Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
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| e. coli rna polymerase determinants of open complex lifetime and structure. | in transcription initiation by escherichia coli rna polymerase (rnap), initial binding to promoter dna triggers large conformational changes, bending downstream duplex dna into the rnap cleft and opening 13bp to form a short-lived open intermediate (i2). subsequent conformational changes increase lifetimes of λpr and t7a1 open complexes (ocs) by >10(5)-fold and >10(2)-fold, respectively. oc lifetime is a target for regulation. to characterize late conformational changes, we determine effects on ... | 2015 | 26055538 |
| r3d-2-msa: the rna 3d structure-to-multiple sequence alignment server. | the rna 3d structure-to-multiple sequence alignment server (r3d-2-msa) is a new web service that seamlessly links rna three-dimensional (3d) structures to high-quality rna multiple sequence alignments (msas) from diverse biological sources. in this first release, r3d-2-msa provides manual and programmatic access to curated, representative ribosomal rna sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3 ... | 2015 | 26048960 |
| structure principles of crispr-cas surveillance and effector complexes. | the pathway of crispr-cas immunity redefines the roles of rna in the flow of genetic information and ignites excitement for next-generation gene therapy tools. crispr-cas machineries offer a fascinating set of new enzyme assemblies from which one can learn principles of molecular interactions and chemical activities. the interference step of the crispr-cas immunity pathway congregates proteins, rna, and dna into a single molecular entity that selectively destroys invading nucleic acids. although ... | 2015 | 26048003 |
| oxidized and reduced [2fe-2s] clusters from an iron(i) synthon. | synthetic [2fe-2s] clusters are often used to elucidate ligand effects on the reduction potentials and spectroscopy of natural electron-transfer sites, which can have anionic cys ligands or neutral his ligands. current synthetic routes to [2fe-2s] clusters are limited in their feasibility with a range of supporting ligands. here, we report a new synthetic route to synthetic [2fe-2s] clusters, through oxidation of an iron(i) source with elemental sulfur. this method yields a neutral diketiminate- ... | 2015 | 26044124 |
| exploring rna polymerase regulation by nmr spectroscopy. | rna synthesis is a central process in all organisms, with rna polymerase (rnap) as the key enzyme. multisubunit rnaps are evolutionary related and are tightly regulated by a multitude of transcription factors. although escherichia coli rnap has been studied extensively, only little information is available about its dynamics and transient interactions. this information, however, are crucial for the complete understanding of transcription regulation in atomic detail. to study rnap by nmr spectros ... | 2015 | 26043358 |
| the impact of drug resistance on mycobacterium tuberculosis physiology: what can we learn from rifampicin? | the emergence of drug-resistant pathogens poses a major threat to public health. although influenced by multiple factors, high-level resistance is often associated with mutations in target-encoding or related genes. the fitness cost of these mutations is, in turn, a key determinant of the spread of drug-resistant strains. rifampicin (rif) is a frontline anti-tuberculosis agent that targets the rpob-encoded β subunit of the dna-dependent rna polymerase (rnap). in mycobacterium tuberculosis (mtb), ... | 2014 | 26038512 |
| structural insights into the translational infidelity mechanism. | the decoding of mrna on the ribosome is the least accurate process during genetic information transfer. here we propose a unified decoding mechanism based on 11 high-resolution x-ray structures of the 70s ribosome that explains the occurrence of missense errors during translation. we determined ribosome structures in rare states where incorrect trnas were incorporated into the peptidyl-trna-binding site. these structures show that in the codon-anticodon duplex, a g·u mismatch adopts the watson-c ... | 2015 | 26037619 |
| cloning and functional characterization of the maize (zea mays l.) carotenoid epsilon hydroxylase gene. | the assignment of functions to genes in the carotenoid biosynthesis pathway is necessary to understand how the pathway is regulated and to obtain the basic information required for metabolic engineering. few carotenoid ε-hydroxylases have been functionally characterized in plants although this would provide insight into the hydroxylation steps in the pathway. we therefore isolated mrna from the endosperm of maize (zea mays l., inbred line b73) and cloned a full-length cdna encoding cyp97c19, a p ... | 2015 | 26030746 |
| a conserved structural chassis for mounting versatile crispr rna-guided immune responses. | bacteria and archaea rely on crispr (clustered regularly interspaced short palindromic repeats) rna-guided adaptive immune systems for targeted elimination of foreign nucleic acids. these immune systems have been divided into three main types, and the first atomic-resolution structure of a type iii rna-guided immune complex provides new insights into the mechanisms of nucleic acid degradation. here we compare the crystal structure of a type iii complex to recently determined structures of dna-ta ... | 2015 | 26028539 |
| distinct trna accommodation intermediates observed on the ribosome with the antibiotics hygromycin a and a201a. | the increase in multi-drug-resistant bacteria is limiting the effectiveness of currently approved antibiotics, leading to a renewed interest in antibiotics with distinct chemical scaffolds. we have solved the structures of the thermus thermophilus 70s ribosome with a-, p-, and e-site trnas bound and in complex with either the aminocyclitol-containing antibiotic hygromycin a (hyga) or the nucleoside antibiotic a201a. both antibiotics bind at the peptidyl transferase center and sterically occlude ... | 2015 | 26028538 |
| structural and mechanistic insights into the pseudomonas fluorescens 2-nitrobenzoate 2-nitroreductase nbaa. | the bacterial 2-nitroreductase nbaa is the primary enzyme initiating the degradation of 2-nitrobenzoate (2-nba), and its activity is controlled by posttranslational modifications. to date, the structure of nbaa remains to be elucidated. in this study, the crystal structure of a cys194ala nbaa mutant was determined to a 1.7-å resolution. the substrate analog 2-nba methyl ester was used to decipher the substrate binding site by inhibition of the wild-type nbaa protein. tandem mass spectrometry sho ... | 2015 | 26025888 |
| molecular detection of bacteria in plant tissues, using universal 16s ribosomal dna degenerated primers. | highly specific, sensitive and rapid tests are required for the detection and identification of covert bacterial contaminations in plant tissue cultures. current methods available for this purpose are tedious, time consuming, highly error prone, expensive, require advanced technical expertise and are sometimes ineffective. we report here the development of a sensitive polymerase chain reaction (pcr) based method for the rapid detection and identification of bacteria occurring in plant tissue cul ... | 2014 | 26019546 |
