| three genomes from the phylum acidobacteria provide insight into the lifestyles of these microorganisms in soils. | the complete genomes of three strains from the phylum acidobacteria were compared. phylogenetic analysis placed them as a unique phylum. they share genomic traits with members of the proteobacteria, the cyanobacteria, and the fungi. the three strains appear to be versatile heterotrophs. genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. the genomes encode low-specificity major facilitator ... | 2009 | 19201974 |
| three-dimensional structure of a1a0 atp synthase from the hyperthermophilic archaeon pyrococcus furiosus by electron microscopy. | the archaeal atp synthase is a multisubunit complex that consists of a catalytic a(1) part and a transmembrane, ion translocation domain a(0). the a(1)a(0) complex from the hyperthermophile pyrococcus furiosus was isolated. mass analysis of the complex by laser-induced liquid bead ion desorption (lilbid) indicated a size of 730 +/- 10 kda. a three-dimensional map was generated by electron microscopy from negatively stained images. the map at a resolution of 2.3 nm shows the a(1) and a(0) domain, ... | 2009 | 19203996 |
| characterization of dna polymerase x from thermus thermophilus hb8 reveals the polxc and php domains are both required for 3'-5' exonuclease activity. | the x-family dna polymerases (polxs) comprise a highly conserved dna polymerase family found in all kingdoms. mammalian polxs are known to be involved in several dna-processing pathways including repair, but the cellular functions of bacterial polxs are less known. many bacterial polxs have a polymerase and histidinol phosphatase (php) domain at their c-termini in addition to a polx core (polxc) domain, and possess 3'-5' exonuclease activity. although both domains are highly conserved in bacteri ... | 2009 | 19211662 |
| functional expression of a bacterial xylose isomerase in saccharomyces cerevisiae. | in industrial fermentation processes, the yeast saccharomyces cerevisiae is commonly used for ethanol production. however, it lacks the ability to ferment pentose sugars like d-xylose and l-arabinose. heterologous expression of a xylose isomerase (xi) would enable yeast cells to metabolize xylose. however, many attempts to express a prokaryotic xi with high activity in s. cerevisiae have failed so far. we have screened nucleic acid databases for sequences encoding putative xis and finally were a ... | 2009 | 19218403 |
| characterization of a mimivirus rna cap guanine-n2 methyltransferase. | a 2,2,7-trimethylguanosine (tmg) cap is a signature feature of eukaryal snrnas, telomerase rnas, and trans-spliced nematode mrnas. tmg and 2,7-dimethylguanosine (dmg) caps are also present on mrnas of two species of alphaviruses (positive strand rna viruses of the togaviridae family). it is presently not known how viral mrnas might acquire a hypermethylated cap. mimivirus, a giant dna virus that infects amoeba, encodes many putative enzymes and proteins implicated in rna transactions, including ... | 2009 | 19218551 |
| reduction of hydrophilic ubiquinones by the flavin in mitochondrial nadh:ubiquinone oxidoreductase (complex i) and production of reactive oxygen species. | nadh:ubiquinone oxidoreductase (complex i) from bovine heart mitochondria is a complicated, energy-transducing, membrane-bound enzyme that contains 45 different subunits, a non-covalently bound flavin mononucleotide, and eight iron-sulfur clusters. the mechanisms of nadh oxidation and intramolecular electron transfer by complex i are gradually being defined, but the mechanism linking ubiquinone reduction to proton translocation remains unknown. studies of ubiquinone reduction by isolated complex ... | 2009 | 19220002 |
| a genetic screen for components of the mammalian rna interference pathway in bloom-deficient mouse embryonic stem cells. | genetic screens performed in model organisms have helped identify key components of the rna interference (rnai) pathway. recessive genetic screens have recently become feasible through the use of mouse embryonic stem (es) cells that are bloom's syndrome protein (blm) deficient. here, we developed and performed a recessive genetic screen to identify components of the mammalian rnai pathway in blm-deficient es cells. genome-wide mutagenesis using a retroviral gene trap strategy resulted in the iso ... | 2009 | 19223321 |
| dodecin is the key player in flavin homeostasis of archaea. | flavins are employed to transform physical input into biological output signals. in this function, flavins catalyze a variety of light-induced reactions and redox processes. however, nature also provides flavoproteins with the ability to uncouple the mediation of signals. such proteins are the riboflavin-binding proteins (rfbps) with their function to store riboflavin for fast delivery of fmn and fad. here we present in vitro and in vivo data showing that the recently discovered archaeal dodecin ... | 2009 | 19224924 |
| idiosyncratic helix-turn-helix motif in methanosarcina barkeri seryl-trna synthetase has a critical architectural role. | all seryl-trna synthetases (serrss) are functional homodimers with a c-terminal active site domain typical for class ii aminoacyl-trna synthetases and an n-terminal domain involved in trna binding. the recently solved three-dimensional structure of methanosarcina barkeri serrs revealed the idiosyncratic features of methanogenic-type serrss; that is, an active site zinc ion, a unique trna binding domain, and an insertion of approximately 30 residues in the catalytic domain, which adopt a helix-tu ... | 2009 | 19228694 |
| gtpase activation of elongation factor ef-tu by the ribosome during decoding. | we have used single-particle reconstruction in cryo-electron microscopy to determine a structure of the thermus thermophilus ribosome in which the ternary complex of elongation factor tu (ef-tu), trna and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. this represents the state in the decoding process just after codon recognition by trna and the resulting gtp hydrolysis by ef-tu, but before the release of ef-tu from the ribosome. progress in sample purificati ... | 2009 | 19229291 |
| a molybdopterin oxidoreductase is involved in h2 oxidation in desulfovibrio desulfuricans g20. | three mutants deficient in hydrogen/formate uptake were obtained through screening of a transposon mutant library containing 5,760 mutants of desulfovibrio desulfuricans g20. mutations were in the genes encoding the type i tetraheme cytochrome c(3) (cyca), fe hydrogenase (hydb), and molybdopterin oxidoreductase (mopb). mutations did not decrease the ability of cells to produce h(2) or formate during growth. complementation of the cyca and mopb mutants with a plasmid carrying the intact cyca and/ ... | 2009 | 19233927 |
| stimulation of expression of a silica-induced protein (sip) in thermus thermophilus by supersaturated silicic acid. | the effects of silicic acid on the growth of thermus thermophilus tmy, an extreme thermophile isolated from a siliceous deposit formed from geothermal water at a geothermal power plant in japan, were examined at 75 degrees c. at concentrations higher than the solubility of amorphous silica (400 to 700 ppm sio(2)), a silica-induced protein (sip) was isolated from the cell envelope fraction of log-phase tmy cells grown in the presence of supersaturated silicic acid. two-dimensional sodium dodecyl ... | 2009 | 19233950 |
