Publications

computing the origin and evolution of the ribosome from its structure - uncovering processes of macromolecular accretion benefiting synthetic biology.	accretion occurs pervasively in nature at widely different timeframes. the process also manifests in the evolution of macromolecules. here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. phylogenetic trees of protein ...	2015	27096056
thiophenecarboxamide derivatives activated by etha kill mycobacterium tuberculosis by inhibiting the ctp synthetase pyrg.	to combat the emergence of drug-resistant strains of mycobacterium tuberculosis, new antitubercular agents and novel drug targets are needed. phenotypic screening of a library of 594 hit compounds uncovered two leads that were active against m. tuberculosis in its replicating, non-replicating, and intracellular states: compounds 7947882 (5-methyl-n-(4-nitrophenyl)thiophene-2-carboxamide) and 7904688 (3-phenyl-n-[(4-piperidin-1-ylphenyl)carbamothioyl]propanamide). mutants resistant to both compou ...	2015	26097035
trna recognition by a bacterial trna xm32 modification enzyme from the spout methyltransferase superfamily.	trmj proteins from the spout methyltransferase superfamily are trna xm32 modification enzymes that occur in bacteria and archaea. unlike archaeal trmj, bacterial trmj require full-length trna molecules as substrates. it remains unknown how bacterial trmjs recognize substrate trnas and specifically catalyze a 2'-o modification at ribose 32. herein, we demonstrate that all six escherichia coli (ec) trnas with 2'-o-methylated nucleosides at position 32 are substrates of ectrmj, and we show that the ...	2015	26202969
recf and recr play critical roles in the homologous recombination and single-strand annealing pathways of mycobacteria.	mycobacteria encode three dna double-strand break repair pathways: (i) reca-dependent homologous recombination (hr), (ii) ku-dependent nonhomologous end joining (nhej), and (iii) recbcd-dependent single-strand annealing (ssa). mycobacterial hr has two presynaptic pathway options that rely on the helicase-nuclease adnab and the strand annealing protein reco, respectively. ablation of adnab or reco individually causes partial impairment of hr, but loss of adnab and reco in combination abolishes hr ...	2015	26195593
argonaute 2: a novel rising star in cancer research.	ago2 (argonaute 2, eif2c2) is the only member in ago family with catalytic activity and of extreme importance during small rnas guided gene silencing processes. the structural investigations have provided insights into details and functional mechanisms of the four major domains within ago2. as a multifunction player, ago2 has been revealed involved in tumorgenesis through mirnas-dependent or independent ways. and nowadays, ago2 has also been more importantly found ectopically over-expressed in c ...	2015	26284139
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
star3d: a stack-based rna 3d structural alignment tool.	the various roles of versatile non-coding rnas typically require the attainment of complex high-order structures. therefore, comparing the 3d structures of rna molecules can yield in-depth understanding of their functional conservation and evolutionary history. recently, many powerful tools have been developed to align rna 3d structures. although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the rna seco ...	2015	26184875
characterization of a mannose-6-phosphate isomerase from bacillus amyloliquefaciens and its application in fructose-6-phosphate production.	the bam6pi gene encoding a mannose-6-phosphate isomerase (m6pi, ec 5.3.1.8) was cloned from bacillus amyloliquefaciens dsm7 and overexpressed in escherichia coli. the enzyme activity of bam6pi was optimal at ph and temperature of 7.5 and 70°c, respectively, with a kcat/km of 13,900 s-1 mm-1 for mannose-6-phosphate (m6p). the purified bam6pi demonstrated the highest catalytic efficiency of all characterized m6pis. although m6pis have been characterized from several other sources, bam6pi is distin ...	2015	26171785
structure and evolution of the archaeal lipid synthesis enzyme sn-glycerol-1-phosphate dehydrogenase.	one of the most critical events in the origins of cellular life was the development of lipid membranes. archaea use isoprenoid chains linked via ether bonds to sn-glycerol 1-phosphate (g1p), whereas bacteria and eukaryotes use fatty acids attached via ester bonds to enantiomeric sn-glycerol 3-phosphate. nad(p)h-dependent g1p dehydrogenase (g1pdh) forms g1p and has been proposed to have played a crucial role in the speciation of the archaea. we present here, to our knowledge, the first structures ...	2015	26175150
md simulations of trna and aminoacyl-trna synthetases: dynamics, folding, binding, and allostery.	while trna and aminoacyl-trna synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. recent molecular dynamics (md) simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. throughout the review, we briefly discuss important historical events to provide a context for how far t ...	2015	26184179
biochemical and structural properties of a thermostable mercuric ion reductase from metallosphaera sedula.	mercuric ion reductase (mera), a mercury detoxification enzyme, has been tuned by evolution to have high specificity for mercuric ions (hg(2+)) and to catalyze their reduction to a more volatile, less toxic elemental form. here, we present a biochemical and structural characterization of mera from the thermophilic crenarchaeon metallosphaera sedula. mera from m. sedula is a thermostable enzyme, and remains active after extended incubation at 97°c. at 37°c, the nadph oxidation-linked hg(2+) reduc ...	2015	26217660