| histidine 114 is critical for atp hydrolysis by the universally conserved atpase ychf. | gtpases perform a wide range of functions, ranging from protein synthesis to cell signaling. of all known gtpases, only eight are conserved across all three domains of life. ychf is one of these eight universally conserved gtpases; however, its cellular function and enzymatic properties are poorly understood. ychf differs from the classical gtpases in that it has a higher affinity for atp than for gtp and is a functional atpase. as a hydrophobic amino acid-substituted atpase, ychf does not posse ... | 2015 | 26018081 |
| enzymological characterization of atm, the first laccase from agrobacterium sp. s5-1, with the ability to enhance in vitro digestibility of maize straw. | laccase is an enzyme that catalyzes oxidation of phenolic compounds, diamines and aromatic amines. in this study, a novel laccase-like gene (atm) in a ligninolyitic isolate agrobacterium sp. s5-1 from soil humus was identified and heterologously expressed in escherichia coli. atm exhibited its maximal activity at ph 4.5 and at 50°c. this enzyme was tolerant to high temperature, a broad range of ph, heavy metal ions (co3+, mn2+, cu2+ and ni2+, 20 mm) and all tested organic solvents. furthermore, ... | 2015 | 26010258 |
| effect of monovalent cations on the kinetics of hypoxic conformational change of mitochondrial complex i. | mitochondrial complex i is a large, membrane-bound enzyme central to energy metabolism, and its dysfunction is implicated in cardiovascular and neurodegenerative diseases. an interesting feature of mammalian complex i is the so-called a/d transition, when the idle enzyme spontaneously converts from the active (a) to the de-active, dormant (d) form. the a/d transition plays an important role in tissue response to ischemia and rate of the conversion can be a crucial factor determining outcome of i ... | 2015 | 26009015 |
| regulation of the type i-f crispr-cas system by crp-camp and galm controls spacer acquisition and interference. | the crispr-cas prokaryotic 'adaptive immune systems' represent a sophisticated defence strategy providing bacteria and archaea with protection from invading genetic elements, such as bacteriophages or plasmids. despite intensive research into their mechanism and application, how crispr-cas systems are regulated is less clear, and nothing is known about the regulation of type i-f systems. we used pectobacterium atrosepticum, a gram-negative phytopathogen, to study crispr-cas regulation, since it ... | 2015 | 26007654 |
| metabolism of β-valine via a coa-dependent ammonia lyase pathway. | pseudomonas species strain sbv1 can rapidly grow on medium containing β-valine as a sole nitrogen source. the tertiary amine feature of β-valine prevents direct deamination reactions catalyzed by aminotransferases, amino acid dehydrogenases, and amino acid oxidases. however, lyase- or aminomutase-mediated conversions would be possible. to identify enzymes involved in the degradation of β-valine, a pssbv1 gene library was prepared and used to complement the β-valine growth deficiency of a closely ... | 2015 | 26004802 |
| analysis of r-protein and rna conformation of 30s subunit intermediates in bacteria. | the ribosome is a large macromolecular complex that must be assembled efficiently and accurately for the viability of all organisms. in bacteria, this process must be robust and tunable to support life in diverse conditions from the ice of arctic glaciers to thermal hot springs. assembly of the small ribosomal subunit (ssu) of escherichia coli has been extensively studied and is highly temperature-dependent. however, a lack of data on ssu assembly for other bacteria is problematic given the impo ... | 2015 | 25999315 |
| structure of a type iv pilus machinery in the open and closed state. | proteins of the secretin family form large macromolecular complexes, which assemble in the outer membrane of gram-negative bacteria. secretins are major components of type ii and iii secretion systems and are linked to extrusion of type iv pili (t4p) and to dna uptake. by electron cryo-tomography of whole thermus thermophilus cells, we determined the in situ structure of a t4p molecular machine in the open and the closed state. comparison reveals a major conformational change whereby the n-termi ... | 2015 | 25997099 |
| mutations in the cre pocket of bacterial rna polymerase affect multiple steps of transcription. | during transcription, the catalytic core of rna polymerase (rnap) must interact with the dna template with low-sequence specificity to ensure efficient enzyme translocation and rna extension. unexpectedly, recent structural studies of bacterial promoter complexes revealed specific interactions between the nontemplate dna strand at the downstream edge of the transcription bubble (cre, core recognition element) and a protein pocket formed by core rnap (cre pocket). we investigated the roles of the ... | 2015 | 25990734 |
| phylogenetic analysis of vitamin b12-related metabolism in mycobacterium tuberculosis. | comparison of genome sequences from clinical isolates of mycobacterium tuberculosis with phylogenetically-related pathogens mycobacterium marinum, mycobacterium kansasii, and mycobacterium leprae reveals diversity amongst genes associated with vitamin b12-related metabolism. diversity is generated by gene deletion events, differential acquisition of genes by horizontal transfer, and single nucleotide polymorphisms (snps) with predicted impact on protein function and transcriptional regulation. d ... | 2015 | 25988174 |
| synergism between a foldase and an unfoldase: reciprocal dependence between the thioredoxin-like activity of dnaj and the polypeptide-unfolding activity of dnak. | the role of bacterial hsp40, dnaj, is to co-chaperone the binding of misfolded or alternatively folded proteins to bacterial hsp70, dnak, which is an atp-fuelled unfolding chaperone. in addition to its dnak targeting activity, dnaj has a weak thiol-reductase activity. in between the substrate-binding domain and the j-domain anchor to dnak, dnaj has a unique domain with four conserved cxxc motives that bind two zn(2+) and partly contribute to polypeptide binding. here, we deleted in dnaj this zn- ... | 2014 | 25988148 |
| a derivative of the thiopeptide ge2270a highly selective against propionibacterium acnes. | a chemical derivative of the thiopeptide ge2270a, designated nai003, was found to possess a substantially reduced antibacterial spectrum in comparison to the parent compound, being active against just a few gram-positive bacteria. in particular, nai003 retained low mics against all tested isolates of propionibacterium acnes and, to a lesser extent, against enterococcus faecalis. furthermore, nai003 showed a time- and dose-dependent killing of both a clindamycin-resistant and a clindamycin-sensit ... | 2015 | 25987631 |
| the mechanism of inhibition of protein synthesis by the proline-rich peptide oncocin. | antibiotic-resistant bacteria are a global health issue necessitating the development of new effective therapeutics. proline-rich antimicrobial peptides (pramps), which include oncocins, are an extensively studied class of amps that counteract bacterial infection at submicromolar concentrations. oncocins enter and kill bacteria by inhibiting certain targets rather than by acting through membrane lysis. although they have recently been reported to bind dnak and the bacterial ribosome, their mode ... | 2015 | 25984972 |
