Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
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| an iron-sulfur cluster loop motif in the archaeoglobus fulgidus uracil-dna glycosylase mediates efficient uracil recognition and removal. | the family 4 uracil-dna glycosylase from the hyperthermophilic organism archaeoglobus fulgidus (afudg) is responsible for the removal of uracil in dna as the first step in the base excision repair (ber) pathway. afudg contains a large solvent-exposed peptide region containing an α helix and loop anchored on each end via ligation of two cysteine thiolates to a [4fe-4s](2+) cluster. we propose that this region plays a similar role in dna damage recognition as a smaller iron-sulfur cluster loop (fc ... | 2012 | 22646210 |
| lessons from high-throughput protein crystallization screening: 10 years of practical experience. | x-ray crystallography provides the majority of our structural biological knowledge at a molecular level and, in terms of pharmaceutical design, is a valuable tool to accelerate discovery. it is the premier technique in the field, but its usefulness is significantly limited by the need to grow well-diffracting crystals. it is for this reason that high-throughput crystallization has become a key technology that has matured over the past 10 years through the field of structural genomics. areas cove ... | 2011 | 22646073 |
| evolution of lysine biosynthesis in the phylum deinococcus-thermus. | thermus thermophilus biosynthesizes lysine through the α-aminoadipate (aaa) pathway: this observation was the first discovery of lysine biosynthesis through the aaa pathway in archaea and bacteria. genes homologous to the t. thermophilus lysine biosynthetic genes are widely distributed in bacteria of the deinococcus-thermus phylum. our phylogenetic analyses strongly suggest that a common ancestor of the deinococcus-thermus phylum had the ancestral genes for bacterial lysine biosynthesis through ... | 2012 | 22645699 |
| structure and function of fusb: an elongation factor g-binding fusidic acid resistance protein active in ribosomal translocation and recycling. | fusidic acid (fa) is a bacteriostatic antibiotic that locks elongation factor g (ef-g) to the ribosome after gtp hydrolysis during elongation and ribosome recycling. the plasmid pub101-encoded protein fusb causes fa resistance in clinical isolates of staphylococcus aureus through an interaction with ef-g. here, we report 1.6 and 2.3 å crystal structures of fusb. we show that fusb is a two-domain protein lacking homology to known structures, where the n-terminal domain is a four-helix bundle and ... | 2012 | 22645663 |
| flexibility of the metal-binding region in apo-cupredoxins. | protein-mediated electron transfer is an essential event in many biochemical processes. efficient electron transfer requires the reorganization energy of the redox event to be minimized, which is ensured by the presence of rigid donor and acceptor sites. electron transfer copper sites are present in the ubiquitous cupredoxin fold, able to bind one or two copper ions. the low reorganization energy in these metal centers has been accounted for by assuming that the protein scaffold creates an entat ... | 2012 | 22645370 |
| resistance to a novel antichlamydial compound is mediated through mutations in chlamydia trachomatis secy. | a novel and quantitative high-throughput screening approach was explored as a tool for the identification of novel compounds that inhibit chlamydial growth in mammalian cells. the assay is based on accumulation of a fluorescent marker by intracellular chlamydiae. its utility was demonstrated by screening 42,000 chemically defined compounds against chlamydia caviae gpic. this analysis led to the identification of 40 primary-hit compounds. five of these compounds were nontoxic to host cells and ha ... | 2012 | 22644029 |
| characterization of the pib-type atpases present in thermus thermophilus. | p(ib)-type atpases transport heavy metals (cu(2+), cu(+), ag(+), zn(2+), cd(2+), co(2+)) across biomembranes, playing a key role in homeostasis and in the mechanisms of biotolerance of these metals. three genes coding for putative p(ib)-type atpases are present in the genome of thermus thermophilus (hb8 and hb27): the ttc1358, ttc1371, and ttc0354 genes; these genes are annotated, respectively, as two copper transporter (copa and copb) genes and a zinc-cadmium transporter (zn(2+)/cd(2+)-atpase) ... | 2012 | 22636781 |
| real-time evidence for ef-g-induced dynamics of helix 44 in 16s rrna. | the penultimate stem-loop of 16s ribosomal rna (rrna), helix 44, plays a central role in ribosome function. using time-resolved dimethyl sulfate (dms) probing, we have analyzed time-dependent modifications that occur at specific bases in this helix near the decoding region, resulting from the binding of elongation factor g (ef-g) in various forms. when ef-g-gtp is bound to 70s ribosomes, bases a1492 and a1493 are immediately protected, while other bases in the region show either no change or enh ... | 2012 | 22634282 |
| engineering rotor ring stoichiometries in the atp synthase. | atp synthase membrane rotors consist of a ring of c-subunits whose stoichiometry is constant for a given species but variable across different ones. we investigated the importance of c/c-subunit contacts by site-directed mutagenesis of a conserved stretch of glycines (gxgxgxgxg) in a bacterial c(11) ring. structural and biochemical studies show a direct, specific influence on the c-subunit stoichiometry, revealing c(<11), c(12), c(13), c(14), and c(>14) rings. molecular dynamics simulations rati ... | 2012 | 22628564 |
| crystal structure of the largest subunit of a bacterial rna-guided immune complex and its role in dna target binding. | prokaryotes make use of small rnas encoded by crispr (clustered regularly interspaced short palindromic repeat) loci to provide immunity against bacteriophage or plasmid invasion. in escherichia coli, the crispr-associated complex for antiviral defense (cascade) utilizes these rnas to target foreign dna for destruction. casa, the largest subunit of cascade, is essential for its function. here we report the crystal structure of thermus thermophilus casa. the structure is composed of two domains t ... | 2012 | 22621933 |
| a study on l-asparaginase of nocardia levis mk-vl_113. | an enzyme-based drug, l-asparaginase, was produced by nocardia levis mk-vl_113 isolated from laterite soils of guntur region. cultural parameters affecting the production of l-asparaginase by the strain were optimized. maximal yields of l-asparaginase were recorded from 3-day-old culture grown in modified asparagine-glycerol salts broth with initial ph 7.0 at temperature 30°c. glycerol (2%) and yeast extract (1.5%) served as good carbon and nitrogen sources for l-asparaginase production, respect ... | 2012 | 22619604 |
| phylogenomics of prokaryotic ribosomal proteins. | archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. we developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 arch ... | 2012 | 22615861 |
| proline oxidase promotes tumor cell survival in hypoxic tumor microenvironments. | proline is a readily released stress substrate that can be metabolized by proline oxidase (pox) to generate either reactive oxygen species (ros) to induce apoptosis or autophagy or atp during times of nutrient stress. however, the contribution of proline metabolism to tumorigenesis in hypoxic microenvironments has not been explored. in this study, we investigated the different functions of pox under hypoxia and glucose depletion. we found that hypoxia induced pox expression in cancer cells in vi ... | 2012 | 22609800 |