| domain architecture of the stator complex of the a1a0-atp synthase from thermoplasma acidophilum. | a key structural element in the ion translocating f-, a-, and v-atpases is the peripheral stalk, an assembly of two polypeptides that provides a structural link between the atpase and ion channel domains. previously, we have characterized the peripheral stalk forming subunits e and h of the a-atpase from thermoplasma acidophilum and demonstrated that the two polypeptides interact to form a stable heterodimer with 1:1 stoichiometry (kish-trier, e., briere, l. k., dunn, s. d., and wilkens, s. (200 ... | 2009 | 19234304 |
| improving the functional expression of a bacillus licheniformis laccase by random and site-directed mutagenesis. | laccases have huge potential for biotechnological applications due to their broad substrate spectrum and wide range of reactions they are able to catalyze. these include, for example, the formation and degradation of dimers, oligomers, polymers, and ring cleavage as well as oxidation of aromatic compounds. potential applications of laccases include detoxification of industrial effluents, decolorization of textile dyes and the synthesis of natural products by, for instance, dimerization of phenol ... | 2009 | 19236694 |
| structures of alternatively spliced isoforms of human ketohexokinase. | a molecular understanding of the unique aspects of dietary fructose metabolism may be the key to understanding and controlling the current epidemic of fructose-related obesity, diabetes and related adverse metabolic states in western populations. fructose catabolism is initiated by its phosphorylation to fructose 1-phosphate, which is performed by ketohexokinase (khk). here, the crystal structures of the two alternatively spliced isoforms of human ketohexokinase, hepatic khk-c and the peripheral ... | 2009 | 19237742 |
| dna uracil repair initiated by the archaeal exoiii homologue mth212 via direct strand incision. | no genes for any of the known uracil dna glycosylases of the udg superfamily are present in the genome of methanothermobacter thermautotrophicus deltah, making it difficult to imagine how dna-u repair might be initiated in this organism. recently, mth212, the exoiii homologue of m. thermautotrophicus deltah has been characterized as a dna uridine endonuclease, which suggested the possibility of a novel endonucleolytic entry mechanism for dna uracil repair. with no system of genetic experimentati ... | 2009 | 19240141 |
| involvement of a carboxylated lysine in uv damage endonuclease. | uv damage endonuclease is a dna repair enzyme that can both recognize damage such as uv lesions and introduce a nick directly 5' to them. recently, the crystal structure of the enzyme from thermus thermophilus was solved. in the electron density map of this structure, unexplained density near the active site was observed at the tip of lys229. based on this finding, it was proposed that lys229 is post-translationally modified. in this article, we give evidence that this modification is a carboxyl ... | 2009 | 19241382 |
| allopatric speciation in ticks: genetic and reproductive divergence between geographic strains of rhipicephalus (boophilus) microplus. | the cattle tick, rhipicephalus (boophilus) microplus, economically impact cattle industry in tropical and subtropical regions of the world. the morphological and genetic differences among r. microplus strains have been documented in the literature, suggesting that biogeographical and ecological separation may have resulted in boophilid ticks from america/africa and those from australia being different species. to test the hypothesis of the presence of different boophilid species, herein we perfo ... | 2009 | 19243585 |
| identification of neisserial dna binding components. | neisseria meningitidis, a causative agent of meningitis and septicaemia, expresses type iv pili, a feature correlating with the uptake of exogenous dna from the environment by natural transformation. the outer membrane complex pilq, through which pili are extruded and retracted, has previously been shown to bind dna in its pore region. in order to further elucidate how dna is transported across the membranes, we searched for dna binding proteins within the meningococcal inner membrane. inner mem ... | 2009 | 19246756 |
| the family x dna polymerase from deinococcus radiodurans adopts a non-standard extended conformation. | deinococcus radiodurans is an extraordinarily radioresistant bacterium that is able to repair hundreds of radiation-induced double-stranded dna breaks. one of the players in this pathway is an x family dna polymerase (polx(dr)). deletion of polx(dr) has been shown to decrease the rate of repair of double-stranded dna breaks and increase cell sensitivity to gamma-rays. a 3'-->5' exonuclease activity that stops cutting close to dna loops has also been demonstrated. the present crystal structure of ... | 2009 | 19251692 |
| crystallization and preliminary characterization of the thermus thermophilus rna helicase hera c-terminal domain. | heat-resistant rna-dependent atpase (hera) from thermus thermophilus is a dead-box rna helicase. two constructs encompassing the second reca-like domain and the c-terminal domain of hera were overproduced in escherichia coli and purified to homogeneity. single crystals of both hera constructs were obtained in three crystal forms. a tetragonal crystal form belonged to space group p4(1)2(1)2, with unit-cell parameters a = 65.5, c = 153.0 a, and contained one molecule per asymmetric unit. two ortho ... | 2009 | 19255475 |
| defects in transient trna translocation bypass trna synthetase quality control mechanisms. | quality control mechanisms during protein synthesis are essential to fidelity and cell survival. leucyl-trna synthetase (leurs) misactivates non-leucine amino acids including isoleucine, methionine, and norvaline. to prevent translational errors, mischarged trna products are translocated 30a from the canonical aminoacylation core to a hydrolytic editing-active site within a completely separate domain. because it is transient, the trna translocation mechanism has been difficult to isolate. we hav ... | 2009 | 19258309 |
| contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis. | superoxide dismutase (sod) enzymes are critical in controlling levels of reactive oxygen species (ros) that are linked to aging, cancer, and neurodegenerative disease. superoxide (o(2)(*-)) produced during respiration is removed by the product of the sod2 gene, the homotetrameric manganese superoxide dismutase (mnsod). here, we examine the structural and catalytic roles of the highly conserved active-site residue tyr34, based upon structure-function studies of mnsod enzymes with mutations at thi ... | 2009 | 19265433 |
| a novel endo-hydrogenase activity recycles hydrogen produced by nitrogen fixation. | nitrogen (n(2)) fixation also yields hydrogen (h(2)) at 1:1 stoichiometric amounts. in aerobic diazotrophic (able to grow on n(2) as sole n-source) bacteria, orthodox respiratory hupsl-encoded hydrogenase activity, associated with the cell membrane but facing the periplasm (exo-hydrogenase), has nevertheless been presumed responsible for recycling such endogenous hydrogen. | 2009 | 19277114 |
| a recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center. | the ribosome is an ancient macromolecular machine responsible for the synthesis of all proteins in all living organisms. here we demonstrate that the ribosomal peptidyl transferase center (ptc) is supported by a framework of magnesium microclusters (mg(2+)-muc's). common features of mg(2+)-muc's include two paired mg(2+) ions that are chelated by a common bridging phosphate group in the form mg((a))(2+)-(o1p-p-o2p)-mg((b))(2+). this bridging phosphate is part of a 10-membered chelation ring in t ... | 2009 | 19279186 |
