of multisubunit rna polymerases: structural analysis.	comprehensive multiple sequence alignments of the multisubunit dna-dependent rna polymerase (rnap) large subunits, including the bacterial beta and beta' subunits and their homologs from archaebacterial rnaps, eukaryotic rnaps i-iii, nuclear-cytoplasmic large double-stranded dna virus rnaps, and plant plastid rnaps, were created [lane, w. j. and darst, s. a. (2009). molecular evolution of multisubunit rna polymerases: sequence analysis. in press]. the alignments were used to delineate sequence r ...	2010	19895816
two distinct regions in staphylococcus aureus gatcab guarantee accurate trna recognition.	in many prokaryotes the biosynthesis of the amide aminoacyl-trnas, gln-trna(gln) and asn-trna(asn), proceeds by an indirect route in which mischarged glu-trna(gln) or asp-trna(asn) is amidated to the correct aminoacyl-trna catalyzed by a trna-dependent amidotransferase (adt). two types of adts exist: bacteria, archaea and organelles possess heterotrimeric gatcab, while heterodimeric gatde occurs exclusively in archaea. bacterial gatcab and gatde recognize the first base pair of the acceptor stem ...	2010	19906721
two distinct regions in staphylococcus aureus gatcab guarantee accurate trna recognition.	in many prokaryotes the biosynthesis of the amide aminoacyl-trnas, gln-trna(gln) and asn-trna(asn), proceeds by an indirect route in which mischarged glu-trna(gln) or asp-trna(asn) is amidated to the correct aminoacyl-trna catalyzed by a trna-dependent amidotransferase (adt). two types of adts exist: bacteria, archaea and organelles possess heterotrimeric gatcab, while heterodimeric gatde occurs exclusively in archaea. bacterial gatcab and gatde recognize the first base pair of the acceptor stem ...	2010	19906721
characterization of chlorophenol 4-monooxygenase (tftd) and nadh:fad oxidoreductase (tftc) of burkholderia cepacia ac1100.	burkholderia cepacia ac1100 completely degrades 2,4,5-trichlorophenol, in which an fadh(2)-dependent monooxygenase (tftd) and an nadh:fad oxidoreductase (tftc) catalyze the initial steps. tftd oxidizes 2,4,5-trichlorophenol (2,4,5-tcp) to 2,5-dichloro-p-benzoquinone, which is chemically reduced to 2,5-dichloro-p-hydroquinone (2,5-dichq). then, tftd oxidizes the latter to 5-chloro-2-hydroxy-p-benzoquinone. in those processes, tftc provides all the required fadh(2). we have determined the crystal ...	2010	19915006
characterization of chlorophenol 4-monooxygenase (tftd) and nadh:fad oxidoreductase (tftc) of burkholderia cepacia ac1100.	burkholderia cepacia ac1100 completely degrades 2,4,5-trichlorophenol, in which an fadh(2)-dependent monooxygenase (tftd) and an nadh:fad oxidoreductase (tftc) catalyze the initial steps. tftd oxidizes 2,4,5-trichlorophenol (2,4,5-tcp) to 2,5-dichloro-p-benzoquinone, which is chemically reduced to 2,5-dichloro-p-hydroquinone (2,5-dichq). then, tftd oxidizes the latter to 5-chloro-2-hydroxy-p-benzoquinone. in those processes, tftc provides all the required fadh(2). we have determined the crystal ...	2010	19915006
unusual diheme conformation of the heme-degrading protein from mycobacterium tuberculosis.	heme degradation plays a pivotal role in the availability of the essential nutrient, iron, in pathogenic bacteria. a previously unannotated protein from mycobacterium tuberculosis, rv3592, which shares homology to heme-degrading enzymes, has been identified. biochemical analyses confirm that rv3592, which we have termed mhud (mycobacterial heme utilization, degrader), is able to bind and degrade heme. interestingly, contrary to previously reported stoichiometry for the staphylococcus aureus heme ...	2010	19917297
unusual diheme conformation of the heme-degrading protein from mycobacterium tuberculosis.	heme degradation plays a pivotal role in the availability of the essential nutrient, iron, in pathogenic bacteria. a previously unannotated protein from mycobacterium tuberculosis, rv3592, which shares homology to heme-degrading enzymes, has been identified. biochemical analyses confirm that rv3592, which we have termed mhud (mycobacterial heme utilization, degrader), is able to bind and degrade heme. interestingly, contrary to previously reported stoichiometry for the staphylococcus aureus heme ...	2010	19917297