| bacterial xylose isomerases from the mammal gut bacteroidetes cluster function in saccharomyces cerevisiae for effective xylose fermentation. | xylose isomerase (xi) catalyzes the conversion of xylose to xylulose, which is the key step for anaerobic ethanolic fermentation of xylose. very few bacterial xis can function actively in saccharomyces cerevisiae. here, we illustrate a group of xis that would function for xylose fermentation in s. cerevisiae through phylogenetic analysis, recombinant yeast strain construction, and xylose fermentation. | 2015 | 25981595 |
| during cytochrome c maturation ccmi chaperones the class i apocytochromes until the formation of their b-type cytochrome intermediates. | the c-type cytochromes are electron transfer proteins involved in energy transduction. they have heme-binding (cxxch) sites that covalently ligate heme b via thioether bonds and are classified into different classes based on their protein folds and the locations and properties of their cofactors. rhodobacter capsulatus produces various c-type cytochromes using the cytochrome c maturation (ccm) system i, formed from the ccmabcdefghi proteins. ccmi, a component of the heme ligation complex ccmfhi, ... | 2015 | 25979338 |
| draft genome sequence of the thermophile thermus filiformis atcc 43280, producer of carotenoid-(di)glucoside-branched fatty acid (di)esters and source of hyperthermostable enzymes of biotechnological interest. | here, we present the draft genome sequence of thermus filiformis strain atcc 43280, a thermophile bacterium capable of producing glycosylated carotenoids acylated with branched fatty acids and enzymes of biotechnological potential. | 2015 | 25977443 |
| the eukaryotic translation initiation regulator cdc123 defines a divergent clade of atp-grasp enzymes with a predicted role in novel protein modifications. | deciphering the origin of uniquely eukaryotic features of sub-cellular systems, such as the translation apparatus, is critical in reconstructing eukaryogenesis. one such feature is the highly conserved, but poorly understood, eukaryotic protein cdc123, which regulates the abundance of the eukaryotic translation initiation eif2 complex and binds one of its components eif2γ. we show that the eukaryotic protein cdc123 defines a novel clade of atp-grasp enzymes distinguished from all other members o ... | 2015 | 25976611 |
| the minor capsid protein vp11 of thermophilic bacteriophage p23-77 facilitates virus assembly by using lipid-protein interactions. | thermus thermophilus bacteriophage p23-77 is the type member of a new virus family of icosahedral, tailless, inner-membrane-containing double-stranded dna (dsdna) viruses infecting thermophilic bacteria and halophilic archaea. the viruses have a unique capsid architecture consisting of two major capsid proteins assembled in various building blocks. we analyzed the function of the minor capsid protein vp11, which is the third known capsid component in bacteriophage p23-77. our findings show that ... | 2015 | 25972558 |
| structural biology of bacterial rna polymerase. | since its discovery and characterization in the early 1960s (hurwitz, j. the discovery of rna polymerase. j. biol. chem. 2005, 280, 42477-42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial rna polymerase (rnap). in the late 1990s, structural information pertaining to bacterial rnap has emerged that provided unprecedented insights into the function and mechanism of rna transcription. in this review, i list all structures related to bacterial rn ... | 2015 | 25970587 |
| conformational plasticity surrounding the active site of nadh oxidase from thermus thermophilus. | biotechnological applications of enzymes can involve the use of these molecules under nonphysiological conditions. thus, it is of interest to understand how environmental variables affect protein structure and dynamics and how this ultimately modulates enzyme function. nadh oxidase (nox) from thermus thermophilus exemplifies how enzyme activity can be tuned by reaction conditions, such as temperature, cofactor substitution, and the addition of cosolutes. this enzyme catalyzes the oxidation of re ... | 2015 | 25970557 |
| the transcription factor carh safeguards use of adenosylcobalamin as a light sensor by altering the photolysis products. | the newly discovered light-dependent transcription factor carh uses adenosylcobalamin as a light sensor to regulate expression of protective genes in bacteria upon exposure to sunlight. this use of adenosylcobalamin is a clever adaptation of a classic enzyme cofactor, taking advantage of its photolabile co-c bond. however, it is also puzzling in that photolysis of adenosylcobalamin generates the 5'-deoxyadenosyl radical that could damage dna. here, using liquid chromatography and spectroscopic t ... | 2015 | 25966286 |
| insights into parb spreading from the complex structure of spo0j and pars. | spo0j (stage 0 sporulation protein j, a member of the parb superfamily) is an essential component of the parabs (partition system of para, parb, and pars)-related bacterial chromosome segregation system. parb (partition protein b) and its regulatory protein, para, act cooperatively through pars (partition s) dna to facilitate chromosome segregation. parb binds to chromosomal dna at specific pars sites as well as the neighboring nonspecific dna sites. various parb molecules can associate together ... | 2015 | 25964325 |
| co-transcriptional dna and rna cleavage during type iii crispr-cas immunity. | immune systems must recognize and destroy different pathogens that threaten the host. crispr-cas immune systems protect prokaryotes from viral and plasmid infection utilizing small crispr rnas that are complementary to the invader's genome and specify the targets of rna-guided cas nucleases. type iii crispr-cas immunity requires target transcription, and whereas genetic studies demonstrated dna targeting, in vitro data have shown crrna-guided rna cleavage. the molecular mechanism behind these di ... | 2015 | 25959775 |
| structural snapshots of actively translating human ribosomes. | macromolecular machines, such as the ribosome, undergo large-scale conformational changes during their functional cycles. although their mode of action is often compared to that of mechanical machines, a crucial difference is that, at the molecular dimension, thermodynamic effects dominate functional cycles, with proteins fluctuating stochastically between functional states defined by energetic minima on an energy landscape. here, we have used cryo-electron microscopy to image ex-vivo-derived hu ... | 2015 | 25957688 |
| structure of a cuta1 divalent-cation tolerance protein from cryptosporidium parvum, the protozoal parasite responsible for cryptosporidiosis. | cryptosporidiosis is an infectious disease caused by protozoan parasites of the cryptosporidium genus. infection is associated with mild to severe diarrhea that usually resolves spontaneously in healthy human adults, but may lead to severe complications in young children and in immunocompromised patients. the genome of c. parvum contains a gene, cuta_crypi, that may play a role in regulating the intracellular concentration of copper, which is a toxic element in excess. here, the crystal structur ... | 2015 | 25945704 |
| role of a ribosomal rna phosphate oxygen during the ef-g-triggered gtp hydrolysis. | elongation factor-catalyzed gtp hydrolysis is a key reaction during the ribosomal elongation cycle. recent crystal structures of g proteins, such as elongation factor g (ef-g) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational gtpases (trgtpases) with the sarcin-ricin loop (srl) of ribosomal rna (rrna) is pivotal for hydrolysis. however, the precise mechanism remains elusive and is intensively debated. based on the close prox ... | 2015 | 25941362 |