| an archaeal rad54 protein remodels dna and stimulates dna strand exchange by rada. | rad54 protein is a key member of the rad52 epistasis group required for homologous recombination in eukaryotes. rad54 is a duplex dna translocase that remodels both dna and protein-dna complexes, and functions at multiple steps in the recombination process. here we use biochemical criteria to demonstrate the existence of this important protein in a prokaryotic organism. the sulfolobus solfataricus rad54 (ssorad54) protein is a double-strand dna-dependent atpase that can alter the topology of dup ... | 2009 | 19282450 |
| the complete genome and proteome of laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. | laribacter hongkongensis is a newly discovered gram-negative bacillus of the neisseriaceae family associated with freshwater fish-borne gastroenteritis and traveler's diarrhea. the complete genome sequence of l. hongkongensis hlhk9, recovered from an immunocompetent patient with severe gastroenteritis, consists of a 3,169-kb chromosome with g+c content of 62.35%. genome analysis reveals different mechanisms potentially important for its adaptation to diverse habitats of human and freshwater fish ... | 2009 | 19283063 |
| the genome of bacillus subtilis bacteriophage spo1. | we report the genome sequence of bacillus subtilis phage spo1. the unique genome sequence is 132,562 bp long, and dna packaged in the virion (the chromosome) has a 13,185-bp terminal redundancy, giving a total of 145,747 bp. we predict 204 protein-coding genes and 5 trna genes, and we correlate these findings with the extensive body of investigations of spo1, including studies of the functions of the 61 previously defined genes and studies of the virion structure. sixty-nine percent of the encod ... | 2009 | 19285085 |
| structural rearrangements in the active site of the thermus thermophilus 16s rrna methyltransferase ksga in a binary complex with 5'-methylthioadenosine. | posttranscriptional modification of ribosomal rna (rrna) occurs in all kingdoms of life. the s-adenosyl-l-methionine-dependent methyltransferase ksga introduces the most highly conserved rrna modification, the dimethylation of a1518 and a1519 of 16s rrna. loss of this dimethylation confers resistance to the antibiotic kasugamycin. here, we report biochemical studies and high-resolution crystal structures of ksga from thermus thermophilus. methylation of 30s ribosomal subunits by t. thermophilus ... | 2009 | 19285505 |
| resampling and editing of mischarged trna prior to translation elongation. | faithful translation of the genetic code depends on the gtpase ef-tu delivering correctly charged aminoacyl-trnas to the ribosome for pairing with cognate codons. the accurate coupling of cognate amino acids and trnas by the aminoacyl-trna synthetases is achieved through a combination of substrate specificity and product editing. once released by aminoacyl-trna synthetases, both cognate and near-cognate aminoacyl-trnas were considered to be committed to ribosomal protein synthesis through their ... | 2009 | 19285947 |
| structure and function of a campylobacter jejuni thioesterase cj0915, a hexameric hot dog fold enzyme. | acyl-coenzyme a (coa) thioesterases are a large family of enzymes that hydrolyze acyl-coa esters to the free fatty acid and coa and thereby regulate essential cellular functions such as lipid metabolism, membrane synthesis, signal transduction, and gene transcription. to better understand the virulence mechanisms of campylobacter jejuni, and its possible link to membrane lipid biosynthesis, we have investigated c. jejuni thioesterases, annotated as putative proteins. while little is known about ... | 2009 | 19303060 |
| mutational analysis of mycobacterium uvrd1 identifies functional groups required for atp hydrolysis, dna unwinding, and chemomechanical coupling. | mycobacterial uvrd1 is a dna-dependent atpase and a ku-dependent 3' to 5' dna helicase. the uvrd1 motor domain resembles that of the prototypal superfamily i helicases uvrd and pcra. here we performed a mutational analysis of uvrd1 guided by the crystal structure of a dna-bound escherichia coli uvrd-adp-mgf(3) transition state mimetic. alanine scanning and conservative substitutions identified amino acids essential for both atp hydrolysis and duplex unwinding, including those implicated in phosp ... | 2009 | 19317511 |
| maintenance of rna-dna hybrid length in bacterial rna polymerases. | during transcription elongation the nascent rna remains base-paired to the template strand of the dna before it is displaced and the two strands of the dna reanneal, resulting in the formation of a transcription "bubble" of approximately 10 bp. to examine how the length of the rna-dna hybrid is maintained, we assembled transcription elongation complexes on synthetic nucleic acid scaffolds that mimic the situation in which transcript displacement is compromised and the polymerase synthesizes an e ... | 2009 | 19321439 |
| connection between stop codon reassignment and frequent use of shifty stop frameshifting. | ciliated protozoa of the genus euplotes have undergone genetic code reassignment, redefining the termination codon uga to encode cysteine. in addition, euplotes spp. genes very frequently employ shifty stop frameshifting. both of these phenomena involve noncanonical events at a termination codon, suggesting they might have a common cause. we recently demonstrated that euplotes octocarinatus peptide release factor erf1 ignores uga termination codons while continuing to recognize uaa and uag. here ... | 2009 | 19329535 |
| parb deficiency in pseudomonas aeruginosa destabilizes the partner protein para and affects a variety of physiological parameters. | deletions leading to complete or partial removal of parb were introduced into the pseudomonas aeruginosa chromosome. fluorescence microscopy of fixed cells showed that parb mutants lacking the c-terminal domain or hth motif formed multiple, less intense foci scattered irregularly, in contrast to the one to four parb foci per cell symmetrically distributed in wild-type p. aeruginosa. all parb mutations affected both bacterial growth and swarming and swimming motilities, and increased the producti ... | 2009 | 19332810 |
| structural insight into the inhibition of human kynurenine aminotransferase i/glutamine transaminase k. | human kynurenine aminotransferase i (hkat i) catalyzes the formation of kynurenic acid, a neuroactive compound. here, we report three high-resolution crystal structures (1.50-1.55 a) of hkat i that are in complex with glycerol and each of two inhibitors of hkat i: indole-3-acetic acid (iac) and tris. because tris is able to occupy the substrate binding position, we speculate that this may be the basis for hkat i inhibition. furthermore, the hkat/iac complex structure reveals that the binding moi ... | 2009 | 19338303 |
| degradation of ppgpp by nudix pyrophosphatase modulates the transition of growth phase in the bacterium thermus thermophilus. | a major bacterial alarmone, guanosine 3',5'-bispyrophosphate (ppgpp), controls cellular growth under conditions of nutritional starvation. for most bacteria, intracellular ppgpp levels are tightly controlled by the synthesis/degradation cycle of rela and spot activities. this study shows a novel ppgpp regulatory protein governing the cellular growth of thermus thermophilus, ndx8, a member of the nudix pyrophosphatase family that degrades ppgpp to yield guanosine 3',5'-bisphosphate. the ndx8-null ... | 2009 | 19346251 |