analysis of acyclic nucleoside modifications in sirnas finds sensitivity at position 1 that is restored by 5'-terminal phosphorylation both in vitro and in vivo.	small interfering rnas (sirnas) are short, double-stranded rnas that use the endogenous rnai pathway to mediate gene silencing. phosphorylation facilitates loading of a sirna into the ago2 complex and subsequent cleavage of the target mrna. in this study, 2', 3' seco nucleoside modifications, which contain an acylic ribose ring and are commonly called unlocked nucleic acids (unas), were evaluated at all positions along the guide strand of a sirna targeting apolipoprotein b (apob). una modificati ...	2010	19917641
analysis of acyclic nucleoside modifications in sirnas finds sensitivity at position 1 that is restored by 5'-terminal phosphorylation both in vitro and in vivo.	small interfering rnas (sirnas) are short, double-stranded rnas that use the endogenous rnai pathway to mediate gene silencing. phosphorylation facilitates loading of a sirna into the ago2 complex and subsequent cleavage of the target mrna. in this study, 2', 3' seco nucleoside modifications, which contain an acylic ribose ring and are commonly called unlocked nucleic acids (unas), were evaluated at all positions along the guide strand of a sirna targeting apolipoprotein b (apob). una modificati ...	2010	19917641
molecular modeling of the bifunctional enzyme udp-glcnac 2-epimerase/mannac kinase and predictions of structural effects of mutations associated with hibm and sialuria.	the bifunctional enzyme udp-glcnac 2-epimerase/ mannac kinase (gne/mnk), encoded by the gne gene, catalyzes the first two committed, rate-limiting steps in the biosynthesis of n-acetylneuraminic acid (sialic acid). gne/mnk is feedback inhibited by binding of the downstream product, cmp-sialic acid in its allosteric site. gne mutations can result in two human disorders, hereditary inclusion body myopathy (hibm) or sialuria. so far, no active site geometry predictions or conformational transitions ...	2010	19917666
molecular modeling of the bifunctional enzyme udp-glcnac 2-epimerase/mannac kinase and predictions of structural effects of mutations associated with hibm and sialuria.	the bifunctional enzyme udp-glcnac 2-epimerase/ mannac kinase (gne/mnk), encoded by the gne gene, catalyzes the first two committed, rate-limiting steps in the biosynthesis of n-acetylneuraminic acid (sialic acid). gne/mnk is feedback inhibited by binding of the downstream product, cmp-sialic acid in its allosteric site. gne mutations can result in two human disorders, hereditary inclusion body myopathy (hibm) or sialuria. so far, no active site geometry predictions or conformational transitions ...	2010	19917666
protein-precursor trna contact leads to sequence-specific recognition of 5' leaders by bacterial ribonuclease p.	bacterial ribonuclease p (rnase p) catalyzes the cleavage of 5' leader sequences from precursor trnas (pre-trnas). previously, all known substrate nucleotide specificities in this system are derived from rna-rna interactions with the rnase p rna subunit. here, we demonstrate that pre-trna binding affinities for bacillus subtilis and escherichia coli rnase p are enhanced by sequence-specific contacts between the fourth pre-trna nucleotide on the 5' side of the cleavage site (n(-4)) and the rnase ...	2010	19932118
protein-precursor trna contact leads to sequence-specific recognition of 5' leaders by bacterial ribonuclease p.	bacterial ribonuclease p (rnase p) catalyzes the cleavage of 5' leader sequences from precursor trnas (pre-trnas). previously, all known substrate nucleotide specificities in this system are derived from rna-rna interactions with the rnase p rna subunit. here, we demonstrate that pre-trna binding affinities for bacillus subtilis and escherichia coli rnase p are enhanced by sequence-specific contacts between the fourth pre-trna nucleotide on the 5' side of the cleavage site (n(-4)) and the rnase ...	2010	19932118
n7-methylguanine at position 46 (m7g46) in trna from thermus thermophilus is required for cell viability at high temperatures through a trna modification network.	n(7)-methylguanine at position 46 (m(7)g46) in trna is produced by trna (m(7)g46) methyltransferase (trmb). to clarify the role of this modification, we made a trmb gene disruptant (deltatrmb) of thermus thermophilus, an extreme thermophilic eubacterium. the absence of trmb activity in cell extract from the deltatrmb strain and the lack of the m(7)g46 modification in trna(phe) were confirmed by enzyme assay, nucleoside analysis and rna sequencing. when the deltatrmb strain was cultured at high t ...	2010	19934251