| a mutation of rna polymerase β' subunit (rpoc) converts heterogeneously vancomycin-intermediate staphylococcus aureus (hvisa) into "slow visa". | various mutations in the rpob gene, which encodes the rna polymerase β subunit, are associated with increased vancomycin (van) resistance in vancomycin-intermediate staphylococcus aureus (visa) and heterogeneously visa (hvisa) strains. we reported that rpob mutations are also linked to the expression of the recently found "slow visa" (svisa) phenotype (m. saito, y. katayama, t. hishinuma, a. iwamoto, y. aiba, k kuwahara-arai, l. cui, m. matsuo, n. aritaka, and k. hiramatsu, antimicrob agents che ... | 2015 | 25941225 |
| structural insights into catalysis and dimerization enhanced exonuclease activity of rnase j. | rnase j is a conserved ribonuclease that belongs to the β-casp family of nucleases. it possesses both endo- and exo-ribonuclease activities, which play a key role in pre-rrna maturation and mrna decay. here we report high-resolution crystal structures of deinococcus radiodurans rnase j complexed with rna or uridine 5'-monophosphate in the presence of manganese ions. biochemical and structural studies revealed that rnase j uses zinc ions for two-metal-ion catalysis. one residue conserved among rn ... | 2015 | 25940620 |
| base flipping in open complex formation at bacterial promoters. | in the process of transcription initiation, the bacterial rna polymerase binds double-stranded (ds) promoter dna and subsequently effects strand separation of 12 to 14 base pairs (bp), including the start site of transcription, to form the so-called "open complex" (also referred to as rp(o)). this complex is competent to initiate rna synthesis. here we will review the role of σ70 and its homologs in the strand separation process, and evidence that strand separation is initiated at the -11a (the ... | 2015 | 25927327 |
| argonaute of the archaeon pyrococcus furiosus is a dna-guided nuclease that targets cognate dna. | functions of prokaryotic argonautes (pago) have long remained elusive. recently, argonautes of the bacteria rhodobacter sphaeroides and thermus thermophilus were demonstrated to be involved in host defense. the argonaute of the archaeon pyrococcus furiosus (pfago) belongs to a different branch in the phylogenetic tree, which is most closely related to that of rna interference-mediating eukaryotic argonautes. here we describe a functional and mechanistic characterization of pfago. like the bacter ... | 2015 | 25925567 |
| crystal structure of the protein at3g01520, a eukaryotic universal stress protein-like protein from arabidopsis thaliana in complex with amp. | members of the universal stress protein (usp) family are conserved in a phylogenetically diverse range of prokaryotes, fungi, protists, and plants and confer abilities to respond to a wide range of environmental stresses. arabidopsis thaliana contains 44 usp domain-containing proteins, and usp domain is found either in a small protein with unknown physiological function or in an n-terminal portion of a multi-domain protein, usually a protein kinase. here, we report the first crystal structure of ... | 2015 | 25921306 |
| crystal structure of the human mitochondrial chaperonin symmetrical football complex. | human mitochondria harbor a single type i chaperonin system that is generally thought to function via a unique single-ring intermediate. to date, no crystal structure has been published for any mammalian type i chaperonin complex. in this study, we describe the crystal structure of a football-shaped, double-ring human mitochondrial chaperonin complex at 3.15 å, which is a novel intermediate, likely representing the complex in an early stage of dissociation. interestingly, the mitochondrial chape ... | 2015 | 25918392 |
| role and function of litr, an adenosyl b12-bound light-sensitive regulator of bacillus megaterium qm b1551, in regulation of carotenoid production. | the litr/carh family of proteins is a light-sensitive merr family of transcriptional regulators that contain an adenosyl b12 (coenzyme b12 or adob12)-binding domain at the c terminus. the genes encoding these proteins are found in phylogenetically diverse bacterial genera; however, the biochemical properties of these proteins from gram-positive bacteria remain poorly understood. we performed genetic and biochemical analyses of a homolog of the litr protein from bacillus megaterium qm b1551, a gr ... | 2015 | 25917914 |
| novel role for pilno in type iv pilus retraction revealed by alignment subcomplex mutations. | type iv pili (t4p) are dynamic protein filaments that mediate bacterial adhesion, biofilm formation, and twitching motility. the highly conserved pilmnop proteins form an inner membrane alignment subcomplex required for function of the t4p system, though their exact roles are unclear. three potential interaction interfaces for pilno were identified: core-core, coiled coils (cc), and the transmembrane segments (tmss). a high-confidence pilno heterodimer model was used to select key residues for m ... | 2015 | 25917913 |
| manual classification strategies in the ecod database. | ecod (evolutionary classification of protein domains) is a comprehensive and up-to-date protein structure classification database. the majority of new structures released from the pdb (protein data bank) each week already have close homologs in the ecod hierarchy and thus can be reliably partitioned into domains and classified by software without manual intervention. however, those proteins that lack confidently detectable homologs require careful analysis by experts. although many bioinformatic ... | 2015 | 25917548 |
| structure-based functional identification of helicobacter pylori hp0268 as a nuclease with both dna nicking and rnase activities. | hp0268 is a conserved, uncharacterized protein from helicobacter pylori. here, we determined the solution structure of hp0268 using three-dimensional nuclear magnetic resonance (nmr) spectroscopy, revealing that this protein is structurally most similar to a small muts-related (smr) domain that exhibits nicking endonuclease activity. we also demonstrated for the first time that hp0268 is a nicking endonuclease and a purine-specific ribonuclease through gel electrophoresis and fluorescence spectr ... | 2015 | 25916841 |
| contribution to the prediction of the fold code: application to immunoglobulin and flavodoxin cases. | folding nucleus of globular proteins formation starts by the mutual interaction of a group of hydrophobic amino acids whose close contacts allow subsequent formation and stability of the 3d structure. these early steps can be predicted by simulation of the folding process through a monte carlo (mc) coarse grain model in a discrete space. we previously defined mirs (most interacting residues), as the set of residues presenting a large number of non-covalent neighbour interactions during such simu ... | 2015 | 25915049 |
| characterization of chromosomal and megaplasmid partitioning loci in thermus thermophilus hb27. | in low-copy-number plasmids, the partitioning loci (par) act to ensure proper plasmid segregation and copy number maintenance in the daughter cells. in many bacterial species, par gene homologues are encoded on the chromosome, but their function is much less understood. in the two-replicon, polyploid genome of the hyperthermophilic bacterium thermus thermophilus, both the chromosome and the megaplasmid encode par gene homologues (parabc and parabm, respectively). the mode of partitioning of the ... | 2015 | 25909452 |