| three-dimensional structure and enzymatic function of proapoptotic human p53-inducible quinone oxidoreductase pig3. | tumor suppressor p53 regulates the expression of p53-induced genes (pig) that trigger apoptosis. pig3 or tp53i3 is the only known member of the medium chain dehydrogenase/reductase superfamily induced by p53 and is used as a proapoptotic marker. although the participation of pig3 in the apoptotic pathway is proven, the protein and its mechanism of action were never characterized. we analyzed human pig3 enzymatic function and found nadph-dependent reductase activity with ortho-quinones, which is ... | 2009 | 19349281 |
| mitochondrial respiratory complex i: structure, function and implication in human diseases. | mitochondria are ubiquitous organelles in eukaryotic cells whose primary function is to generate energy supplies in the form of atp through oxidative phosphorylation. as the entry point for most electrons into the respiratory chain, nadh:ubiquinone oxidoreductase, or complex i, is the largest and least understood component of the mitochondrial oxidative phosphorylation system. substantial progress has been made in recent years in understanding its subunit composition, its assembly, the interacti ... | 2009 | 19355884 |
| deciphering peculiar protein-protein interacting modules in deinococcus radiodurans. | interactomes of proteins under positive selection from ionizing-radiation-resistant bacteria (irrb) might be a part of the answer to the question as to how irrb, particularly deinococcus radiodurans r1 (deira), resist ionizing radiation. here, using the database of interacting proteins (dip) and the protein structural interactome (psi)-base server for psi map, we have predicted novel interactions of orthologs of the 58 proteins under positive selection in deira and other irrb, but which are abse ... | 2009 | 19356244 |
| bioinformatics analysis suggests base modifications of trnas and mirnas in arabidopsis thaliana. | modifications of rna bases have been found in some mrnas and non-coding rnas including rrnas, trnas, and snrnas, where modified bases are important for rna function. little is known about rna base modifications in arabidopsis thaliana. | 2009 | 19358740 |
| allostery in hsp70 chaperones is transduced by subdomain rotations. | hsp70s (heat shock protein 70 kda) are central to protein folding, refolding, and trafficking in organisms ranging from archaea to homo sapiens under both normal and stressed cellular conditions. hsp70s are comprised of a nucleotide-binding domain (nbd) and a substrate-binding domain (sbd). the nucleotide binding site in the nbd and the substrate binding site in the sbd are allosterically linked: adp binding promotes substrate binding, while atp binding promotes substrate release. hsp70s have be ... | 2009 | 19361428 |
| molecular dynamism of fe-s cluster biosynthesis implicated by the structure of the sufc(2)-sufd(2) complex. | maturation of iron-sulfur (fe-s) proteins is achieved by the suf machinery in a wide number of eubacteria and archaea, as well as eukaryotic chloroplasts. this machinery is encoded in escherichia coli by the sufabcdse operon, where three suf components, sufb, sufc, and sufd, form a complex and appear to provide an intermediary site for the fe-s cluster assembly. here, we report the quaternary structure of the sufc(2)-sufd(2) complex in which sufc is bound to the c-terminal domain of sufd. compar ... | 2009 | 19361433 |
| structural and motional contributions of the bacillus subtilis clpc n-domain to adaptor protein interactions. | the aaa(+) (atpases associated with a variety of cellular activities) superfamily protein clpc is a key regulator of cell development in bacillus subtilis. as part of a large oligomeric complex, clpc controls an array of cellular processes by recognizing, unfolding, and providing misfolded and aggregated proteins as substrates for the clpp peptidase. clpc is unique compared to other hsp100/clp proteins, as it requires an adaptor protein for all fundamental activities. the nmr solution structure ... | 2009 | 19361434 |
| the lateral gate of secyeg opens during protein translocation. | the secyeg translocon of escherichia coli mediates the translocation of preproteins across the cytoplasmic membrane. here, we have examined the role of the proposed lateral gate of the translocon in translocation. a dual cysteine cross-linking approach allowed the introduction of cross-linker arms of various lengths between adjoining aminoacyl positions of transmembrane segments 2b and 7 of the lateral gate. oxidation and short spacer linkers that fix the gate in the closed state abolished prepr ... | 2009 | 19366685 |
| alliance of proteomics and genomics to unravel the specificities of sahara bacterium deinococcus deserti. | to better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, deinococcus deserti vcd115, isolated from sahara surface sand. its genome consists of a 2.8-mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. from the large corpus of ms/ms spectra recorded, 1,348 proteins w ... | 2009 | 19370165 |
| functional characterization of excision repair and reca-dependent recombinational dna repair in campylobacter jejuni. | the presence and functionality of dna repair mechanisms in campylobacter jejuni are largely unknown. in silico analysis of the complete translated genome of c. jejuni nctc 11168 suggests the presence of genes involved in methyl-directed mismatch repair (mmr), nucleotide excision repair, base excision repair (ber), and recombinational repair. to assess the functionality of these putative repair mechanisms in c. jejuni, muts, uvrb, ung, and reca knockout mutants were constructed and analyzed for t ... | 2009 | 19376866 |
| from a consortium sequence to a unified sequence: the bacillus subtilis 168 reference genome a decade later. | comparative genomics is the cornerstone of identification of gene functions. the immense number of living organisms precludes experimental identification of functions except in a handful of model organisms. the bacterial domain is split into large branches, among which the firmicutes occupy a considerable space. bacillus subtilis has been the model of firmicutes for decades and its genome has been a reference for more than 10 years. sequencing the genome involved more than 30 laboratories, with ... | 2009 | 19383706 |
| the crystal structures of chikungunya and venezuelan equine encephalitis virus nsp3 macro domains define a conserved adenosine binding pocket. | macro domains (also called "x domains") constitute a protein module family present in all kingdoms of life, including viruses of the coronaviridae and togaviridae families. crystal structures of the macro domain from the chikungunya virus (an "old world" alphavirus) and the venezuelan equine encephalitis virus (a "new world" alphavirus) were determined at resolutions of 1.65 and 2.30 a, respectively. these domains are active as adenosine di-phosphoribose 1''-phosphate phosphatases. both the chik ... | 2009 | 19386706 |
| accuracy modulating mutations of the ribosomal protein s4-s5 interface do not necessarily destabilize the rps4-rps5 protein-protein interaction. | during the process of translation, an aminoacyl trna is selected in the a site of the decoding center of the small subunit based on the correct codon-anticodon base pairing. though selection is usually accurate, mutations in the ribosomal rna and proteins and the presence of some antibiotics like streptomycin alter translational accuracy. recent crystallographic structures of the ribosome suggest that cognate trnas induce a "closed conformation" of the small subunit that stabilizes the codon-ant ... | 2009 | 19386726 |