| mobility of xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase. | we use a form of "freeze-trap, kinetic crystallography" to explore the migration of xe atoms away from the dinuclear heme a(3)/cu(b) center in thermus thermophilus cytochrome ba(3) oxidase. this enzyme is a member of the heme-copper oxidase superfamily and is thus crucial for dioxygen-dependent life. the mechanisms involved in the migration of oxygen, water, electrons, and protons into and/or out of the specialized channels of the heme-copper oxidases are generally not well understood. pressuriz ... | 2012 | 22607023 |
| how hibernation factors rmf, hpf, and yfia turn off protein synthesis. | eubacteria inactivate their ribosomes as 100s dimers or 70s monomers upon entry into stationary phase. in escherichia coli, 100s dimer formation is mediated by ribosome modulation factor (rmf) and hibernation promoting factor (hpf), or alternatively, the yfia protein inactivates ribosomes as 70s monomers. here, we present high-resolution crystal structures of the thermus thermophilus 70s ribosome in complex with each of these stationary-phase factors. the binding site of rmf overlaps with that o ... | 2012 | 22605777 |
| distinct functions of regions 1.1 and 1.2 of rna polymerase σ subunits from escherichia coli and thermus aquaticus in transcription initiation. | rna polymerase (rnap) from thermophilic thermus aquaticus is characterized by higher temperature of promoter opening, lower promoter complex stability, and higher promoter escape efficiency than rnap from mesophilic escherichia coli. we demonstrate that these differences are in part explained by differences in the structures of the n-terminal regions 1.1 and 1.2 of the e. coli σ(70) and t. aquaticus σ(a) subunits. in particular, region 1.1 and, to a lesser extent, region 1.2 of the e. coli σ(70) ... | 2012 | 22605342 |
| absence of helicobacter pylori high tetracycline resistant 16s rdna aga926-928ttc genotype in gastric biopsy specimens from dyspeptic patients of a city in the interior of são paulo, brazil. | treatment effectiveness of helicobacter pylori varies regionally and is decreasing worldwide, principally as a result of antibiotic resistant bacterium. tetracycline is generally included in second line h. pylori eradication regimens. in brazil, a high level of tetracycline resistance (tetr) is mainly associated with aga926-928ttc 16 s rdna nucleotide substitutions. as h. pylori culture is fastidious, we investigated the primary occurrence of h. pylori 16 s rdna high level tetr genotype using a ... | 2012 | 22594560 |
| role of apoptosis-inducing factor, proline dehydrogenase, and nadph oxidase in apoptosis and oxidative stress. | flavoproteins catalyze a variety of reactions utilizing flavin mononucleotide or flavin adenine dinucleotide as cofactors. the oxidoreductase properties of flavoenzymes implicate them in redox homeostasis, oxidative stress, and various cellular processes, including programmed cell death. here we explore three critical flavoproteins involved in apoptosis and redox signaling, ie, apoptosis-inducing factor (aif), proline dehydrogenase, and nadph oxidase. these proteins have diverse biochemical func ... | 2012 | 22593641 |
| structure and conservation of the periplasmic targeting factor tic22 protein from plants and cyanobacteria. | mitochondria and chloroplasts are of endosymbiotic origin. their integration into cells entailed the development of protein translocons, partially by recycling bacterial proteins. we demonstrate the evolutionary conservation of the translocon component tic22 between cyanobacteria and chloroplasts. tic22 in anabaena sp. pcc 7120 is essential. the protein is localized in the thylakoids and in the periplasm and can be functionally replaced by a plant orthologue. tic22 physically interacts with the ... | 2012 | 22593581 |
| structural insights into the substrate specificity of streptococcus pneumoniae β(1,3)-galactosidase bgac. | the surface-exposed β-galactosidase bgac from streptococcus pneumoniae was reported to be a virulence factor because of its specific hydrolysis activity toward the β(1,3)-linked galactose and n-acetylglucosamine (galβ(1,3)nag) moiety of oligosaccharides on the host molecules. here we report the crystal structure of bgac at 1.8 å and its complex with galactose at 1.95 å. at ph 5.5-8.0, bgac exists as a stable homodimer, each subunit of which consists of three distinct domains: a catalytic domain ... | 2012 | 22593580 |
| structure, function and inhibition of the two- and three-domain 4fe-4s ispg proteins. | ispg is a 4fe4s protein involved in isoprenoid biosynthesis. most bacterial ispgs contain two domains: a tim barrel (a) and a 4fe4s domain (b), but in plants and malaria parasites, there is a large insert domain (a*) whose structure and function are unknown. we show that bacterial ispgs function in solution as (ab)(2) dimers and that mutations in either both a or both b domains block activity. chimeras harboring an a-mutation in one chain and a b-mutation in the other have 50% of the activity se ... | 2012 | 22586085 |
| corallopyronin a specifically targets and depletes essential obligate wolbachia endobacteria from filarial nematodes in vivo. | doxycycline and rifampicin deplete essential wolbachia from filarial nematodes that cause lymphatic filariasis or onchocerciasis, resulting in blocked worm development and death. however, doxycycline is contraindicated for children and pregnant/breastfeeding women, as is rifampicin in the latter group with the additional specter of possible resistance development in mycobacterium spp. novel antibiotics with a narrower spectrum would aid in eliminating filarial diseases. corallococcus coralloides ... | 2012 | 22586066 |
| reconstitution of vacuolar-type rotary h+-atpase/synthase from thermus thermophilus. | vacuolar-type rotary h(+)-atpase/synthase (v(o)v(1)) from thermus thermophilus, composed of nine subunits, a, b, d, f, c, e, g, i, and l, has been reconstituted from individually isolated v(1) (a(3)b(3)d(1)f(1)) and v(o) (c(1)e(2)g(2)i(1)l(12)) subcomplexes in vitro. a(3)b(3)d and a(3)b(3) also reconstituted with v(o), resulting in a holoenzyme-like complexes. however, a(3)b(3)d-v(o) and a(3)b(3)-v(o) did not show atp synthesis and dicyclohexylcarbodiimide-sensitive atpase activity. the reconsti ... | 2012 | 22582389 |
| codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids. | synonymous codons are unevenly distributed among genes, a phenomenon termed codon usage bias. understanding the patterns of codon bias and the forces shaping them is a major step towards elucidating the adaptive advantage codon choice can confer at the level of individual genes and organisms. here, we perform a large-scale analysis to assess codon usage bias pattern of pyrimidine-ending codons in highly expressed genes in prokaryotes. we find a bias pattern linked to the degeneracy of the encode ... | 2012 | 22581775 |
| staphylococcus aureus fabi: inhibition, substrate recognition, and potential implications for in vivo essentiality. | methicillin-resistant staphylococcus aureus (mrsa) infections constitute a serious health threat worldwide, and novel antibiotics are therefore urgently needed. the enoyl-acp reductase (safabi) is essential for the s. aureus fatty acid biosynthesis and, hence, serves as an attractive drug target. we have obtained a series of snapshots of this enzyme that provide a mechanistic picture of ligand and inhibitor binding, including a dimer-tetramer transition combined with extensive conformational cha ... | 2012 | 22579249 |
