| purification and characterization of dr_2577 (slpa) a major s-layer protein from deinococcus radiodurans. | the protein dr_2577 is a major surface layer component of the radio-resistant bacterium deinococcus radiodurans. in the present study dr_2577 has been purified and its oligomeric profile characterized by means of size exclusion chromatography and gel electrophoresis. dr_2577 was found to be organized into three hierarchical orders characterized by monomers, stable dimers formed by the occurrence of disulfide bonds, and hexamers resulting from a combination of dimers. the structural implications ... | 2015 | 26074883 |
| the orisome: structure and function. | during the cell division cycle of all bacteria, dna-protein complexes termed orisomes trigger the onset of chromosome duplication. orisome assembly is both staged and stringently regulated to ensure that dna synthesis begins at a precise time and only once at each origin per cycle. orisomes comprise multiple copies of the initiator protein dnaa, which oligomerizes after interacting with specifically positioned recognition sites in the unique chromosomal replication origin, oric. since dnaa is hi ... | 2015 | 26082765 |
| seca: a potential antimicrobial target. | there is a consensus in the medical profession of the pressing need for novel antimicrobial agents due to issues related to drug resistance. in practice, solutions to this problem to a large degree lie with the identification of new and vital targets in bacteria and subsequently designing their inhibitors. we consider seca a very promising antimicrobial target. in this review, we compile and analyze information available on seca to show that inhibition of seca has a multitude of consequences. fu ... | 2015 | 26062397 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 3-sulfinopropionyl-coenzyme a (3sp-coa) desulfinase from advenella mimigardefordensis dpn7(t): crystal structure and function of a desulfinase with an acyl-coa dehydrogenase fold. | 3-sulfinopropionyl-coenzyme a (3sp-coa) desulfinase (acddpn7; ec 3.13.1.4) was identified during investigation of the 3,3'-dithiodipropionic acid (dtdp) catabolic pathway in the betaproteobacterium advenella mimigardefordensis strain dpn7(t). dtdp is an organic disulfide and a precursor for the synthesis of polythioesters (ptes) in bacteria, and is of interest for biotechnological pte production. acddpn7 catalyzes sulfur abstraction from 3sp-coa, a key step during the catabolism of dtdp. here, t ... | 2015 | 26057676 |
| activation of gtp hydrolysis in mrna-trna translocation by elongation factor g. | during protein synthesis, elongation of the polypeptide chain by each amino acid is followed by a translocation step in which mrna and transfer rna (trna) are advanced by one codon. this crucial step is catalyzed by elongation factor g (ef-g), a guanosine triphosphatase (gtpase), and accompanied by a rotation between the two ribosomal subunits. a mutant of ef-g, h91a, renders the factor impaired in guanosine triphosphate (gtp) hydrolysis and thereby stabilizes it on the ribosome. we use cryogeni ... | 2015 | 26229983 |
| 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 |
| 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 of c19orf12, coding for a transmembrane glycine zipper containing mitochondrial protein, cause mis-localization of the protein, inability to respond to oxidative stress and increased mitochondrial ca²⁺. | mutations in c19orf12 have been identified in patients affected by neurodegeneration with brain iron accumulation (nbia), a clinical entity characterized by iron accumulation in the basal ganglia. by using western blot analysis with specific antibody and confocal studies, we showed that wild-type c19orf12 protein was not exclusively present in mitochondria, but also in the endoplasmic reticulum (er) and mam (mitochondria associated membrane), while mutant c19orf12 variants presented a different ... | 2015 | 26136767 |
| 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 |
| 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 |
| 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 |
| structure and heme-binding properties of hemq (chlorite dismutase-like protein) from listeria monocytogenes. | chlorite dismutase-like proteins are structurally closely related to functional chlorite dismutases which are heme b-dependent oxidoreductases capable of reducing chlorite to chloride with simultaneous production of dioxygen. chlorite dismutase-like proteins are incapable of performing this reaction and their biological role is still under discussion. recently, members of this large protein family were shown to be involved in heme biosynthesis in gram-positive bacteria, and thus the protein was ... | 2015 | 25602700 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| regulation of the rply gene encoding 5s rrna binding protein l25 in escherichia coli and related bacteria. | ribosomal protein (r-protein) l25 is one of the three r-proteins (l25, l5, l18) that interact with 5s rrna in eubacteria. specific binding of l25 with a certain domain of 5s r-rna, a so-called loop e, has been studied in detail, but information about regulation of l25 synthesis has remained totally lacking. in contrast to the rple (l5) and rplr (l18) genes that belong to the polycistronic spc-operon and are regulated at the translation level by r-protein s8, the rply (l25) gene forms an independ ... | 2015 | 25749694 |