| resonance raman studies of the (his)(cys)3 2fe-2s cluster of mitoneet: comparison to the (cys)4 mutant and implications of the effects of ph on the labile metal center. | mitoneet is a 2fe-2s outer mitochondrial membrane protein that was initially identified as a target for anti-diabetic drugs. it exhibits a novel protein fold, and in contrast to other 2fe-2s proteins such as rieske proteins and ferredoxins, the metal clusters in the mitoneet homodimer are each coordinated by one histidine residue and three cysteine residues. the interaction of the ligating his87 residue with the 2fe-2s moiety is especially significant because previous studies have shown that rep ... | 2009 | 19388667 |
| molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of transport. | we have examined the network of connected internal cavities in cytochrome c oxidase along which water produced at the catalytic center is removed from the enzyme. using combination of structural analysis, molecular dynamics simulations, and free energy calculations we have identified two exit pathways that connect the mg2+ ion cavity to the outside of the enzyme. each pathway has a well-defined bottleneck, which determines the overall rate of water traffic along the exit pathway, and a specific ... | 2009 | 19393218 |
| redox-dependent conformational changes in cytochrome c oxidase suggest a gating mechanism for proton uptake. | a role for conformational change in the coupling mechanism of cytochrome c oxidase is the subject of controversy. relatively small conformational changes have been reported in comparisons of reduced and oxidized crystal structures of bovine oxidase but none in bacterial oxidases. comparing the x-ray crystal structures of the reduced (at 2.15 a resolution) and oxidized forms of cytochrome c oxidase from rhodobacter sphaeroides, we observe a displacement of heme a(3) involving both the porphyrin r ... | 2009 | 19397279 |
| structure of ttha1623, a novel metallo-beta-lactamase superfamily protein from thermus thermophilus hb8. | ttha1623 is a metallo-beta-lactamase superfamily protein from the extremely thermophilic bacterium thermus thermophilus hb8. homologues of ttha1623 exist in a wide range of bacteria and archaea and one eukaryote, giardia lamblia, but their function remains unknown. to analyze the structural properties of ttha1623, the crystal structures of its iron-bound and zinc-bound forms have been determined to 2.8 and 2.2 a resolution, respectively. ttha1623 possesses an alphabetabetaalpha-fold similar to t ... | 2009 | 19407375 |
| crystallization and preliminary x-ray crystallographic analysis of a novel histidinol-phosphate phosphatase from thermococcus onnurineus na1. | the ton_0887 gene product from thermococcus onnurineus na1 is a 240-residue protein that has histidinol-phosphate phosphatase (holpase) activity. according to analysis of its primary structure, the ton_0887 gene product is a monofunctional holpase that belongs to the dddd superfamily. this contrasts with the generally accepted classification that bifunctional holpases belong to the dddd superfamily. the ton_0887 gene product was purified and crystallized at 295 k. a 2.2 a resolution data set was ... | 2009 | 19407379 |
| cloning, expression, purification and crystallization as well as x-ray fluorescence and preliminary x-ray diffraction analyses of human adp-ribosylhydrolase 1. | human adp-ribosylhydrolase 1 (harh1, adprh) cleaves the glycosidic bond of adp-ribose attached to an arg residue of a protein. harh1 has been cloned, expressed heterologously in escherichia coli, purified and crystallized in complex with k(+) and adp. the orthorhombic crystals contained one monomer per asymmetric unit, exhibited a solvent content of 43% and diffracted x-rays to a resolution of 1.9 a. a prerequisite for obtaining well diffracting crystals was the performance of x-ray fluorescence ... | 2009 | 19407395 |
| structure, stability, and folding of ribonuclease h1 from the moderately thermophilic chlorobium tepidum: comparison with thermophilic and mesophilic homologues. | proteins from thermophilic organisms are able to function under conditions that render a typical mesophilic protein inactive. pairwise comparisons of homologous mesophilic and thermophilic proteins can help to identify the energetic features of a protein's energy landscape that lead to such thermostability. previous studies of bacterial ribonucleases h (rnases h) from the thermophile thermus thermophilus and the mesophile escherichia coli revealed that the thermostability arises in part from an ... | 2009 | 19408959 |
| versatile solidified nanofibrous cellulose-containing media for growth of extremophiles. | solidified media that employ a porous matrix of nanofibrous cellulose are described. the physicochemical stability of the porous structure allows the development of solidified media that can support the growth of extremophiles, such as acidophilic acidiphilium, alkaliphilic bacillus, thermophilic geobacillus and thermus, alkalithermophilic bacillus, and acidothermophilic sulfolobus microbes. the cellulose-supported media have several advantages over agar- and gellan gum-derived media, including ... | 2009 | 19411423 |
| diversity of 23s rrna genes within individual prokaryotic genomes. | the concept of ribosomal constraints on rrna genes is deduced primarily based on the comparison of consensus rrna sequences between closely related species, but recent advances in whole-genome sequencing allow evaluation of this concept within organisms with multiple rrna operons. | 2009 | 19415112 |
| allosteric regulation of the primase (dnag) activity by the clamp-loader (tau) in vitro. | during dna replication the helicase (dnab) recruits the primase (dnag) in the replisome to initiate the polymerization of new dna strands. dnab is attached to the tau subunit of the clamp-loader that loads the beta clamp and interconnects the core polymerases on the leading and lagging strands. the tau-dnab-dnag ternary complex is at the heart of the replisome and its function is likely to be modulated by a complex network of allosteric interactions. using a stable ternary complex comprising the ... | 2009 | 19415803 |
| xylose reductase from pichia stipitis with altered coenzyme preference improves ethanolic xylose fermentation by recombinant saccharomyces cerevisiae. | xylose reductase (xr) and xylitol dehydrogenase (xdh) from pichia stipitis are the two enzymes most commonly used in recombinant saccharomyces cerevisiae strains engineered for xylose utilization. the availability of nad+ for xdh is limited during anaerobic xylose fermentation because of the preference of xr for nadph. this in turn results in xylitol formation and reduced ethanol yield. the coenzyme preference of p. stipitis xr was changed by site-directed mutagenesis with the aim to engineer it ... | 2009 | 19416504 |
| atomic structure of a folate/fad-dependent trna t54 methyltransferase. | trnas from all 3 phylogenetic domains have a 5-methyluridine at position 54 (t54) in the t-loop. the methyl group is transferred from s-adenosylmethionine by trma methyltransferase in most gram-negative bacteria and some archaea and eukaryotes, whereas it is transferred from 5,10-methylenetetrahydrofolate (mthf) by trmfo, a folate/fad-dependent methyltransferase, in most gram-positive bacteria and some gram-negative bacteria. however, the catalytic mechanism remains unclear, because the crystal ... | 2009 | 19416846 |