| one ring to rule them all: trafficking of heme and heme synthesis intermediates in the metazoans. | the appearance of heme, an organic ring surrounding an iron atom, in evolution forever changed the efficiency with which organisms were able to generate energy, utilize gasses and catalyze numerous reactions. because of this, heme has become a near ubiquitous compound among living organisms. in this review we have attempted to assess the current state of heme synthesis and trafficking with a goal of identifying crucial missing information, and propose hypotheses related to trafficking that may g ... | 2012 | 22575458 |
| mycobacterium tuberculosis rbpa protein is a new type of transcriptional activator that stabilizes the σ a-containing rna polymerase holoenzyme. | rbpa is an rna polymerase (rnap)-binding protein whose presence increases the tolerance levels of mycobacteria to the first-line anti-tuberculosis drug rifampicin by an unknown mechanism. here, we show that the role of mycobacterium tuberculosis rbpa in resistance is indirect because it does not affect the sensitivity of rnap to rifampicin while it stimulates transcription controlled by the housekeeping σ(a)-factor. the transcription regulated by the stress-related σ(f) was not affected by rbpa. ... | 2012 | 22570422 |
| active site opening and closure control translocation of multisubunit rna polymerase. | multisubunit rna polymerase (rnap) is the central information-processing enzyme in all cellular life forms, yet its mechanism of translocation along the dna molecule remains conjectural. here, we report direct monitoring of bacterial rnap translocation following the addition of a single nucleotide. time-resolved measurements demonstrated that translocation is delayed relative to nucleotide incorporation and occurs shortly after or concurrently with pyrophosphate release. an investigation of tran ... | 2012 | 22570421 |
| structure based hypothesis of a mitochondrial ribosome rescue mechanism. | mtrf1 is a vertebrate mitochondrial protein with an unknown function that arose from a duplication of the mitochondrial release factor mtrf1a. to elucidate the function of mtrf1, we determined the positions that are conserved among mtrf1 sequences but that are different in their mtrf1a paralogs. we subsequently modeled the 3d structure of mtrf1a and mtrf1 bound to the ribosome, highlighting the structural implications of these differences to derive a hypothesis for the function of mtrf1. | 2012 | 22569235 |
| ispe inhibitors identified by a combination of in silico and in vitro high-throughput screening. | cdp-me kinase (ispe) contributes to the non-mevalonate or deoxy-xylulose phosphate (doxp) pathway for isoprenoid precursor biosynthesis found in many species of bacteria and apicomplexan parasites. ispe has been shown to be essential by genetic methods and since it is absent from humans it constitutes a promising target for antimicrobial drug development. using in silico screening directed against the substrate binding site and in vitro high-throughput screening directed against both, the substr ... | 2012 | 22563402 |
| metallation state of human manganese superoxide dismutase expressed in saccharomyces cerevisiae. | human manganese superoxide dismutase (sod2p) has been expressed in yeast and the protein purified from isolated yeast mitochondria, yielding both the metallated protein and the less stable apoprotein in a single chromatographic step. at 30 °c growth temperature, more than half of the purified enzyme is apoprotein that can be fully activated following reconstitution, while the remainder contains a mixture of manganese and iron. in contrast, only fully metallated enzyme was isolated from a similar ... | 2012 | 22561997 |
| comparing the similarity of different groups of bacteria to the human proteome. | numerous aspects of the relationship between bacteria and human have been investigated. one aspect that has recently received attention is sequence overlap at the proteomic level. however, there has not yet been a study that comprehensively characterizes the level of sequence overlap between bacteria and human, especially as it relates to bacterial characteristics like pathogenicity, g-c content, and proteome size. in this study, we began by performing a general characterization of the range of ... | 2012 | 22558081 |
| cellular function and molecular structure of ecto-nucleotidases. | ecto-nucleotidases play a pivotal role in purinergic signal transmission. they hydrolyze extracellular nucleotides and thus can control their availability at purinergic p2 receptors. they generate extracellular nucleosides for cellular reuptake and salvage via nucleoside transporters of the plasma membrane. the extracellular adenosine formed acts as an agonist of purinergic p1 receptors. they also can produce and hydrolyze extracellular inorganic pyrophosphate that is of major relevance in the c ... | 2012 | 22555564 |
| stabilizing proteins from sequence statistics: the interplay of conservation and correlation in triosephosphate isomerase stability. | understanding the determinants of protein stability remains one of protein science's greatest challenges. there are still no computational solutions that calculate the stability effects of even point mutations with sufficient reliability for practical use. amino acid substitutions rarely increase the stability of native proteins; hence, large libraries and high-throughput screens or selections are needed to stabilize proteins using directed evolution. consensus mutations have proven effective fo ... | 2012 | 22555051 |
| structure, function, and assembly of heme centers in mitochondrial respiratory complexes. | the sequential flow of electrons in the respiratory chain, from a low reduction potential substrate to o(2), is mediated by protein-bound redox cofactors. in mitochondria, hemes-together with flavin, iron-sulfur, and copper cofactors-mediate this multi-electron transfer. hemes, in three different forms, are used as a protein-bound prosthetic group in succinate dehydrogenase (complex ii), in bc(1) complex (complex iii) and in cytochrome c oxidase (complex iv). the exact function of heme b in comp ... | 2012 | 22554985 |
| when ribonucleases come into play in pathogens: a survey of gram-positive bacteria. | it is widely acknowledged that rna stability plays critical roles in bacterial adaptation and survival in different environments like those encountered when bacteria infect a host. bacterial ribonucleases acting alone or in concert with regulatory rnas or rna binding proteins are the mediators of the regulatory outcome on rna stability. we will give a current update of what is known about ribonucleases in the model gram-positive organism bacillus subtilis and will describe their established role ... | 2012 | 22550495 |
| the structure and function of the eukaryotic ribosome. | structures of the bacterial ribosome have provided a framework for understanding universal mechanisms of protein synthesis. however, the eukaryotic ribosome is much larger than it is in bacteria, and its activity is fundamentally different in many key ways. recent cryo-electron microscopy reconstructions and x-ray crystal structures of eukaryotic ribosomes and ribosomal subunits now provide an unprecedented opportunity to explore mechanisms of eukaryotic translation and its regulation in atomic ... | 2012 | 22550233 |