solution structures and backbone dynamics of the ribosomal protein s6 and its permutant p(54-55).	the ribosomal protein s6 from thermus thermophilus has served as a model system for the study of protein folding, especially for understanding the effects of circular permutations of secondary structure elements. this study presents the structure of a permutant protein, the 96-residue p(54-55), and the structure of its 101-residue parent protein s6(wt) in solution. the data also characterizes the effects of circular permutation on the backbone dynamics of s6. consistent with crystallographic dat ...	2010	19937661
catalytic mechanism of human alpha-galactosidase.	the enzyme alpha-galactosidase (alpha-gal, also known as alpha-gal a; e.c. 3.2.1.22) is responsible for the breakdown of alpha-galactosides in the lysosome. defects in human alpha-gal lead to the development of fabry disease, a lysosomal storage disorder characterized by the buildup of alpha-galactosylated substrates in the tissues. alpha-gal is an active target of clinical research: there are currently two treatment options for fabry disease, recombinant enzyme replacement therapy (approved in ...	2010	19940122
catalytic mechanism of human alpha-galactosidase.	the enzyme alpha-galactosidase (alpha-gal, also known as alpha-gal a; e.c. 3.2.1.22) is responsible for the breakdown of alpha-galactosides in the lysosome. defects in human alpha-gal lead to the development of fabry disease, a lysosomal storage disorder characterized by the buildup of alpha-galactosylated substrates in the tissues. alpha-gal is an active target of clinical research: there are currently two treatment options for fabry disease, recombinant enzyme replacement therapy (approved in ...	2010	19940122
trna-dependent pre-transfer editing by prokaryotic leucyl-trna synthetase.	to prevent genetic code ambiguity due to misincorporation of amino acids into proteins, aminoacyl-trna synthetases have evolved editing activities to eliminate intermediate or final non-cognate products. in this work we studied the different editing pathways of class ia leucyl-trna synthetase (leurs). different mutations and experimental conditions were used to decipher the editing mechanism, including the recently developed compound an2690 that targets the post-transfer editing site of leurs. t ...	2010	19940155
trna-dependent pre-transfer editing by prokaryotic leucyl-trna synthetase.	to prevent genetic code ambiguity due to misincorporation of amino acids into proteins, aminoacyl-trna synthetases have evolved editing activities to eliminate intermediate or final non-cognate products. in this work we studied the different editing pathways of class ia leucyl-trna synthetase (leurs). different mutations and experimental conditions were used to decipher the editing mechanism, including the recently developed compound an2690 that targets the post-transfer editing site of leurs. t ...	2010	19940155
peptide-based antibodies against glutathione-binding domains suppress superoxide production mediated by mitochondrial complex i.	complex i (nqr) is a critical site of superoxide (o2-*) production and the major host of redox protein thiols in mitochondria. in response to oxidative stress, nqr-derived protein thiols at the 51- and 75-kda subunits are known to be reversibly s-glutathionylated. although several glutathionylated domains from nqr 51 and 75 kda have been identified, their roles in the regulatory functions remain to be explored. to gain further insights into protein s-glutathionylation of complex i, we used two p ...	2010	19940158
peptide-based antibodies against glutathione-binding domains suppress superoxide production mediated by mitochondrial complex i.	complex i (nqr) is a critical site of superoxide (o2-*) production and the major host of redox protein thiols in mitochondria. in response to oxidative stress, nqr-derived protein thiols at the 51- and 75-kda subunits are known to be reversibly s-glutathionylated. although several glutathionylated domains from nqr 51 and 75 kda have been identified, their roles in the regulatory functions remain to be explored. to gain further insights into protein s-glutathionylation of complex i, we used two p ...	2010	19940158
solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase.	due to its potential as an antibiotic target, e. coli peptide deformylase (pdf(ec)) serves as a model enzyme system for inhibitor design. while investigating the structural-functional and inhibitory features of this enzyme, we unexpectedly discovered that 2-amino-5-mercapto-1,3,4-thiadiazole (amt) served as a slow-binding inhibitor of pdf(ec) when the above compound was dissolved only in dimethylformamide (dmf), but not in any other solvent, and allowed to age. the time dependent inhibitory pote ...	2010	19922819
solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase.	due to its potential as an antibiotic target, e. coli peptide deformylase (pdf(ec)) serves as a model enzyme system for inhibitor design. while investigating the structural-functional and inhibitory features of this enzyme, we unexpectedly discovered that 2-amino-5-mercapto-1,3,4-thiadiazole (amt) served as a slow-binding inhibitor of pdf(ec) when the above compound was dissolved only in dimethylformamide (dmf), but not in any other solvent, and allowed to age. the time dependent inhibitory pote ...	2010	19922819
structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis.	nonribosomal peptide synthetases (nrpss) are large, multidomain proteins that are involved in the biosynthesis of an array of secondary metabolites. we report the structure of the third adenylation domain from the siderophore-synthesizing nrps, sidn, from the endophytic fungus neotyphodium lolii. this is the first structure of a eukaryotic nrps domain, and it reveals a large binding pocket required to accommodate the unusual amino acid substrate, n(delta)-cis-anhydromevalonyl-n(delta)-hydroxy-l- ...	2010	19923209
structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis.	nonribosomal peptide synthetases (nrpss) are large, multidomain proteins that are involved in the biosynthesis of an array of secondary metabolites. we report the structure of the third adenylation domain from the siderophore-synthesizing nrps, sidn, from the endophytic fungus neotyphodium lolii. this is the first structure of a eukaryotic nrps domain, and it reveals a large binding pocket required to accommodate the unusual amino acid substrate, n(delta)-cis-anhydromevalonyl-n(delta)-hydroxy-l- ...	2010	19923209
crystal structure of pyrococcus horikoshii tryptophanyl-trna synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-trna synthetase.	the ancient and ubiquitous aminoacyl-trna synthetases constitute a valuable model system for studying early evolutionary events. so far, the evolutionary relationship of tryptophanyl- and tyrosyl-trna synthetase (trprs and tyrrs) remains controversial. as trprs and tyrrs share low sequence homology but high structural similarity, a structure-based method would be advantageous for phylogenetic analysis of the enzymes. here, we present the first crystal structure of an archaeal trprs, the structur ...	2010	19942682
crystal structure of pyrococcus horikoshii tryptophanyl-trna synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-trna synthetase.	the ancient and ubiquitous aminoacyl-trna synthetases constitute a valuable model system for studying early evolutionary events. so far, the evolutionary relationship of tryptophanyl- and tyrosyl-trna synthetase (trprs and tyrrs) remains controversial. as trprs and tyrrs share low sequence homology but high structural similarity, a structure-based method would be advantageous for phylogenetic analysis of the enzymes. here, we present the first crystal structure of an archaeal trprs, the structur ...	2010	19942682
stereochemical mechanisms of trna methyltransferases.	methylation of trna on the four canonical bases adds structural complexity to the molecule, and improves decoding specificity and efficiency. while many trna methylases are known, detailed insight into the catalytic mechanism is only available in a few cases. of interest among all trna methylases is the structural basis for nucleotide selection, by which the specificity is limited to a single site, or broadened to multiple sites. general themes in catalysis include the basis for rate acceleratio ...	2010	19944101
synergistic cooperation between two clpb isoforms in aggregate reactivation.	bacterial aaa+ atpase clpb cooperates with dnak during reactivation of aggregated proteins. the clpb-mediated disaggregation is linked to translocation of polypeptides through the channel in the oligomeric clpb. two isoforms of clpb are produced in vivo: the full-length clpb95 and clpb80, which does not contain the substrate-interacting n-terminal domain. the biological role of the truncated isoform clpb80 is unknown. we found that resolubilization of aggregated proteins in escherichia coli afte ...	2010	19961856
synergistic cooperation between two clpb isoforms in aggregate reactivation.	bacterial aaa+ atpase clpb cooperates with dnak during reactivation of aggregated proteins. the clpb-mediated disaggregation is linked to translocation of polypeptides through the channel in the oligomeric clpb. two isoforms of clpb are produced in vivo: the full-length clpb95 and clpb80, which does not contain the substrate-interacting n-terminal domain. the biological role of the truncated isoform clpb80 is unknown. we found that resolubilization of aggregated proteins in escherichia coli afte ...	2010	19961856