| mechanism of sequence-specific pausing of bacterial rna polymerase. | sequence-specific pausing of multisubunit rna polymerases (rnaps) represents a rate-limiting step during transcription elongation. pausing occurs on average every 100 bases of dna. several models have been proposed to explain pausing, including backtracking of the ternary elongation complex, delay of translocation of the enzyme along dna, or a conformational change in the active site preventing formation of the phosphodiester bond. here, we performed biochemical characterization of previously-re ... | 2009 | 19416863 |
| contribution of ribosomal residues to p-site trna binding. | structural studies have revealed multiple contacts between the ribosomal p site and trna, but how these contacts contribute to p-trna binding remains unclear. in this study, the effects of ribosomal mutations on the dissociation rate (k(off)) of various trnas from the p site were measured. mutation of the 30s p site destabilized trnas to various degrees, depending on the mutation and the species of trna. these data support the idea that ribosome-trna interactions are idiosyncratically tuned to e ... | 2009 | 19417061 |
| structural insights into erf3 and stop codon recognition by erf1. | eukaryotic translation termination is mediated by two interacting release factors, erf1 and erf3, which act cooperatively to ensure efficient stop codon recognition and fast polypeptide release. the crystal structures of human and schizosaccharomyces pombe full-length erf1 in complex with erf3 lacking the gtpase domain revealed details of the interaction between these two factors and marked conformational changes in erf1 that occur upon binding to erf3, leading erf1 to resemble a trna molecule. ... | 2009 | 19417105 |
| yeast mitochondrial gln-trna(gln) is generated by a gatfab-mediated transamidation pathway involving arc1p-controlled subcellular sorting of cytosolic glurs. | it is impossible to predict which pathway, direct glutaminylation of trna(gln) or trna-dependent transamidation of glutamyl-trna(gln), generates mitochondrial glutaminyl-trna(gln) for protein synthesis in a given species. the report that yeast mitochondria import both cytosolic glutaminyl-trna synthetase and trna(gln) has challenged the widespread use of the transamidation pathway in organelles. here we demonstrate that yeast mitochondrial glutaminyl-trna(gln) is in fact generated by a transamid ... | 2009 | 19417106 |
| identification of genes contributing to the virulence of francisella tularensis schu s4 in a mouse intradermal infection model. | francisella tularensis is a highly virulent human pathogen. the most virulent strains belong to subspecies tularensis and these strains cause a sometimes fatal disease. despite an intense recent research effort, there is very limited information available that explains the unique features of subspecies tularensis strains that distinguish them from other f. tularensis strains and that explain their high virulence. here we report the use of targeted mutagenesis to investigate the roles of various ... | 2009 | 19424499 |
| roles of rel(spn) in stringent response, global regulation and virulence of serotype 2 streptococcus pneumoniae d39. | rela/spot homologue (rsh) proteins have (p)ppgpp synthetase and hydrolase activities that mediate major global responses to nutrient limitation and other stresses. rsh proteins are conserved in most bacteria and play diverse roles in bacterial pathogenesis. we report here that the rsh protein of streptococcus pneumoniae, rel(spn), can be deleted and is the primary source of (p)ppgpp synthesis in virulent strain d39 under some conditions. a d39 deltarel(spn) mutant grew well in complex medium, bu ... | 2009 | 19426208 |
| structure, stability, and flexibility of ribosomal protein l14e from sulfolobus solfataricus. | ribosomal protein l14e is a component of the large ribosomal subunit in both archaea and eukaryotes. we report here a high-resolution nmr solution structure of recombinant l14e and show that the n-terminal 57 residues adopt a classic sh3 fold. the protein contains a tight turn between strands 1 and 2 instead of the typical sh3 rt-loop, indicating that it is unlikely to interact with neighboring ribosomal proteins using the common sh3 site for proline-rich sequences. the remainder of the protein ... | 2009 | 19432457 |
| a spectroscopic investigation of a tridentate cu-complex mimicking the tyrosine-histidine cross-link of cytochrome c oxidase. | heme-copper oxidases have a crucial role in the energy transduction mechanism, catalyzing the reduction of dioxygen to water. the reduction of dioxygen takes place at the binuclear center, which contains heme a3 and cub. the x-ray crystal structures have revealed that the c6' of tyrosine 244 (bovine heart numbering) is cross-linked to a nitrogen of histidine 240, a ligand to cub. the role of the cross-linked tyrosine at the active site still remains unclear. in order to provide insight into the ... | 2009 | 19438285 |
| solution conformation of wild-type e. coli hsp70 (dnak) chaperone complexed with adp and substrate. | dnak is the canonical hsp70 molecular chaperone protein from escherichia coli. like other hsp70s, dnak comprises two main domains: a 44-kda n-terminal nucleotide-binding domain (nbd) that contains atpase activity, and a 25-kda substrate-binding domain (sbd) that harbors the substrate-binding site. here, we report an experimental structure for wild-type, full-length dnak, complexed with the peptide nrllltg and with adp. it was obtained in aqueous solution by using nmr residual dipolar coupling an ... | 2009 | 19439666 |
| plasmodial aspartyl-trna synthetases and peculiarities in plasmodium falciparum. | distinctive features of aspartyl-transfer rna (trna) synthetases (asprs) from the protozoan plasmodium genus are described. these apicomplexan asprss contain 29-31 amino acid insertions in their anticodon binding domains, a remarkably long n-terminal appendix that varies in size from 110 to 165 amino acids and two potential initiation codons. this article focuses on the atypical functional and structural properties of plasmodium falciparum cytosolic asprs, the causative parasite of human malaria ... | 2009 | 19443655 |
| electrostatics of the fes clusters in respiratory complex i. | respiratory complex i couples the transfer of electrons from nadh to ubiquinone and the translocation of protons across the mitochondrial membrane. a detailed understanding of the midpoint reduction potentials (e(m)) of each redox center and the factors which influence those potentials are critical in the elucidation of the mechanism of electron transfer in this enzyme. we present accurate electrostatic interaction energies for the iron-sulfur (fes) clusters of complex i to facilitate the develo ... | 2009 | 19445896 |
| regulation of translation by the redox state of elongation factor g in the cyanobacterium synechocystis sp. pcc 6803. | elongation factor g (ef-g), a key protein in translational elongation, was identified as a primary target of inactivation by reactive oxygen species within the translational machinery of the cyanobacterium synechocystis sp. pcc 6803 (kojima, k., oshita, m., nanjo, y., kasai, k., tozawa, y., hayashi, h., and nishiyama, y. (2007) mol. microbiol. 65, 936-947). in the present study, we found that inactivation of ef-g (slr1463) by h(2)o(2) was attributable to the oxidation of two specific cysteine re ... | 2009 | 19447882 |
| transcription activity of individual rrn operons in bacillus subtilis mutants deficient in (p)ppgpp synthetase genes, rela, yjbm, and ywac. | in bacillus subtilis a null mutation of the rela gene, whose gene product is involved in the synthesis and/or hydrolysis of (p)ppgpp, causes a growth defect that can be suppressed by mutation(s) of yjbm and/or ywac coding for small (p)ppgpp synthetases. all 35 suppressor mutations newly isolated were classified into two groups, either yjbm or ywac, by mapping and sequencing their mutations, suggesting that there are no (p)ppgpp synthetases other than rela, yjbm, and ywac in b. subtilis. in order ... | 2009 | 19447912 |