| goniometer-based femtosecond x-ray diffraction of mutant 30s ribosomal subunit crystals. | in this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30s ribosomal subunit mutant using goniometer-based femtosecond crystallography. crystal quality assessment for these samples was conducted at the x-ray pump probe end-station of the linac coherent light source (lcls) using recently introduced goniometer-based instrumentation. these 30s subunit crystals were genetically engineered to omit a 26-residue protein, thx, which is present in the wild-ty ... | 2015 | 26798805 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| challenges and opportunities for customizing polyhydroxyalkanoates. | polyhydroxyalkanoates (phas) as an alternative to synthetic plastics have been gaining increasing attention. being natural in their origin, phas are completely biodegradable and eco-friendly. however, consistent efforts to exploit this biopolymer over the last few decades have not been able to pull phas out of their nascent stage, inspite of being the favorite of the commercial world. the major limitations are: (1) the high production cost, which is due to the high cost of the feed and (2) poor ... | 2015 | 26063933 |
| 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 |
| 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 |
| structural characterization of an alternative mode of tigecycline binding to the bacterial ribosome. | although both tetracycline and tigecycline inhibit protein synthesis by sterically hindering the binding of trna to the ribosomal a site, tigecycline shows increased efficacy in both in vitro and in vivo activity assays and escapes the most common resistance mechanisms associated with the tetracycline class of antibiotics. these differences in activities are attributed to the tert-butyl-glycylamido side chain found in tigecycline. our structural analysis by x-ray crystallography shows that tigec ... | 2015 | 25753625 |
| 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 |
| structural insights into a key carotenogenesis related enzyme phytoene synthase of p. falciparum: a novel drug target for malaria. | carotenoids represent a diverse group of pigments derived from the common isoprenoid precursors and fulfill a variety of critical functions in plants and animals. phytoene synthase (psy), a transferase enzyme that catalyzes the first specific step in carotenoid biosynthesis plays a central role in the regulation of a number of essential functions mediated via carotenoids. psys have been deeply investigated in plants, bacteria and algae however in apicomplexans it is poorly studied. in an effort ... | 2015 | 26702306 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| how fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization. | maximization of growth rate is an important fitness strategy for bacteria. bacteria can achieve this by expressing proteins at optimal concentrations, such that resources are not wasted. this is exemplified for escherichia coli by the increase of its ribosomal protein-fraction with growth rate, which precisely matches the increased protein synthesis demand. these findings and others have led to the hypothesis that e. coli aims to maximize its growth rate in environments that support growth. howe ... | 2015 | 25754869 |
| crystal structure of the c-terminal 2',5'-phosphodiesterase domain of group a rotavirus protein vp3. | in response to viral infections, the mammalian innate immune system induces the production of the second messenger 2'-5' oligoadenylate (2-5a) to activate latent ribonuclease l (rnase l) that restricts viral replication and promotes apoptosis. a subset of rotaviruses and coronaviruses encode 2',5'-phosphodiesterase enzymes that hydrolyze 2-5a, thereby inhibiting rnase l activation. we report the crystal structure of the 2',5'-phosphodiesterase domain of group a rotavirus protein vp3 at 1.39 å re ... | 2015 | 25758703 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| high-resolution structure of the escherichia coli ribosome. | protein synthesis by the ribosome is highly dependent on the ionic conditions in the cellular environment, but the roles of ribosome solvation have remained poorly understood. moreover, the functions of modifications to ribosomal rna and ribosomal proteins have also been unclear. here we present the structure of the escherichia coli 70s ribosome at 2.4-å resolution. the structure reveals details of the ribosomal subunit interface that are conserved in all domains of life, and it suggests how sol ... | 2015 | 25775265 |