| structural features of a 3' splice site in influenza a. | influenza a is an rna virus with a genome of eight negative sense segments. segment 7 mrna contains a 3' splice site for alternative splicing to encode the essential m2 protein. on the basis of sequence alignment and chemical mapping experiments, the secondary structure surrounding the 3' splice site has an internal loop, adenine bulge, and hairpin loop when it is in the hairpin conformation that exposes the 3' splice site. we report structural features of a three-dimensional model of the hairpi ... | 2015 | 25909229 |
| real-time submillisecond single-molecule fret dynamics of freely diffusing molecules with liposome tethering. | single-molecule fluorescence resonance energy transfer (smfret) is one of the powerful techniques for deciphering the dynamics of unsynchronized biomolecules. however, smfret is limited in its temporal resolution for observing dynamics. here, we report a novel method for observing real-time dynamics with submillisecond resolution by tethering molecules to freely diffusing 100-nm-sized liposomes. the observation time for a diffusing molecule is extended to 100 ms with a submillisecond resolution, ... | 2015 | 25908552 |
| identification of novel esterase-active enzymes from hot environments by use of the host bacterium thermus thermophilus. | functional metagenomic screening strategies, which are independent of known sequence information, can lead to the identification of truly novel genes and enzymes. since e. coli has been used exhaustively for this purpose as a host, it is important to establish alternative expression hosts and to use them for functional metagenomic screening for new enzymes. in this study we show that thermus thermophilus hb27 is an excellent screening host and can be used as an alternative provider of truly nove ... | 2015 | 25904908 |
| dna interference: dna-induced gene silencing in the appendicularian oikopleura dioica. | rna interference is widely employed as a gene-silencing system in eukaryotes for host defence against invading nucleic acids. in response to invading double-stranded rna (dsrna), mrna is degraded in sequence-specific manner. so far, however, dna interference (dnai) has been reported only in plants, ciliates and archaea, and has not been explored in metazoa. here, we demonstrate that linear double-stranded dna promotes both sequence-specific transcription blocking and mrna degradation in developi ... | 2015 | 25904672 |
| major reorientation of trna substrates defines specificity of dihydrouridine synthases. | the reduction of specific uridines to dihydrouridine is one of the most common modifications in trna. increased levels of the dihydrouridine modification are associated with cancer. dihydrouridine synthases (dus) from different subfamilies selectively reduce distinct uridines, located at spatially unique positions of folded trna, into dihydrouridine. because the catalytic center of all dus enzymes is conserved, it is unclear how the same protein fold can be reprogrammed to ensure that nucleotide ... | 2015 | 25902496 |
| effects of argonaute on gene expression in thermus thermophilus. | eukaryotic argonaute proteins mediate rna-guided rna interference, allowing both regulation of host gene expression and defense against invading mobile genetic elements. recently, it has become evident that prokaryotic argonaute homologs mediate dna-guided dna interference, and play a role in host defense. argonaute of the bacterium thermus thermophilus (ttago) targets invading plasmid dna during and after transformation. using small interfering dna guides, ttago can cleave single and double str ... | 2015 | 25902012 |
| biosynthesis of l-sorbose and l-psicose based on c-c bond formation catalyzed by aldolases in an engineered corynebacterium glutamicum strain. | the property of loose stereochemical control at aldol products from aldolases helped to synthesize multiple polyhydroxylated compounds with nonnatural stereoconfiguration. in this study, we discovered for the first time that some fructose 1,6-diphosphate aldolases (frua) and tagatose 1,6-diphosphate (taga) aldolases lost their strict stereoselectivity when using l-glyceraldehyde and synthesized not only l-sorbose but also a high proportion of l-psicose. among the aldolases tested, taga from baci ... | 2015 | 25888171 |
| structural effects of protein aging: terminal marking by deamidation in human triosephosphate isomerase. | deamidation, the loss of the ammonium group of asparagine and glutamine to form aspartic and glutamic acid, is one of the most commonly occurring post-translational modifications in proteins. since deamidation rates are encoded in the protein structure, it has been proposed that they can serve as molecular clocks for the timing of biological processes such as protein turnover, development and aging. despite the importance of this process, there is a lack of detailed structural information explai ... | 2015 | 25884638 |
| identification of a laccase glac15 from ganoderma lucidum 77002 and its application in bioethanol production. | laccases have potential applications in detoxification of lignocellulosic biomass after thermochemical pretreatment and production of value-added products or biofuels from renewable biomass. however, their application in large-scale industrial and environmental processes has been severely thwarted by the high cost of commercial laccases. therefore, it is necessary to identify new laccases with lower cost but higher activity to detoxify lignocellulosic hydrolysates and better efficiency to produc ... | 2015 | 25883681 |
| a novel family of integrases associated with prophages and genomic islands integrated within the trna-dihydrouridine synthase a (dusa) gene. | genomic islands play a key role in prokaryotic genome plasticity. genomic islands integrate into chromosomal loci such as transfer rna genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. a gene encoding a putative integrase was identified at a single site within the 5' end of the dusa gene in the genomes of over 200 bacteria. this integrase was discovered to be a component of numerous genomic islands, which appear to ... | 2015 | 25883135 |
| applications of cas9 as an rna-programmed rna-binding protein. | the streptococcus pyogenes crispr-cas system has gained widespread application as a genome editing and gene regulation tool as simultaneous cellular delivery of the cas9 protein and guide rnas enables recognition of specific dna sequences. the recent discovery that cas9 can also bind and cleave rna in an rna-programmable manner indicates the potential utility of this system as a universal nucleic acid-recognition technology. rna-targeted cas9 (rcas9) could allow identification and manipulation o ... | 2015 | 25880497 |
| structural basis for 2'-5'-oligoadenylate binding and enzyme activity of a viral rnase l antagonist. | synthesis of 2'-5'-oligoadenylates (2-5a) by oligoadenylate synthetase (oas) is an important innate cellular response that limits viral replication by activating the latent cellular rnase, rnase l, to degrade single-stranded rna. some rotaviruses and coronaviruses antagonize the oas/rnase l pathway through the activity of an encoded 2h phosphoesterase domain that cleaves 2-5a. these viral 2h phosphoesterases are phylogenetically related to the cellular a kinase anchoring protein 7 (akap7) and sh ... | 2015 | 25878106 |