| substrate specificity of a mannose-6-phosphate isomerase from bacillus subtilis and its application in the production of l-ribose. | the uncharacterized gene previously proposed as a mannose-6-phosphate isomerase from bacillus subtilis was cloned and expressed in escherichia coli. the maximal activity of the recombinant enzyme was observed at ph 7.5 and 40 degrees c in the presence of 0.5 mm co(2+). the isomerization activity was specific for aldose substrates possessing hydroxyl groups oriented in the same direction at the c-2 and c-3 positions, such as the d and l forms of ribose, lyxose, talose, mannose, and allose. the en ... | 2009 | 19447949 |
| sequential processing of the toxoplasma apicoplast membrane protein ftsh1 in topologically distinct domains during intracellular trafficking. | ftsh proteins are hexameric transmembrane proteases found in chloroplasts, mitochondria and bacteria. in the protozoan toxoplasma gondii, ftsh1 is localized to membranes of the apicoplast, a relict chloroplast present in many apicomplexan parasites. we have shown that although t. gondii ftsh1 lacks the typical bipartite targeting presequence seen on apicoplast luminal proteins, it is targeted to the apicoplast via the endoplasmic reticulum. in this report, we show that ftsh1 undergoes processing ... | 2009 | 19450729 |
| translocation of proteins through the sec61 and secyeg channels. | the sec61 and secyeg translocation channels mediate the selective transport of proteins across the endoplasmic reticulum and bacterial inner membrane, respectively. these channels are also responsible for the integration of membrane proteins. to accomplish these two critical events in protein expression, the transport channels undergo conformational changes to permit the export of lumenal domains and the integration of transmembrane spans. novel insight into how these channels open during protei ... | 2009 | 19450960 |
| understanding the sequence specificity of trna binding to elongation factor tu using trna mutagenesis. | measuring the binding affinities of 42 single-base-pair mutants in the acceptor and t psi c stems of saccharomyces cerevisiae trna phe to thermus thermophilus elongation factor tu (ef-tu) revealed that much of the specificity for trna occurs at the 49-65, 50-64, and 51-63 base pairs. introducing the same mutations at the three positions into escherichia coli trna cag leu resulted in similar changes in binding affinity. swapping the three pairs from several e. coli trnas into yeast trna phe resul ... | 2009 | 19452597 |
| structural basis for adp-mediated transcriptional regulation by p1 and p7 para. | the accurate segregation of dna is essential for the faithful inheritance of genetic information. segregation of the prototypical p1 plasmid par system requires two proteins, para and parb, and a centromere. when bound to atp, para mediates segregation by interacting with centromere-bound parb, but when bound to adp, para fulfils a different function: dna-binding transcription autoregulation. the structure of para is unknown as is how distinct nucleotides arbitrate its different functions. to ad ... | 2009 | 19461582 |
| comprehensive analysis of phosphorylated proteins of escherichia coli ribosomes. | phosphorylation of bacterial ribosomal proteins has been known for decades; however, there is still very limited information available on specific locations of the phosphorylation sites in ribosomal proteins and the role they might play in protein synthesis. in this study, we have mapped the specific phosphorylation sites in 24 escherichia coli ribosomal proteins by tandem mass spectrometry. detection of phosphorylation was achieved by either phosphorylation specific visualization techniques, pr ... | 2009 | 19469554 |
| compressing the free energy range of substructure stabilities in iso-1-cytochrome c. | evolutionary conservation of substructure architecture between yeast iso-1-cytochrome c and the well-characterized horse cytochrome c is studied with limited proteolysis, the alkaline conformational transition and global unfolding with guanidine-hcl. mass spectral analysis of limited proteolysis cleavage products for iso-1-cytochrome c show that its least stable substructure is the same as horse cytochrome c. the limited proteolysis data yield a free energy of 3.8 +/- 0.4 kcal mol(-1) to unfold ... | 2009 | 19472325 |
| the genome sequence of geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to geobacter sulfurreducens. | the genome sequence of geobacter metallireducens is the second to be completed from the metal-respiring genus geobacter, and is compared in this report to that of geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences. | 2009 | 19473543 |
| analysis of proteins with the 'hot dog' fold: prediction of function and identification of catalytic residues of hypothetical proteins. | the hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. the fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme a-binding enzymes with a variety of substrates located at their active sites. | 2009 | 19473548 |
| isolation, crystallization and preliminary x-ray analysis of the transamidosome, a ribonucleoprotein involved in asparagine formation. | thermus thermophilus deprived of asparagine synthetase synthesizes asn on trna(asn) via a trna-dependent pathway involving a nondiscriminating aspartyl-trna synthetase that charges asp onto trna(asn) prior to conversion of the asp to asn by gatcab, a trna-dependent amidotransferase. this pathway also constitutes the route of asn-trna(asn) formation by bacteria and archaea deprived of asparaginyl-trna synthetase. the partners involved in trna-dependent asn formation in t. thermophilus assemble in ... | 2009 | 19478435 |
| crystallization of mycobacterium smegmatis methionyl-trna synthetase in the presence of methionine and adenosine. | methionyl-trna synthetase (metrs) from mycobacterium smegmatis was recombinantly expressed in escherichia coli and purified using ni(2+)-affinity and size-exclusion chromatography. crystals formed readily in the presence of the ligands methionine and adenosine. these two ligands are components of an intermediate in the two-step catalytic mechanism of metrs. the crystals were produced using the vapour-diffusion method and a full data set to 2.1 a resolution was collected from a single crystal. th ... | 2009 | 19478446 |
| cloning and analysis of a bifunctional methyltransferase/restriction endonuclease tspgwi, the prototype of a thermus sp. enzyme family. | restriction-modification systems are a diverse class of enzymes. they are classified into four major types: i, ii, iii and iv. we have previously proposed the existence of a thermus sp. enzyme family, which belongs to type ii restriction endonucleases (reases), however, it features also some characteristics of types i and iii. members include related thermophilic endonucleases: tspgwi, taqii, tspdti, and tth111ii. | 2009 | 19480701 |
| asymmetric amino acid activation by class ii histidyl-trna synthetase from escherichia coli. | aminoacyl-trna synthetases (arss) join amino acids to their cognate trnas to initiate protein synthesis. class ii ars possess a unique catalytic domain fold, possess active site signature sequences, and are dimers or tetramers. the dimeric class i enzymes, notably tyrrs, exhibit half-of-sites reactivity, but its mechanistic basis is unclear. in class ii histidyl-trna synthetase (hisrs), amino acid activation occurs at different rates in the two active sites when trna is absent, but half-of-sites ... | 2009 | 19487703 |