| bacterial toxin-antitoxin systems: translation inhibitors everywhere. | toxin-antitoxin (ta) systems are composed of two elements: a toxic protein and an antitoxin which is either an rna (type i and iii) or a protein (type ii). type ii systems are abundant in bacterial genomes in which they move via horizontal gene transfer. they are generally composed of two genes organized in an operon, encoding a toxin and a labile antitoxin. when carried by mobile genetic elements, these small modules contribute to their stability by a phenomenon denoted as addiction. recently, ... | 2011 | 22545240 |
| characterization of multi-functional properties and conformational analysis of muts2 from thermotoga maritima msb8. | the muts2 homologues have received attention because of their unusual activities that differ from those of muts. in this work, we report on the functional characteristics and conformational diversities of thermotoga maritima muts2 (tmmuts2). various biochemical features of the protein were demonstrated via diverse techniques such as scanning probe microscopy (spm), atpase assays, analytical ultracentrifugation, dna binding assays, size chromatography, and limited proteolytic analysis. dimeric tm ... | 2012 | 22545085 |
| crystal structure of dnak protein complexed with nucleotide exchange factor grpe in dnak chaperone system: insight into intermolecular communication. | the conserved, atp-dependent bacterial dnak chaperones process client substrates with the aid of the co-chaperones dnaj and grpe. however, in the absence of structural information, how these proteins communicate with each other cannot be fully delineated. for the study reported here, we solved the crystal structure of a full-length geobacillus kaustophilus hta426 grpe homodimer in complex with a nearly full-length g. kaustophilus hta426 dnak that contains the interdomain linker (acting as a pseu ... | 2012 | 22544739 |
| mycobacterium thermoresistibile as a source of thermostable orthologs of mycobacterium tuberculosis proteins. | the genus mycobacterium comprises major human pathogens such as the causative agent of tuberculosis, mycobacterium tuberculosis (mtb), and many environmental species. tuberculosis claims ~1.5 million lives every year, and drug resistant strains of mtb are rapidly emerging. to aid the development of new tuberculosis drugs, major efforts are currently under way to determine crystal structures of mtb drug targets and proteins involved in pathogenicity. however, a major obstacle to obtaining crystal ... | 2012 | 22544630 |
| structure and folding of a rare, natural kink turn in rna with an a*a pair at the 2b*2n position. | the kink turn (k-turn) is a frequently occurring motif, comprising a bulge followed by g•a and a•g pairs that introduces a sharp axial bend in duplex rna. natural k-turn sequences exhibit significant departures from the consensus, including the a•g pairs that form critical interactions stabilizing the core of the structure. kt-23 found in the small ribosomal subunit differs from the consensus in many organisms, particularly in the second a•g pair distal to the bulge (2b•2n). analysis of many kt- ... | 2012 | 22539525 |
| identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. | the identification of ligand binding sites is a key task in the annotation of proteins with known structure but uncharacterized function. here we describe a knowledge-based method exploiting the observation that unrelated binding sites share small structural motifs that bind the same chemical fragments irrespective of the nature of the ligand as a whole. | 2012 | 22536963 |
| biological applications of hybrid quantum mechanics/molecular mechanics calculation. | since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. accordingly, qm calculations that are jointed with mm calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. a unix-shell-based interface program connecting the quantum mechanics ... | 2012 | 22536015 |
| hd-rnas: an automated hierarchical database of rna structures. | one of the important goals of most biological investigations is to classify and organize the experimental findings so that they are readily useful for deriving generalized rules. although there is a huge amount of information on rna structures in pdb, there are redundant files, ambiguous synthetic sequences etc. moreover, a systematic hierarchical organization, reflecting rna classification, is missing in pdb. in this investigation, we have classified all the available rna structures from pdb th ... | 2012 | 22529851 |
| mechanistic stoichiometry of proton translocation by cytochrome cbb3. | cytochrome cbb(3) belongs to the superfamily of respiratory heme-copper oxidases that couple the reduction of molecular oxygen to proton translocation across the bacterial or mitochondrial membrane. the cbb(3)-type enzymes are found only in bacteria, and are both structurally and functionally the most distant from their mitochondrial counterparts. the mechanistic h(+)/e(-) stoichiometry of proton translocation in these cbb(3)-type cytochrome c oxidases has remained controversial. a stoichiometri ... | 2012 | 22529361 |
| ribosome engineering to promote new crystal forms. | crystallographic studies of the ribosome have provided molecular details of protein synthesis. however, the crystallization of functional complexes of ribosomes with gtpase translation factors proved to be elusive for a decade after the first ribosome structures were determined. analysis of the packing in different 70s ribosome crystal forms revealed that regardless of the species or space group, a contact between ribosomal protein l9 from the large subunit and 16s rrna in the shoulder of a neig ... | 2012 | 22525755 |
| mechanism of foreign dna selection in a bacterial adaptive immune system. | in bacterial and archaeal crispr immune pathways, dna sequences from invading bacteriophage or plasmids are integrated into crispr loci within the host genome, conferring immunity against subsequent infections. the ribonucleoprotein complex cascade utilizes rnas generated from these loci to target complementary "nonself" dna sequences for destruction, while avoiding binding to "self" sequences within the crispr locus. here we show that casa, the largest protein subunit of cascade, is required fo ... | 2012 | 22521690 |
| crispr immunity relies on the consecutive binding and degradation of negatively supercoiled invader dna by cascade and cas3. | the prokaryotic crispr/cas immune system is based on genomic loci that contain incorporated sequence tags from viruses and plasmids. using small guide rna molecules, these sequences act as a memory to reject returning invaders. both the cascade ribonucleoprotein complex and the cas3 nuclease/helicase are required for crispr interference in escherichia coli, but it is unknown how natural target dna molecules are recognized and neutralized by their combined action. here we show that cascade effici ... | 2012 | 22521689 |
| comparative analyses of homocitrate synthase genes of ascomycetous yeasts. | most ascomycetous yeasts have 2 homocitrate synthases (hcss). among the fungal lysine biosynthesis-related genes, only the hcs gene was duplicated in the course of evolution. it was recently reported that hcs of saccharomyces cerevisiae has an additional function in nuclear activities involving chromatin regulation related to dna damage repair, which is not related to lysine biosynthesis. thus, it is possible that the bifunctionality is associated with hcs gene duplication. phylogenetic analysis ... | 2012 | 22518332 |