| major centers of motion in the large ribosomal rnas. | major centers of motion in the rrnas of thermus thermophilus are identified by alignment of crystal structures of ef-g bound and ef-g unbound ribosomal subunits. small rigid helices upstream of these 'pivots' are aligned, thereby decoupling their motion from global rearrangements. of the 21 pivots found, six are observed in the large subunit rrna and 15 in the small subunit rrna. although the magnitudes of motion differ, with only minor exceptions equivalent pivots are seen in comparisons of esc ... | 2015 | 25870411 |
| semiquinone intermediates are involved in the energy coupling mechanism of e. coli complex i. | complex i (nadh:quinone oxidoreductase) is central to cellular aerobic energy metabolism, and its deficiency is involved in many human mitochondrial diseases. complex i translocates protons across the membrane using electron transfer energy. semiquinone (sq) intermediates appearing during catalysis are suggested to be key for the coupling mechanism in complex i. however, the existence of sq has remained controversial due to the extreme difficulty in detecting unstable and low intensity sq signal ... | 2015 | 25868873 |
| atomic-resolution structures of discrete stages on the reaction coordinate of the [fe4s4] enzyme ispg (gcpe). | ispg is the penultimate enzyme in non-mevalonate biosynthesis of the universal terpene building blocks isopentenyl diphosphate and dimethylallyl diphosphate. its mechanism of action has been the subject of numerous studies but remained unresolved due to difficulties in identifying distinct reaction intermediates. using a moderate reducing agent and an epoxide substrate analogue, we were now able to trap and crystallographically characterize various stages in the ispg-catalyzed conversion of 2-c- ... | 2015 | 25868383 |
| multiple mutations and increased rna expression in tetracycline-resistant streptococcus pneumoniae as determined by genome-wide dna and mrna sequencing. | the objective of this study was to characterize chromosomal mutations associated with resistance to tetracycline in streptococcus pneumoniae. | 2015 | 25862682 |
| isolation and characterization of a hybrid respiratory supercomplex consisting of mycobacterium tuberculosis cytochrome bcc and mycobacterium smegmatis cytochrome aa3. | recently, energy production pathways have been shown to be viable antitubercular drug targets to combat multidrug-resistant tuberculosis and eliminate pathogen in the dormant state. one family of drugs currently under development, the imidazo[1,2-a]pyridine derivatives, is believed to target the pathogen's homolog of the mitochondrial bc1 complex. this complex, denoted cytochrome bcc, is highly divergent from mitochondrial complex iii both in subunit structure and inhibitor sensitivity, making i ... | 2015 | 25861988 |
| parallel structural evolution of mitochondrial ribosomes and oxphos complexes. | the five macromolecular complexes that jointly mediate oxidative phosphorylation (oxphos) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which evolutionary mechanism(s) these novel subunits were recruited. even less well understood is the structural evolution of mitochondrial ribosomes (mitoribosomes): while it was long thought that their exceptionally high protein content would physically compensate for their uniquely low amount of ribosomal rna ... | 2015 | 25861818 |
| trnaglu increases the affinity of glutamyl-trna synthetase for its inhibitor glutamyl-sulfamoyl-adenosine, an analogue of the aminoacylation reaction intermediate glutamyl-amp: mechanistic and evolutionary implications. | for trna-dependent protein biosynthesis, amino acids are first activated by aminoacyl-trna synthetases (aarss) yielding the reaction intermediates aminoacyl-amp (aa-amp). stable analogues of aa-amp, such as aminoacyl-sulfamoyl-adenosines, inhibit their cognate aarss. glutamyl-sulfamoyl-adenosine (glu-ams) is the best known inhibitor of escherichia coli glutamyl-trna synthetase (glurs). thermodynamic parameters of the interactions between glu-ams and e. coli glurs were measured in the presence an ... | 2015 | 25860020 |
| zinc regulates a switch between primary and alternative s18 ribosomal proteins in mycobacterium tuberculosis. | the mycobacterium tuberculosis genome encodes five putative 'alternative' ribosomal proteins whose expression is repressed at high zn(2+) concentration. each alternative protein has a primary homologue that is predicted to bind zn(2+). we hypothesized that zinc triggers a switch between these paired homologous proteins and therefore chose one of these pairs, s18-1/s18-2, to study mechanisms of the predicted competition for their incorporation into ribosomes. our data show that zn(2+)-depletion c ... | 2015 | 25858183 |
| molecular determinants of the interactions between proteins and ssdna. | ssdna binding proteins (ssbs) protect ssdna from chemical and enzymatic assault that can derail dna processing machinery. complexes between ssbs and ssdna are often highly stable, but predicting their structures is challenging, mostly because of the inherent flexibility of ssdna and the geometric and energetic complexity of the interfaces that it forms. here, we report a newly developed coarse-grained model to predict the structure of ssb-ssdna complexes. the model is successfully applied to pre ... | 2015 | 25855635 |
| marine extremophiles: a source of hydrolases for biotechnological applications. | the marine environment covers almost three quarters of the planet and is where evolution took its first steps. extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. the ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. hydrolases including amylases, cellulases, peptidases and lipases from hyper ... | 2015 | 25854643 |
| recent functional insights into the role of (p)ppgpp in bacterial physiology. | the alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppgpp) are involved in regulating growth and several different stress responses in bacteria. in recent years, substantial progress has been made in our understanding of the molecular mechanisms of (p)ppgpp metabolism and (p)ppgpp-mediated regulation. in this review, we summarize these recent insights, with a focus on the molecular mechanisms governing the activity of the rela/spot homologue (rsh) ... | 2015 | 25853779 |
| salinity regulation of the interaction of halovirus snj1 with its host and alteration of the halovirus replication strategy to adapt to the variable ecosystem. | halovirus is a major force that affects the evolution of extreme halophiles and the biogeochemistry of hypersaline environments. however, until now, the systematic studies on the halovirus ecology and the effects of salt concentration on virus-host systems are lacking. to provide more valuable information for understanding ecological strategies of a virus-host system in the hypersaline ecosystem, we studied the interaction between halovirus snj1 and its host natrinema sp.j7-2 under various nacl ... | 2015 | 25853566 |
| the phenotypic expression of mitochondrial trna-mutations can be modulated by either mitochondrial leucyl-trna synthetase or the c-terminal domain thereof. | mutations in mitochondrial (mt) dna determine important human diseases. the majority of the known pathogenic mutations are located in transfer rna (trna) genes and are responsible for a wide range of currently untreatable disorders. experimental evidence both in yeast and in human cells has shown that the detrimental effects of mt-trna point mutations can be attenuated by increasing the expression of the cognate mt-aminoacyl-trna synthetases (aarss). in addition, constitutive high levels of isol ... | 2015 | 25852750 |