| aquifex aeolicus trna (n2,n2-guanine)-dimethyltransferase (trm1) catalyzes transfer of methyl groups not only to guanine 26 but also to guanine 27 in trna. | transfer rna (n2,n2-guanine)-dimethyltransferase (trm1) catalyzes n2,n2-dimethylguanine formation at position 26 (m(2)(2)g26) in trna. in the reaction, n2-guanine at position 26 (m(2)g26) is generated as an intermediate. the trm1 genes are found only in archaea and eukaryotes, although it has been reported that aquifex aeolicus, a hyper-thermophilic eubacterium, has a putative trm1 gene. to confirm whether a. aeolicus trm1 has trna methyltransferase activity, we purified recombinant trm1 protein ... | 2009 | 19491098 |
| characterization of three beta-galactoside phosphorylases from clostridium phytofermentans: discovery of d-galactosyl-beta1->4-l-rhamnose phosphorylase. | we characterized three d-galactosyl-beta1-->3-n-acetyl-d-hexosamine phosphorylase (ec 2.4.1.211) homologs from clostridium phytofermentans (cphy0577, cphy1920, and cphy3030 proteins). cphy0577 and cphy3030 proteins exhibited similar activity on galacto-n-biose (gnb; d-gal-beta1-->3-d-galnac) and lacto-n-biose i (lnb; d-gal-beta1-->3-d-glcnac), thus indicating that they are d-galactosyl-beta1-->3-n-acetyl-d-hexosamine phosphorylases, subclassified as gnb/lnb phosphorylase. in contrast, cphy1920 p ... | 2009 | 19491100 |
| vibriobactin antibodies: a vaccine strategy. | a new target strategy in the development of bacterial vaccines, the induction of antibodies to microbial outer membrane ferrisiderophore complexes, is explored. a vibriobactin (vib) analogue, with a thiol tether, 1-(2,3-dihydroxybenzoyl)-5,9-bis[[(4s,5r)-2-(2,3-dihydroxyphenyl)-4,5-dihydro-5-methyl-4-oxazolyl]carbonyl]-14-(3-mercaptopropanoyl)-1,5,9,14-tetraazatetradecane, was synthesized and linked to ovalbumin (ova) and bovine serum albumin (bsa). the antigenicity of the vib microbial iron che ... | 2009 | 19492834 |
| two structurally independent domains of e. coli nusg create regulatory plasticity via distinct interactions with rna polymerase and regulators. | nusg is a conserved regulatory protein that interacts with elongation complexes (ecs) of rna polymerase, dna, and rna to modulate transcription in multiple and sometimes opposite ways. in escherichia coli, nusg suppresses pausing and increases elongation rate, enhances termination by e. coli rho and phage hk022 nun protein, and promotes antitermination by lambdan and in ribosomal rna operons. we report nmr studies that suggest that e. coli nusg consists of two largely independent n- and c-termin ... | 2009 | 19500594 |
| the folding trajectory of rnase h is dominated by its topology and not local stability: a protein engineering study of variants that fold via two-state and three-state mechanisms. | proteins can sample a variety of partially folded conformations during the transition between the unfolded and native states. some proteins never significantly populate these high-energy states and fold by an apparently two-state process. however, many proteins populate detectable, partially folded forms during the folding process. the role of such intermediates is a matter of considerable debate. a single amino acid change can convert escherichia coli ribonuclease h from a three-state folder th ... | 2009 | 19501596 |
| toward the catalytic mechanism of a cysteine ligase (mshc) from mycobacterium smegmatis: an enzyme involved in the biosynthetic pathway of mycothiol. | mycobacterium tuberculosis and other members of the actinomycete family produce mycothiol (msh or acetylcysteine-glucosamine-inositol, accys-glcn-ins) to protect the organism against oxidative and antibiotic stress. the biosynthesis of msh proceeds via a five-step process that involves four unique enzymes, msha-d, which represent specific targets for inhibitor design. recombinant mycobacterium smegmatis mshc catalyzes the atp-dependent condensation of glucosamine-inositol (glcn-ins) and cysteine ... | 2009 | 19505149 |
| the 5' terminal uracil of let-7a is critical for the recruitment of mrna to argonaute2. | small rnas modulate gene expression by forming a ribonucleoprotein complex with argonaute proteins and directing them to specific complementary sites in target nucleic acids. however, the interactions required for the recruitment of the target nucleic acid to the ribonucleoprotein complex are poorly understood. in the present manuscript we have investigated this question by using let-7a, argonaute2 and a fully complementary mrna target. importantly, we have found that recombinant argonaute2 is s ... | 2009 | 19508234 |
| hsp70 structure, function, regulation and influence on yeast prions. | heat shock proteins protect cells from various conditions of stress. hsp70, the most ubiquitous and highly conserved hsp, helps proteins adopt native conformation or regain function after misfolding. various co-chaperones specify hsp70 function and broaden its substrate range. we discuss hsp70 structure and function, regulation by co-factors and influence on propagation of yeast prions. | 2009 | 19519514 |
| hsp104 and prion propagation. | high-ordered aggregates (amyloids) may disrupt cell functions, cause toxicity at certain conditions and provide a basis for self-perpetuated, protein-based infectious heritable agents (prions). heat shock proteins acting as molecular chaperones counteract protein aggregation and influence amyloid propagation. the yeast hsp104/hsp70/hsp40 chaperone complex plays a crucial role in interactions with both ordered and unordered aggregates. the main focus of this review will be on the hsp104 chaperone ... | 2009 | 19519517 |
| insights into trna-dependent amidotransferase evolution and catalysis from the structure of the aquifex aeolicus enzyme. | many bacteria form gln-trna(gln) and asn-trna(asn) by conversion of the misacylated glu-trna(gln) and asp-trna(asn) species catalyzed by the gatcab amidotransferase in the presence of atp and an amide donor (glutamine or asparagine). here, we report the crystal structures of gatcab from the hyperthermophilic bacterium aquifex aeolicus, complexed with glutamine, asparagine, aspartate, adp, or atp. in contrast to the staphylococcus aureus gatcab, the a. aeolicus enzyme formed acyl-enzyme intermedi ... | 2009 | 19520089 |
| insights into the role of val45 and gln182 of escherichia coli muty in dna substrate binding and specificity. | escherichia coli muty (ecmuty) reduces mutagenesis by removing adenines paired with guanines or 7,8-dihydro-8-oxo-guanines (8-oxog). v45 and q182 of ecmuty are considered to be the key determinants of adenine specificity. both residues are spatially close to each other in the active site and are conserved in muty family proteins but not in methanobacterium thermoautotrophicum mig.mthi t/g mismatch dna glycosylase (a50 and l187 at the corresponding respective positions). | 2009 | 19523222 |
| a link between hinge-bending domain motions and the temperature dependence of catalysis in 3-isopropylmalate dehydrogenase. | enzyme function depends on specific conformational motions. we show that the temperature dependence of enzyme kinetic parameters can provide insight into these functionally relevant motions. while investigating the catalytic properties of ipmdh from escherichia coli, we found that its catalytic efficiency (k(cat)/k(m,ipm)) for the substrate ipm has an unusual temperature dependence, showing a local minimum at approximately 35 degrees c. in search of an explanation, we measured the individual con ... | 2009 | 19527660 |