| structural insights into the role of rrna modifications in protein synthesis and ribosome assembly. | we report crystal structures of the thermus thermophilus ribosome at 2.3- to 2.5-å resolution, which have enabled modeling of rrna modifications. the structures reveal contacts of modified nucleotides with mrna and trnas or protein py, and contacts within the ribosome interior stabilizing the functional fold of rrna. our work provides a resource to explore the roles of rrna modifications and yields a more comprehensive atomic model of a bacterial ribosome. | 2015 | 25775268 |
| universal pathway for posttransfer editing reactions: insights from the crystal structure of ttphers with puromycin. | at the amino acid binding and recognition step, phenylalanyl-trna synthetase (phers) faces the challenge of discrimination between cognate phenylalanine and closely similar noncognate tyrosine. resampling of tyr-trna(phe) to phers increasing the number of correctly charged trna molecules has recently been revealed. thus, the very same editing site of phers promotes hydrolysis of misacylated trna species, associated both with cis- and trans-editing pathways. here we report the crystal structure o ... | 2015 | 25775602 |
| 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 |
| the ingenious structure of central rotor apparatus in vov1; key for both complex disassembly and energy coupling between v1 and vo. | vacuolar type rotary h+-atpases (vov1) couple atp synthesis/hydrolysis by v1 with proton translocation by vo via rotation of a central rotor apparatus composed of the v1-df rotor shaft, a socket-like vo-c (eukaryotic vo-d) and the hydrophobic rotor ring. reconstitution experiments using subcomplexes revealed a weak binding affinity of v1-df to vo-c despite the fact that torque needs to be transmitted between v1-df and vo-c for the tight energy coupling between v1 and vo. mutation of a short heli ... | 2015 | 25756791 |
| a prime/boost strategy using dna/fowlpox recombinants expressing the genetically attenuated e6 protein as a putative vaccine against hpv-16-associated cancers. | considering the high number of new cases of cervical cancer each year that are caused by human papilloma viruses (hpvs), the development of an effective vaccine for prevention and therapy of hpv-associated cancers, and in particular against the high-risk hpv-16 genotype, remains a priority. vaccines expressing the e6 and e7 proteins that are detectable in all hpv-positive pre-cancerous and cancer cells might support the treatment of hpv-related lesions and clear already established tumors. | 2015 | 25763880 |
| 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 |
| evolution of the metazoan mitochondrial replicase. | the large number of complete mitochondrial dna (mtdna) sequences available for metazoan species makes it a good system for studying genome diversity, although little is known about the mechanisms that promote and/or are correlated with the evolution of this organellar genome. by investigating the molecular evolutionary history of the catalytic and accessory subunits of the mtdna polymerase, pol γ, we sought to develop mechanistic insight into its function that might impact genome structure by ex ... | 2015 | 25740821 |
| structure of the vacuolar h+-atpase rotary motor reveals new mechanistic insights. | vacuolar h(+)-atpases are multisubunit complexes that operate with rotary mechanics and are essential for membrane proton transport throughout eukaryotes. here we report a ∼ 1 nm resolution reconstruction of a v-atpase in a different conformational state from that previously reported for a lower-resolution yeast model. the stator network of the v-atpase (and by implication that of other rotary atpases) does not change conformation in different catalytic states, and hence must be relatively rigid ... | 2015 | 25661654 |
| supramolecular protein assembly supports immobilization of a cytochrome p450 monooxygenase system as water-insoluble gel. | diverse applications of the versatile bacterial cytochrome p450 enzymes (p450s) are hampered by their requirement for the auxiliary proteins, ferredoxin reductases and ferredoxins, that transfer electrons to p450s. notably, this limits the use of p450s as immobilized enzymes for industrial purposes. herein, we demonstrate the immobilization of a bacterial p450 and its redox protein partners by supramolecular complex formation using a self-assembled heterotrimeric protein. employment of homodimer ... | 2015 | 25733255 |
| heterotrimeric nadh-oxidizing methylenetetrahydrofolate reductase from the acetogenic bacterium acetobacterium woodii. | the methylenetetrahydrofolate reductase (mthfr) of acetogenic bacteria catalyzes the reduction of methylene-thf, which is highly exergonic with nadh as the reductant. therefore, the enzyme was suggested to be involved in energy conservation by reducing ferredoxin via electron bifurcation, followed by na(+) translocation by the rnf complex. the enzyme was purified from acetobacterium woodii and shown to have an unprecedented subunit composition containing the three subunits rnfc2, metf, and metv. ... | 2015 | 25733614 |