| the human 18s rrna base methyltransferases dimt1l and wbscr22-trmt112 but not rrna modification are required for ribosome biogenesis. | at the heart of the ribosome lie rrnas, whose catalytic function in translation is subtly modulated by posttranscriptional modifications. in the small ribosomal subunit of budding yeast, on the 18s rrna, two adjacent adenosines (a1781/a1782) are n(6)-dimethylated by dim1 near the decoding site, and one guanosine (g1575) is n(7)-methylated by bud23-trm112 at a ridge between the p- and e-site trnas. here we establish human dimt1l and wbscr22-trmt112 as the functional homologues of yeast dim1 and b ... | 2015 | 25851604 |
| productive mrna stem loop-mediated transcriptional slippage: crucial features in common with intrinsic terminators. | escherichia coli and yeast dna-dependent rna polymerases are shown to mediate efficient nascent transcript stem loop formation-dependent rna-dna hybrid realignment. the realignment was discovered on the heteropolymeric sequence t5c5 and yields transcripts lacking a c residue within a corresponding u5c4. the sequence studied is derived from a roseiflexus insertion sequence (is) element where the resulting transcriptional slippage is required for transposase synthesis. the stability of the rna str ... | 2015 | 25848054 |
| two duplicated genes ddi2 and ddi3 in budding yeast encode a cyanamide hydratase and are induced by cyanamide. | two dna damage-inducible genes in saccharomyces cerevisiae, ddi2 and ddi3, are identical and encode putative hd domain-containing proteins, whose functions are currently unknown. because ddi2/3 also shows limited homology to a fungal cyanamide hydratase that converts cyanamide to urea, we tested the enzymatic activity of recombinant ddi2. to this end, we developed a novel enzymatic assay and determined that the km value of the recombinant ddi2/3 for cyanamide is 17.3 ± 0.05 mm, and its activity ... | 2015 | 25847245 |
| a functional role of rv1738 in mycobacterium tuberculosis persistence suggested by racemic protein crystallography. | protein 3d structure can be a powerful predictor of function, but it often faces a critical roadblock at the crystallization step. rv1738, a protein from mycobacterium tuberculosis that is strongly implicated in the onset of nonreplicating persistence, and thereby latent tuberculosis, resisted extensive attempts at crystallization. chemical synthesis of the l- and d-enantiomeric forms of rv1738 enabled facile crystallization of the d/l-racemic mixture. the structure was solved by an ab initio ap ... | 2015 | 25831534 |
| interaction of trna with eukaryotic ribosome. | this paper is a review of currently available data concerning interactions of trnas with the eukaryotic ribosome at various stages of translation. these data include the results obtained by means of cryo-electron microscopy and x-ray crystallography applied to various model ribosomal complexes, site-directed cross-linking with the use of trna derivatives bearing chemically or photochemically reactive groups in the cca-terminal fragment and chemical probing of 28s rrna in the region of the peptid ... | 2015 | 25830484 |
| the vrra srna controls a stationary phase survival factor vrp of vibrio cholerae. | small non-coding rnas (srnas) are emerging regulatory elements in bacteria. the vibrio cholerae srna vrra has previously been shown to down-regulate outer membrane proteins (ompa and ompt) and biofilm matrix protein (rbmc) by base-pairing with the 5' region of the corresponding mrnas. in this study, we present an additional target of vrra in v. cholerae, the mrna coding for the ribosome binding protein vrp. vrp is homologous to ribosome-associated inhibitor a (raia) of escherichia coli which fac ... | 2015 | 25826569 |
| triaminopyrimidine is a fast-killing and long-acting antimalarial clinical candidate. | the widespread emergence of plasmodium falciparum (pf) strains resistant to frontline agents has fuelled the search for fast-acting agents with novel mechanism of action. here, we report the discovery and optimization of novel antimalarial compounds, the triaminopyrimidines (taps), which emerged from a phenotypic screen against the blood stages of pf. the clinical candidate (compound 12) is efficacious in a mouse model of pf malaria with an ed99 <30 mg kg(-1) and displays good in vivo safety mar ... | 2015 | 25823686 |
| structure-function dissection of myxococcus xanthus card n-terminal domain, a defining member of the card_cdnl_trcf family of rna polymerase interacting proteins. | two prototypes of the large card_cdnl_trcf family of bacterial rna polymerase (rnap)-binding proteins, myxococcus xanthus card and cdnl, have distinct functions whose molecular basis remain elusive. card, a global regulator linked to the action of several extracytoplasmic function (ecf) σ-factors, binds to the rnap β subunit (rnap-β) and to protein carg via an n-terminal domain, cardnt, and to dna via an intrinsically unfolded c-terminal domain resembling eukaryotic high-mobility-group a (hmga) ... | 2015 | 25811865 |
| the conserved endoribonuclease ybey is required for chloroplast ribosomal rna processing in arabidopsis. | maturation of chloroplast ribosomal rnas (rrnas) comprises several endoribonucleolytic and exoribonucleolytic processing steps. however, little is known about the specific enzymes involved and the cleavage steps they catalyze. here, we report the functional characterization of the single arabidopsis (arabidopsis thaliana) gene encoding a putative ybey endoribonuclease. atybey null mutants are seedling lethal, indicating that atybey function is essential for plant growth. knockdown plants display ... | 2015 | 25810095 |
| deinococcus as new chassis for industrial biotechnology: biology, physiology and tools. | deinococcus spp are among the most radiation-resistant micro-organisms that have been discovered. they show remarkable resistance to a range of damage caused by ionizing radiation, desiccation, uv radiation and oxidizing agents. traditionally, escherichia coli and saccharomyces cerevisiae have been the two platforms of choice for engineering micro-organisms for biotechnological applications, because they are well understood and easy to work with. however, in recent years, researchers have begun ... | 2015 | 25809882 |
| glycosylation of phenolic compounds by the site-mutated β-galactosidase from lactobacillus bulgaricus l3. | β-galactosidases can transfer the galactosyl from lactose or galactoside donors to various acceptors and thus are especially useful for the synthesis of important glycosides. however, these enzymes have limitations in the glycosylation of phenolic compounds that have many physiological functions. in this work, the β-galactosidase from lactobacillus bulgaricus l3 was subjected to site-saturation mutagenesis at the w980 residue. the recombinant pet-21b plasmid carrying the enzyme gene was used as ... | 2015 | 25803778 |