| product-controlled steady-state kinetics between cytochrome aa(3) from rhodobacter sphaeroides and equine ferrocytochrome c analyzed by a novel spectrophotometric approach. | cytochrome c oxidase (cco) catalyzes the reduction of molecular oxygen to water using ferrocytochrome c (cyt c(2+)) as the electron donor. in this study, the oxidation of horse cyt c(2+) by cco from rhodobacter sphaeroides, was monitored using stopped-flow spectrophotometry. a novel analytic procedure was applied in which the spectra were deconvoluted into the reduced and oxidized forms of cyt c by a least-squares fitting method, yielding the reaction rates at various concentrations of cyt c(2+) ... | 2012 | 22516686 |
| the three-dimensional structural basis of type ii hyperprolinemia. | type ii hyperprolinemia is an autosomal recessive disorder caused by a deficiency in δ(1)-pyrroline-5-carboxylate dehydrogenase (p5cdh; also known as aldh4a1), the aldehyde dehydrogenase that catalyzes the oxidation of glutamate semialdehyde to glutamate. here, we report the first structure of human p5cdh (hsp5cdh) and investigate the impact of the hyperprolinemia-associated mutation of ser352 to leu on the structure and catalytic properties of the enzyme. the 2. 5-å-resolution crystal structure ... | 2012 | 22516612 |
| dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from thermococcus kodakarensis kod1. | ribose-1,5-bisphosphate isomerase (r15pi) is a novel enzyme recently identified as a member of an amp metabolic pathway in archaea. the enzyme converts d-ribose 1,5-bisphosphate into ribulose 1,5-bisphosphate, providing the substrate for archaeal ribulose-1,5-bisphosphate carboxylase/oxygenases. we here report the crystal structures of r15pi from thermococcus kodakarensis kod1 (tk-r15pi) with and without its substrate or product. tk-r15pi is a hexameric enzyme formed by the trimerization of dime ... | 2012 | 22511789 |
| bactquant: an enhanced broad-coverage bacterial quantitative real-time pcr assay. | bacterial load quantification is a critical component of bacterial community analysis, but a culture-independent method capable of detecting and quantifying diverse bacteria is needed. based on our analysis of a diverse collection of 16 s rrna gene sequences, we designed a broad-coverage quantitative real-time pcr (qpcr) assay--bactquant--for quantifying 16 s rrna gene copy number and estimating bacterial load. we further utilized in silico evaluation to complement laboratory-based qpcr characte ... | 2012 | 22510143 |
| snapshot of virus evolution in hypersaline environments from the characterization of a membrane-containing salisaeta icosahedral phage 1. | the multitude of archaea and bacteria inhabiting extreme environments has only become evident during the last decades. as viruses apply a significant evolutionary force to their hosts, there is an inherent value in learning about viruses infecting these extremophiles. in this study, we have focused on one such unique virus-host pair isolated from a hypersaline environment: an icosahedral, membrane-containing double-stranded dna virus--salisaeta icosahedral phage 1 (ssip-1) and its halophilic hos ... | 2012 | 22509017 |
| riboswitch (t-box)-mediated control of trna-dependent amidation in clostridium acetobutylicum rationalizes gene and pathway redundancy for asparagine and asparaginyl-trnaasn synthesis. | analysis of the gram-positive clostridium acetobutylicum genome reveals an inexplicable level of redundancy for the genes putatively involved in asparagine (asn) and asn-trna(asn) synthesis. besides a duplicated set of gatcab trna-dependent amidotransferase genes, there is a triplication of aspartyl-trna synthetase genes and a duplication of asparagine synthetase b genes. this genomic landscape leads to the suspicion of the incoherent simultaneous use of the direct and indirect pathways of asn a ... | 2012 | 22505715 |
| substrate-induced change in the quaternary structure of type 2 isopentenyl diphosphate isomerase from sulfolobus shibatae. | type 2 isopentenyl diphosphate isomerase catalyzes the interconversion between two active units for isoprenoid biosynthesis, i.e., isopentenyl diphosphate and dimethylallyl diphosphate, in almost all archaea and in some bacteria, including human pathogens. the enzyme is a good target for discovery of antibiotics because it is essential for the organisms that use only the mevalonate pathway to produce the active isoprene units and because humans possess a nonhomologous isozyme, type 1 isopentenyl ... | 2012 | 22505674 |
| structure of escherichia coli aspartate α-decarboxylase asn72ala: probing the role of asn72 in pyruvoyl cofactor formation. | the crystal structure of the asn72ala site-directed mutant of escherichia coli aspartate α-decarboxylase (adc) has been determined at 1.7 å resolution. the refined structure is consistent with the presence of a hydrolysis product serine in the active site in place of the pyruvoyl group required for catalysis, which suggests that the role of asn72 is to protect the ester formed during adc activation from hydrolysis. in previously determined structures of activated adc, including the wild type and ... | 2012 | 22505409 |
| genome signature difference between deinococcus radiodurans and thermus thermophilus. | the extremely radioresistant bacteria of the genus deinococcus and the extremely thermophilic bacteria of the genus thermus belong to a common taxonomic group. considering the distinct living environments of deinococcus and thermus, different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor. their guanine-cytosine (gc) contents are similar; however, we hypothesized that their genomic signatures would be different. our findings indicate ... | 2012 | 22500246 |
| para-like protein uses nonspecific chromosomal dna binding to partition protein complexes. | recent data have shown that plasmid partitioning par-like systems are used by some bacterial cells to control localization of protein complexes. here we demonstrate that one of these homologs, ppfa, uses nonspecific chromosome binding to separate cytoplasmic clusters of chemotaxis proteins upon division. using fluorescent microscopy and point mutations, we show dynamic chromosome binding and walker-type atpase activity are essential for cluster segregation. the n-terminal domain of a cytoplasmic ... | 2012 | 22496588 |
| rhodanese functions as sulfur supplier for key enzymes in sulfur energy metabolism. | how microorganisms obtain energy is a challenging topic, and there have been numerous studies on the mechanisms involved. here, we focus on the energy substrate traffic in the hyperthermophilic bacterium aquifex aeolicus. this bacterium can use insoluble sulfur as an energy substrate and has an intricate sulfur energy metabolism involving several sulfur-reducing and -oxidizing supercomplexes and enzymes. we demonstrate that the cytoplasmic rhodanese sbdp participates in this sulfur energy metabo ... | 2012 | 22496367 |
| life under multiple extreme conditions: diversity and physiology of the halophilic alkalithermophiles. | around the world, there are numerous alkaline, hypersaline environments that are heated either geothermally or through intense solar radiation. it was once thought that such harsh environments were inhospitable and incapable of supporting a variety of life. however, numerous culture-dependent and -independent studies revealed the presence of an extensive diversity of aerobic and anaerobic bacteria and archaea that survive and grow under these multiple harsh conditions. this diversity includes th ... | 2012 | 22492435 |