the effect of spermine on the initiation of mitochondrial protein synthesis.	polyamines are important in both prokaryotic and eukaryotic translational systems. spermine is a quaternary aliphatic amine that is cationic under physiological conditions. in this paper, we demonstrate that spermine stimulates fmet-trna binding to mammalian mitochondrial 55s ribosomes. the stimulatory effect of spermine is independent of the identity of the mrna. the degree of stimulation of spermine is the same at all concentrations of mitochondrial initiation factor 2 (if2(mt)) and mitochondr ...	2010	19962967
the effect of spermine on the initiation of mitochondrial protein synthesis.	polyamines are important in both prokaryotic and eukaryotic translational systems. spermine is a quaternary aliphatic amine that is cationic under physiological conditions. in this paper, we demonstrate that spermine stimulates fmet-trna binding to mammalian mitochondrial 55s ribosomes. the stimulatory effect of spermine is independent of the identity of the mrna. the degree of stimulation of spermine is the same at all concentrations of mitochondrial initiation factor 2 (if2(mt)) and mitochondr ...	2010	19962967
lcca, an archaeal laccase secreted as a highly stable glycoprotein into the extracellular medium by haloferax volcanii.	laccases couple the oxidation of phenolic compounds to the reduction of molecular oxygen and thus span a wide variety of applications. while laccases of eukaryotes and bacteria are well characterized, these enzymes have not been described in archaea. here, we report the purification and characterization of a laccase (lcca) from the halophilic archaeon haloferax volcanii. lcca was secreted at high levels into the culture supernatant of a recombinant h. volcanii strain, with peak activity (170 +/- ...	2010	19966030
lcca, an archaeal laccase secreted as a highly stable glycoprotein into the extracellular medium by haloferax volcanii.	laccases couple the oxidation of phenolic compounds to the reduction of molecular oxygen and thus span a wide variety of applications. while laccases of eukaryotes and bacteria are well characterized, these enzymes have not been described in archaea. here, we report the purification and characterization of a laccase (lcca) from the halophilic archaeon haloferax volcanii. lcca was secreted at high levels into the culture supernatant of a recombinant h. volcanii strain, with peak activity (170 +/- ...	2010	19966030
the structure of the proline utilization a proline dehydrogenase domain inactivated by n-propargylglycine provides insight into conformational changes induced by substrate binding and flavin reduction.	proline utilization a (puta) from escherichia coli is a flavoprotein that has mutually exclusive roles as a transcriptional repressor of the put regulon and a membrane-associated enzyme that catalyzes the oxidation of proline to glutamate. previous studies have shown that the binding of proline in the proline dehydrogenase (prodh) active site and subsequent reduction of the fad trigger global conformational changes that enhance puta-membrane affinity. these events cause puta to switch from its r ...	2010	19994913
the effect of primer-template mismatches on the detection and quantification of nucleic acids using the 5' nuclease assay.	real-time polymerase chain reaction (pcr) is the current method of choice for detection and quantification of nucleic acids, especially for molecular diagnostics. complementarity between primers and template is often crucial for pcr applications, as mismatches can severely reduce priming efficiency. however, little quantitative data on the effect of these mismatches is available. we quantitatively investigated the effects of primer-template mismatches within the 3'-end primer region on real-time ...	2010	19948821
dynamics of the base of ribosomal a-site finger revealed by molecular dynamics simulations and cryo-em.	helix 38 (h38) of the large ribosomal subunit, with a length of 110 a, reaches the small subunit through intersubunit bridge b1a. previous cryo-em studies revealed that the tip of h38 moves by more than 10 a from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible h38 in attenuation of translocation and in dynamical signaling between ribosomal functional centers. we investigate a region including the elbow-shaped kink-turn (kt-38) i ...	2010	19952067