| autonomously folding protein fragments reveal differences in the energy landscapes of homologous rnases h. | an important approach to understanding how a protein sequence encodes its energy landscape is to compare proteins with different sequences that fold to the same general native structure. in this work, we compare e. coli and t. thermophilus homologs of the protein rnase h. using protein fragments, we create equilibrium mimics of two different potential partially-folded intermediates (i(core) and i(core+1)) hypothesized to be present on the energy landscapes of these two proteins. we observe that ... | 2015 | 25803034 |
| a universal stress protein (usp) in mycobacteria binds camp. | mycobacteria are endowed with rich and diverse machinery for the synthesis, utilization, and degradation of camp. the actions of cyclic nucleotides are generally mediated by binding of camp to conserved and well characterized cyclic nucleotide binding domains or structurally distinct cgmp-specific and -regulated cyclic nucleotide phosphodiesterase, adenylyl cyclase, and e. coli transcription factor fhla (gaf) domain-containing proteins. proteins with cyclic nucleotide binding and gaf domains can ... | 2015 | 25802331 |
| inducible expression of a resistance-nodulation-division-type efflux pump in staphylococcus aureus provides resistance to linoleic and arachidonic acids. | although staphylococcus aureus is exposed to antimicrobial fatty acids on the skin, in nasal secretions, and in abscesses, a specific mechanism of inducible resistance to this important facet of innate immunity has not been identified. here, we have sequenced the genome of s. aureus usa300 variants selected for their ability to grow at an elevated concentration of linoleic acid. the fatty acid-resistant clone far7 had a single nucleotide polymorphism resulting in an h₁₂₁y substitution in an unch ... | 2015 | 25802299 |
| ph dependence of the stress regulator dksa. | dksa controls transcription of genes associated with diverse stress responses, such as amino acid and carbon starvation, oxidative stress, and iron starvation. dksa binds within the secondary channel of rna polymerase, extending its long coiled-coil domain towards the active site. the cellular expression of dksa remains constant due to a negative feedback autoregulation, raising the question of whether dksa activity is directly modulated during stress. here, we show that escherichia coli dksa is ... | 2015 | 25799498 |
| structural and functional studies of phosphoenolpyruvate carboxykinase from mycobacterium tuberculosis. | tuberculosis, the second leading infectious disease killer after hiv, remains a top public health priority. the causative agent of tuberculosis, mycobacterium tuberculosis (mtb), which can cause both acute and clinically latent infections, reprograms metabolism in response to the host niche. phosphoenolpyruvate carboxykinase (pck) is the enzyme at the center of the phosphoenolpyruvate-pyruvate-oxaloacetate node, which is involved in regulating the carbon flow distribution to catabolism, anabolis ... | 2015 | 25798914 |
| x-ray crystal structures of escherichia coli rna polymerase with switch region binding inhibitors enable rational design of squaramides with an improved fraction unbound to human plasma protein. | squaramides constitute a novel class of rna polymerase inhibitors of which genetic evidence and computational modeling previously have suggested an inhibitory mechanism mediated by binding to the rna polymerase switch region. an iterative chemistry program increased the fraction unbound to human plasma protein from below minimum detection levels, i.e., <1% to 4-6%, while retaining biochemical potency. since in vitro antimicrobial activity against an efflux-negative strain of haemophilus influenz ... | 2015 | 25798859 |
| bacterial transfer rnas. | transfer rna is an essential adapter molecule that is found across all three domains of life. the primary role of transfer rna resides in its critical involvement in the accurate translation of messenger rna codons during protein synthesis and, therefore, ultimately in the determination of cellular gene expression. this review aims to bring together the results of intensive investigations into the synthesis, maturation, modification, aminoacylation, editing and recycling of bacterial transfer rn ... | 2015 | 25796611 |
| unraveling the specific regulation of the central pathway for anaerobic degradation of 3-methylbenzoate. | the mbd cluster encodes the anaerobic degradation of 3-methylbenzoate in the β-proteobacterium azoarcus sp. cib. the specific transcriptional regulation circuit that controls the expression of the mbd genes was investigated. the po, pb 1, and p3 r promoters responsible for the expression of the mbd genes, their cognate mbdr transcriptional repressor, as well as the mbdr operator regions (atacn10gtat) have been characterized. the three-dimensional structure of mbdr has been solved revealing a con ... | 2015 | 25795774 |
| asc1, homolog of human rack1, prevents frameshifting in yeast by ribosomes stalled at cga codon repeats. | quality control systems monitor and stop translation at some ribosomal stalls, but it is unknown if halting translation at such stalls actually prevents synthesis of abnormal polypeptides. in yeast, ribosome stalling occurs at arg cga codon repeats, with even two consecutive cga codons able to reduce translation by up to 50%. the conserved eukaryotic asc1 protein limits translation through internal arg cga codon repeats. we show that, in the absence of asc1 protein, ribosomes continue translatin ... | 2015 | 25792604 |
| overexpression of a novel thermostable and chloride-tolerant laccase from thermus thermophilus sg0.5jp17-16 in pichia pastoris and its application in synthetic dye decolorization. | laccases have been used for the decolorization and detoxification of synthetic dyes due to their ability to oxidize a wide variety of dyes with water as the sole byproduct. a putative laccase gene (lactt) from thermus thermophilus sg0.5jp17-16 was screened using the genome mining approach, and it was highly expressed in pichia pastoris, yielding a high laccase activity of 6130 u/l in a 10-l fermentor. the lactt open reading frame encoded a protein of 466 amino acid residues with four putative cu ... | 2015 | 25790466 |
| the class iii cyclobutane pyrimidine dimer photolyase structure reveals a new antenna chromophore binding site and alternative photoreduction pathways. | photolyases are proteins with an fad chromophore that repair uv-induced pyrimidine dimers on the dna in a light-dependent manner. the cyclobutane pyrimidine dimer class iii photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. here we present the crystal structure of a class iii photolyase termed photolyase-related protein a (phra) of agrobacterium tumefaciens at 1.67-å resolution. phra contains 5,10-methenyltetrahydrofolate (m ... | 2015 | 25784552 |
| ribosome biochemistry in crystal structure determination. | 2015 | 25780230 | |
| rrna--the evolution of that magic molecule. | 2015 | 25780167 | |
| reflections on the 20th anniversary of rna. | 2015 | 25780133 | |
| substrate, product, and cofactor: the extraordinarily flexible relationship between the cde superfamily and heme. | pfam clan 0032, also known as the cde superfamily, is a diverse group of at least 20 protein families sharing a common α,β-barrel domain. of these, six different groups bind heme inside the barrel's interior, using it alternately as a cofactor, substrate, or product. focusing on these six, an integrated picture of structure, sequence, taxonomy, and mechanism is presented here, detailing how a single structural motif might be able to mediate such an array of functions with one of nature's most im ... | 2015 | 25778630 |