| related bifunctional restriction endonuclease-methyltransferase triplets: tspdti, tth111ii/tthhb27i and tsoi with distinct specificities. | we previously defined a family of restriction endonucleases (reases) from thermus sp., which share common biochemical and biophysical features, such as the fusion of both the nuclease and methyltransferase (mtase) activities in a single polypeptide, cleavage at a distance from the recognition site, large molecular size, modulation of activity by s-adenosylmethionine (sam), and incomplete cleavage of the substrate dna. members include related thermophilic reases with five distinct specificities: ... | 2012 | 22489904 |
| structural and functional consequences of phosphate-arsenate substitutions in selected nucleotides: dna, rna, and atp. | a recent finding of a bacterial strain (gfaj-1) that can rely on arsenic instead of phosphorus raised the questions of if and how arsenate can replace phosphate in biomolecules that are essential to sustain cell life. apart from questions related to chemical stability, there are those of the structural and functional consequences of phosphate-arsenate substitutions in vital nucleotides in gfaj1-like cells. in this study we selected three types of molecules (atp/adp as energy source and replicati ... | 2012 | 22480264 |
| response of methicillin-resistant staphylococcus aureus to amicoumacin a. | amicoumacin a exhibits strong antimicrobial activity against methicillin-resistant staphylococcus aureus (mrsa), hence we sought to uncover its mechanism of action. genome-wide transcriptome analysis of s. aureus col in response to amicoumacin a showed alteration in transcription of genes specifying several cellular processes including cell envelope turnover, cross-membrane transport, virulence, metabolism, and general stress response. the most highly induced gene was lrga, encoding an antiholin ... | 2012 | 22479511 |
| development of a shutterless continuous rotation method using an x-ray cmos detector for protein crystallography. | a new shutterless continuous rotation method using an x-ray complementary metal-oxide semiconductor (cmos) detector has been developed for high-speed, precise data collection in protein crystallography. the principle of operation and the basic performance of the x-ray cmos detector (hamamatsu photonics kk c10158dk) have been shown to be appropriate to the shutterless continuous rotation method. the data quality of the continuous rotation method is comparable to that of the conventional oscillati ... | 2009 | 22477775 |
| structural and mechanistic analysis of the membrane-embedded glycosyltransferase waaa required for lipopolysaccharide synthesis. | waaa is a key enzyme in the biosynthesis of lps, a critical component of the outer envelope of gram-negative bacteria. embedded in the cytoplasmic face of the inner membrane, waaa catalyzes the transfer of 3-deoxy-d-manno-oct-2-ulosonic acid (kdo) to the lipid a precursor of lps. here we present crystal structures of the free and cmp-bound forms of waaa from aquifex aeolicus, an ancient gram-negative hyperthermophile. these structures reveal details of the cmp-binding site and implicate a unique ... | 2012 | 22474366 |
| electron transfer in subunit nuoi (tyky) of escherichia coli nadh:quinone oxidoreductase (ndh-1). | bacterial proton-translocating nadh:quinone oxidoreductase (ndh-1) consists of a peripheral and a membrane domain. the peripheral domain catalyzes the electron transfer from nadh to quinone through a chain of seven iron-sulfur (fe/s) clusters. subunit nuoi in the peripheral domain contains two [4fe-4s] clusters (n6a and n6b) and plays a role in bridging the electron transfer from cluster n5 to the terminal cluster n2. we constructed mutants for eight individual cys-coordinating fe/s clusters. wi ... | 2012 | 22474289 |
| genome sequence and transcriptome analysis of the radioresistant bacterium deinococcus gobiensis: insights into the extreme environmental adaptations. | the desert is an excellent model for studying evolution under extreme environments. we present here the complete genome and ultraviolet (uv) radiation-induced transcriptome of deinococcus gobiensis i-0, which was isolated from the cold gobi desert and shows higher tolerance to gamma radiation and uv light than all other known microorganisms. nearly half of the genes in the genome encode proteins of unknown function, suggesting that the extreme resistance phenotype may be attributed to unknown ge ... | 2012 | 22470573 |
| chemoinformatic identification of novel inhibitors against mycobacterium tuberculosis l-aspartate α-decarboxylase. | l-aspartate α-decarboxylase (adc) belongs to a class of pyruvoyl dependent enzymes and catalyzes the conversion of aspartate to β-alanine in the pantothenate pathway, which is critical for the growth of several micro-organisms, including mycobacterium tuberculosis (mtb). its presence only in micro-organisms, fungi and plants and its absence in animals, particularly human, make it a promising drug target. we have followed a chemoinformatics-based approach to identify potential drug-like inhibitor ... | 2012 | 22470451 |
| solution nuclear magnetic resonance analyses of the anticodon arms of proteinogenic and nonproteinogenic trna(gly). | although the fate of most trna molecules in the cell is aminoacylation and delivery to the ribosome, some trnas are destined to fulfill other functional roles. in addition to their central role in translation, trna molecules participate in processes such as regulation of gene expression, bacterial cell wall biosynthesis, viral replication, antibiotic biosynthesis, and suppression of alternative splicing. in bacteria, glycyl-trna molecules with anticodon sequences gcc and ucc exhibit multiple ext ... | 2012 | 22468768 |
| posttranslational modification of cellular proteins by a ubiquitin-like protein in bacteria. | posttranslational modification of proteins with ubiquitin and ubiquitin-like proteins plays important regulatory roles in eukaryotes. although a homologous conjugation system has recently been reported in archaea, there is no similar report in bacteria. this report describes the identification of a ubiquitin-like conjugation system in the bacterium thermus thermophilus. a series of in vivo analyses revealed that ttub, a bacterial ubiquitin-like protein that functions as a sulfur carrier in trna ... | 2012 | 22467871 |
| the type ii secretion system: biogenesis, molecular architecture and mechanism. | many gram-negative bacteria use the sophisticated type ii secretion system (t2ss) to translocate a wide range of proteins from the periplasm across the outer membrane. the inner-membrane platform of the t2ss is the nexus of the system and orchestrates the secretion process through its interactions with the periplasmic filamentous pseudopilus, the dodecameric outer-membrane complex and a cytoplasmic secretion atpase. here, recent structural and biochemical information is reviewed to describe our ... | 2012 | 22466878 |
| substrate and enzyme functional groups contribute to translational quality control by bacterial prolyl-trna synthetase. | aminoacyl-trna synthetases activate specific amino acid substrates and attach them via an ester linkage to cognate trna molecules. in addition to cognate proline, prolyl-trna synthetase (prors) can activate cysteine and alanine and misacylate trna(pro). editing of the misacylated aminoacyl-trna is required for error-free protein synthesis. an editing domain (ins) appended to bacterial prors selectively hydrolyzes ala-trna(pro), whereas cys-trna(pro) is cleared by a freestanding editing domain, y ... | 2012 | 22458656 |
| deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen. | standard genotypic antiretroviral resistance testing, performed by bulk sequencing, does not readily detect variants that comprise <20% of the circulating hiv-1 rna population. nevertheless, it is valuable in selecting an antiretroviral regimen after antiretroviral failure. in patients with poor adherence, resistant variants may not reach this threshold. therefore, deep sequencing would be potentially valuable for detecting minority resistant variants. we compared bulk sequencing and deep sequen ... | 2012 | 22457522 |
| folding without charges. | surface charges of proteins have in several cases been found to function as "structural gatekeepers," which avoid unwanted interactions by negative design, for example, in the control of protein aggregation and binding. the question is then if side-chain charges, due to their desolvation penalties, play a corresponding role in protein folding by avoiding competing, misfolded traps? to find out, we removed all 32 side-chain charges from the 101-residue protein s6 from thermus thermophilus. the re ... | 2012 | 22454493 |
| response to copper stress in streptomyces lividans extends beyond genes under direct control of a copper-sensitive operon repressor protein (csor). | a copper-sensitive operon repressor protein (csor) has been identified in streptomyces lividans (csor(sl)) and found to regulate copper homeostasis with attomolar affinity for cu(i). solution studies reveal apo- and cu(i)-csor(sl) to be a tetramer assembly, and a 1.7-å resolution crystal structure of apo-csor(sl) reveals that a significant conformational change is necessary to enable cu(i) binding. in silico prediction of the csor regulon was confirmed in vitro (emsa) and in vivo (rna-seq), whic ... | 2012 | 22451651 |
| ultrafast excited-state deactivation of flavins bound to dodecin. | dodecins, a group of flavin-binding proteins with a dodecameric quaternary structure, are able to incorporate two flavins within each of their six identical binding pockets building an aromatic tetrade with two tryptophan residues. dodecin from the archaeal halobacterium salinarum is a riboflavin storage device. we demonstrate that unwanted side reactions induced by reactive riboflavin species and degradation of riboflavin are avoided by ultrafast depopulation of the reactive excited state of ri ... | 2012 | 22451648 |
| role of trehalose in salinity and temperature tolerance in the model halophilic bacterium chromohalobacter salexigens. | the disaccharide trehalose is considered as a universal stress molecule, protecting cells and biomolecules from injuries imposed by high osmolarity, heat, oxidation, desiccation and freezing. chromohalobacter salexigens is a halophilic and extremely halotolerant γ-proteobacterium of the family halomonadaceae. in this work, we have investigated the role of trehalose as a protectant against salinity, temperature and desiccation in c. salexigens. a mutant deficient in the trehalose-6-phosphate synt ... | 2012 | 22448254 |
| production of l-ribose from l-ribulose by a triple-site variant of mannose-6-phosphate isomerase from geobacillus thermodenitrificans. | a triple-site variant (w17q n90a l129f) of mannose-6-phosphate isomerase from geobacillus thermodenitrificans was obtained by combining variants with residue substitutions at different positions after random and site-directed mutagenesis. the specific activity and catalytic efficiency (k(cat)/k(m)) for l-ribulose isomerization of this variant were 3.1- and 7.1-fold higher, respectively, than those of the wild-type enzyme at ph 7.0 and 70°c in the presence of 1 mm co(2+). the triple-site variant ... | 2012 | 22447612 |
| cloning, purification, crystallization and preliminary x-ray analysis of the burkholderia pseudomallei l1 ribosomal protein. | the gene encoding the l1 ribosomal protein from burkholderia pseudomallei strain d286 has been cloned into the petblue-1 vector system, overexpressed in escherichia coli and purified. crystals of the native protein were grown by the hanging-drop vapour-diffusion technique using peg 3350 as a precipitant and diffracted to beyond 1.65 å resolution. the crystals belonged to space group p2(1)2(1)2, with unit-cell parameters a = 53.6, b = 127.1, c = 31.8 å and with a single molecule in the asymmetric ... | 2012 | 22442241 |
| crystallization and preliminary x-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase. | dihydrouridine synthases catalyse the reduction of uridine to dihydrouridine in the d-loop and variable loop of trna. the human dihydrouridine synthase hsdus2l has been implicated in the development of pulmonary carcinogenesis. here, the purification, crystallization and preliminary x-ray characterization of the hsdus2l catalytic domain are reported. the crystals belonged to space group p2(1) and contained a single molecule of hsdus2l in the asymmetric unit. a complete data set was collected to ... | 2012 | 22442237 |
| structure and activity of the pseudomonas aeruginosa hotdog-fold thioesterases pa5202 and pa2801. | the hotdog fold is one of the basic protein folds widely present in bacteria, archaea and eukaryotes. many of these proteins exhibit thioesterase activity against fatty acyl-coas and play important roles in lipid metabolism, cellular signalling and degradation of xenobiotics. the genome of the opportunistic pathogen pseudomonas aeruginosa contains over 20 genes encoding predicted hotdog-fold proteins, none of which have been experimentally characterized. we have found that two p. aeruginosa hotd ... | 2012 | 22439787 |
| saccharomyces cerevisiae possesses a stress-inducible glycyl-trna synthetase gene. | aminoacyl-trna synthetases are a large family of housekeeping enzymes that are pivotal in protein translation and other vital cellular processes. saccharomyces cerevisiae possesses two distinct nuclear glycyl-trna synthetase (glyrs) genes, grs1 and grs2. grs1 encodes both cytoplasmic and mitochondrial activities, while grs2 is essentially silent and dispensable under normal conditions. we herein present evidence that expression of grs2 was drastically induced upon heat shock, ethanol or hydrogen ... | 2012 | 22438917 |
| exploring the proton pump and exit pathway for pumped protons in cytochrome ba3 from thermus thermophilus. | the heme-copper oxygen reductases are redox-driven proton pumps. in the current work, the effects of mutations in a proposed exit pathway for pumped protons are examined in the ba(3)-type oxygen reductase from thermus thermophilus, leading from the propionates of heme a(3) to the interface between subunits i and ii. recent studies have proposed important roles for his376 and asp372, both of which are hydrogen-bonded to propionate-a of heme a(3), and for glu126(ii) (subunit ii), which is hydrogen ... | 2012 | 22431640 |
| structural basis for the rescue of stalled ribosomes: structure of yaej bound to the ribosome. | in bacteria, the hybrid transfer-messenger rna (tmrna) rescues ribosomes stalled on defective messenger rnas (mrnas). however, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmrna-independent manner. here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor yaej bound to the thermus thermophilus 70s ribosome in complex with the initiator trna(i)(fmet) and a short mrna. the structure reveals that the c-terminal tail ... | 2012 | 22422986 |
| decoding in the absence of a codon by tmrna and smpb in the ribosome. | in bacteria, ribosomes stalled at the end of truncated messages are rescued by transfer-messenger rna (tmrna), a bifunctional molecule that acts as both a transfer rna (trna) and a messenger rna (mrna), and smpb, a small protein that works in concert with tmrna. here, we present the crystal structure of a tmrna fragment, smpb and elongation factor tu bound to the ribosome at 3.2 angstroms resolution. the structure shows how smpb plays the role of both the anticodon loop of trna and portions of m ... | 2012 | 22422985 |