| role of nad⁺-dependent malate dehydrogenase in the metabolism of methylomicrobium alcaliphilum 20z and methylosinus trichosporium ob3b. | we have expressed the l-malate dehydrogenase (mdh) genes from aerobic methanotrophs methylomicrobium alcaliphilum 20z and methylosinus trichosporium ob3b as his-tagged proteins in escherichia coli. the substrate specificities, enzymatic kinetics and oligomeric states of the mdhs have been characterized. both mdhs were nad⁺-specific and thermostable enzymes not affected by metal ions or various organic metabolites. the mdh from m. alcaliphilum 20z was a homodimeric (2 × 35 kda) enzyme displaying ... | 2015 | 27682078 |
| trna biology in mitochondria. | mitochondria are the powerhouses of eukaryotic cells. they are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. these organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. among them, mitochondria use many specific pathways to obtain complete and functional sets of trnas as required for translatio ... | 2015 | 25734984 |
| bactobolin a binds to a site on the 70s ribosome distinct from previously seen antibiotics. | the ribosome is the target of a large number of antibiotics. here, we report a 3.4-å-resolution crystal structure of bactobolin a bound to 70s ribosome-trna complex. the antibiotic binds at a previously unseen site in the 50s subunit and displaces trna bound at the p-site. it thus likely has a similar mechanism of action as blasticidin s despite binding to a different site. the structure also rationalizes previously identified resistance mutations. | 2015 | 25562208 |
| unraveling the mechanistic features of rna polymerase ii termination by the 5'-3' exoribonuclease rat1. | within a complex with rai1, the 5'-3' exoribonuclease rat1 promotes termination of rna polymerase ii (rnapii) on protein-coding genes, but its underlying molecular mechanism is still poorly understood. using in vitro transcription termination assays, we have found that rnapii is prone to more effective termination by rat1/rai1 when its catalytic site is disrupted due to ntp misincorporation, implying that paused rnapii, which is often found in vivo near termination sites, could adopt a similar c ... | 2015 | 25722373 |
| structural basis for recognition of g-1-containing trna by histidyl-trna synthetase. | aminoacyl-trna synthetases (aarss) play a crucial role in protein translation by linking trnas with cognate amino acids. among all the trnas, only trna(his) bears a guanine base at position -1 (g-1), and it serves as a major recognition element for histidyl-trna synthetase (hisrs). despite strong interests in the histidylation mechanism, the trna recognition and aminoacylation details are not fully understood. we herein present the 2.55 å crystal structure of hisrs complexed with trna(his), whic ... | 2015 | 25722375 |
| an intermolecular binding mechanism involving multiple lysm domains mediates carbohydrate recognition by an endopeptidase. | lysm domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing n-acetylglucosamine (glcnac) moieties, such as chitin and peptidoglycan. in bacteria, the functional significance of the involvement of multiple lysm domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. here, a structural study of the thermus thermophilus nlpc/p60 endopeptidase cont ... | 2015 | 25760608 |
| identification of two structural elements important for ribosome-dependent gtpase activity of elongation factor 4 (ef4/lepa). | the bacterial translational gtpase ef4/lepa is structurally similar to the canonical elongation factor ef-g. while sharing core structural features with other translational gtpases, the function of ef4 remains unknown. recent structural data locates the unique c-terminal domain (ctd) of ef4 in proximity to the ribosomal peptidyl transferase center (ptc). to investigate the functional role of ef4's ctd we have constructed three c-terminal truncation variants. these variants are fully functional w ... | 2015 | 25712150 |
| analysis of the cooperative atpase cycle of the aaa+ chaperone clpb from thermus thermophilus by using ordered heterohexamers with an alternating subunit arrangement. | the clpb/hsp104 chaperone solubilizes and reactivates protein aggregates in cooperation with dnak/hsp70 and its cofactors. the clpb/hsp104 protomer has two aaa+ modules, aaa-1 and aaa-2, and forms a homohexamer. in the hexamer, these modules form a two-tiered ring in which each tier consists of homotypic aaa+ modules. by atp binding and its hydrolysis at these aaa+ modules, clpb/hsp104 exerts the mechanical power required for protein disaggregation. although atpase cycle of this chaperone has be ... | 2015 | 25713084 |