| the binding site and mechanism of the rna polymerase inhibitor tagetitoxin: an issue open to debate. | in a recent paper in the journal of biological chemistry, artsimovitch et al. report a major revision of a crystallographic model and proposed mechanism of the rna polymerase inhibitor, tagetitoxin. this reassessment is based on theoretical modeling using molecular dynamics simulations. here, we argue that this theoretical model contradicts experimental results and a published crystal structure cannot exclude several mechanistically distinct alternative models and does not support some major con ... | 2012 | 22414754 |
| response to klyuyev and vassylyev: on the mechanism of tagetitoxin inhibition of transcription. | in their commentary, klyuyev and vassylyev dispute a model of transcription inhibition by tagetitoxin (tgt) proposed by us based on biochemical analysis and computational docking. we maintain that, although an alternative explanation can be provided for any single observation reported by us, taken together our results support a model in which tgt acts by trapping the trigger loop (tl) in an inactive state (artsimovitch et al.). this model is consistent with all the data collected with a physiolo ... | 2012 | 22414748 |
| the bacterial sec-translocase: structure and mechanism. | most bacterial secretory proteins pass across the cytoplasmic membrane via the translocase, which consists of a protein-conducting channel secyeg and an atp-dependent motor protein seca. the ancillary secdf membrane protein complex promotes the final stages of translocation. recent years have seen a major advance in our understanding of the structural and biochemical basis of protein translocation, and this has led to a detailed model of the translocation mechanism. | 2012 | 22411975 |
| pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of rna gene sizes and inferred structures, yet typical nucleotide composition bias. | pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. no mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of chelicerata possess unusual features, including short rrna genes and trna genes that lack sequence to encode arms of the canonical cloverleaf-shaped trna. additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the m ... | 2012 | 22409411 |
| structural and enzymatic characterization of bacd, an l-amino acid dipeptide ligase from bacillus subtilis. | bacd is an atp-dependent dipeptide ligase responsible for the biosynthesis of l-alanyl-l-anticapsin, a precursor of an antibiotic produced by bacillus spp. in contrast to the well-studied and phylogenetically related d-alanine: d-alanine ligase (ddl), bacd synthesizes dipeptides using l-amino acids as substrates and has a low substrate specificity in vitro. the enzyme is of great interest because of its potential application in industrial protein engineering for the environmentally friendly biol ... | 2012 | 22407814 |
| 2011 william allan award: development and evolution. | 2012 | 22405084 | |
| the variable subdomain of escherichia coli seca functions to regulate seca atpase activity and adp release. | bacterial seca proteins can be categorized by the presence or absence of a variable subdomain (var) located within nucleotide-binding domain ii of the seca dead motor. here we show that var is dispensable for seca function, since the var deletion mutant secaδ519-547 displayed a wild-type rate of cellular growth and protein export. loss or gain of var is extremely rare in the history of bacterial evolution, indicating that it appears to contribute to seca function within the relevant species in t ... | 2012 | 22389482 |
| activity, stability, and structure of metagenome-derived lc11-rnase h1, a homolog of sulfolobus tokodaii rnase h1. | metagenome-derived lc11-rnase h1 is a homolog of sulfolobus tokodaii rnase h1 (sto-rnase h1). it lacks a c-terminal tail, which is responsible for hyperstabilization of sto-rnase h1. sto-rnase h1 is characterized by its ability to cleave not only an rna/dna hybrid but also a double-stranded rna (dsrna). to examine whether lc11-rnase h1 also exhibits both rnase h and dsrnase activities, lc11-rnase h1 was overproduced in escherichia coli, purified, and characterized. lc11-rnase h1 exhibited rnase ... | 2012 | 22389131 |
| structural insights into initial and intermediate steps of the ribosome-recycling process. | the ribosome-recycling factor (rrf) and elongation factor-g (ef-g) disassemble the 70s post-termination complex (potc) into mrna, trna, and two ribosomal subunits. we have determined cryo-electron microscopic structures of the potc·rrf complex, with and without ef-g. we find that domain ii of rrf initially interacts with universally conserved residues of the 23s rrna helices 43 and 95, and protein l11 within the 50s ribosomal subunit. upon ef-g binding, both rrf and trna are driven towards the t ... | 2012 | 22388519 |
| interpreting protein structural dynamics from nmr chemical shifts. | in this investigation, semiempirical nmr chemical shift prediction methods are used to evaluate the dynamically averaged values of backbone chemical shifts obtained from unbiased molecular dynamics (md) simulations of proteins. md-averaged chemical shift predictions generally improve agreement with experimental values when compared to predictions made from static x-ray structures. improved chemical shift predictions result from population-weighted sampling of multiple conformational states and f ... | 2012 | 22381384 |
| mapping hidden potential identity elements by computing the average discriminating power of individual trna positions. | the recently published discrete mathematical method, extended consensus partition (ecp), identifies nucleotide types at each position that are strictly absent from a given sequence set, while occur in other sets. these are defined as discriminating elements (des). in this study using the ecp approach, we mapped potential hidden identity elements that discriminate the 20 different trna identities. we filtered the tdna data set for the obligatory presence of well-established trna features, and the ... | 2012 | 22378766 |
| acyl carrier protein structural classification and normal mode analysis. | all acyl carrier protein primary and tertiary structures were gathered into the thyme database. they are classified into 16 families by amino acid sequence similarity, with members of the different families having sequences with statistically highly significant differences. these classifications are supported by tertiary structure superposition analysis. tertiary structures from a number of families are very similar, suggesting that these families may come from a single distant ancestor. normal ... | 2012 | 22374859 |
| genetic recombination in bacillus subtilis: a division of labor between two single-strand dna-binding proteins. | we have investigated the structural, biochemical and cellular roles of the two single-stranded (ss) dna-binding proteins from bacillus subtilis, ssba and ssbb. during transformation, ssbb localizes at the dna entry pole where it binds and protects internalized ssdna. the 2.8-å resolution structure of ssbb bound to ssdna reveals a similar overall protein architecture and ssdna-binding surface to that of escherichia coli ssb. ssba, which binds ssdna with higher affinity than ssbb, co-assembles ont ... | 2012 | 22373918 |