the extended at-hook is a novel rna binding motif.	the at-hook has been defined as a dna binding peptide motif that contains a glycine-arginine-proline (g-r-p) tripeptide core flanked by basic amino acids. recent reports documented variations in the sequence of at-hooks and revealed rna binding activity of some canonical at-hooks, suggesting a higher structural and functional variability of this protein domain than previously anticipated. here we describe the discovery and characterization of the extended at-hook peptide motif (eat-hook), in whi ...	2015	26156556
crystal structures of a hyperthermophilic archaeal homoserine dehydrogenase suggest a novel cofactor binding mode for oxidoreductases.	nad(p)-dependent dehydrogenases differ according to their coenzyme preference: some prefer nad, others nadp, and still others exhibit dual cofactor specificity. the structure of a newly identified archaeal homoserine dehydrogenase showed this enzyme to have a strong preference for nadp. however, nadp did not act as a cofactor with this enzyme, but as a strong inhibitor of nad-dependent homoserine oxidation. structural analysis and site-directed mutagenesis showed that the large number of interac ...	2015	26154028
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
phenotypic suppression of streptomycin resistance by mutations in multiple components of the translation apparatus.	the bacterial ribosome and its associated translation factors are frequent targets of antibiotics, and antibiotic resistance mutations have been found in a number of these components. such mutations can potentially interact with one another in unpredictable ways, including the phenotypic suppression of one mutation by another. these phenotypic interactions can provide evidence of long-range functional interactions throughout the ribosome and its functional complexes and potentially give insights ...	2015	26148717
structure and mechanism of the atpase that powers viral genome packaging.	many viruses package their genomes into procapsids using an atpase machine that is among the most powerful known biological motors. however, how this motor couples atp hydrolysis to dna translocation is still unknown. here, we introduce a model system with unique properties for studying motor structure and mechanism. we describe crystal structures of the packaging motor atpase domain that exhibit nucleotide-dependent conformational changes involving a large rotation of an entire subdomain. we al ...	2015	26150523
ecophysiology of an uncultivated lineage of aigarchaeota from an oxic, hot spring filamentous 'streamer' community.	the candidate archaeal phylum 'aigarchaeota' contains microorganisms from terrestrial and subsurface geothermal ecosystems. the phylogeny and metabolic potential of aigarchaeota has been deduced from several recent single-cell amplified genomes; however, a detailed description of their metabolic potential and in situ transcriptional activity is absent. here, we report a comprehensive metatranscriptome-based reconstruction of the in situ metabolism of aigarchaeota in an oxic, hot spring filamento ...	2015	26140529
ecophysiology of an uncultivated lineage of aigarchaeota from an oxic, hot spring filamentous 'streamer' community.	the candidate archaeal phylum 'aigarchaeota' contains microorganisms from terrestrial and subsurface geothermal ecosystems. the phylogeny and metabolic potential of aigarchaeota has been deduced from several recent single-cell amplified genomes; however, a detailed description of their metabolic potential and in situ transcriptional activity is absent. here, we report a comprehensive metatranscriptome-based reconstruction of the in situ metabolism of aigarchaeota in an oxic, hot spring filamento ...	2015	26140529
a dynamic search process underlies microrna targeting.	argonaute proteins play a central role in mediating post-transcriptional gene regulation by micrornas (mirnas). argonautes use the nucleotide sequences in mirnas as guides for identifying target messenger rnas for repression. here, we used single-molecule fret to directly visualize how human argonaute-2 (ago2) searches for and identifies target sites in rnas complementary to its mirna guide. our results suggest that ago2 initially scans for target sites with complementarity to nucleotides 2-4 of ...	2015	26140593
single-molecule imaging reveals that argonaute reshapes the binding properties of its nucleic acid guides.	argonaute proteins repress gene expression and defend against foreign nucleic acids using short rnas or dnas to specify the correct target rna or dna sequence. we have developed single-molecule methods to analyze target binding and cleavage mediated by the argonaute:guide complex, risc. we find that both eukaryotic and prokaryotic argonaute proteins reshape the fundamental properties of rna:rna, rna:dna, and dna:dna hybridization—a small rna or dna bound to argonaute as a guide no longer follows ...	2015	26140592
constraining the lateral helix of respiratory complex i by cross-linking does not impair enzyme activity or proton translocation.	complex i (nadh:ubiquinone oxidoreductase) is a multisubunit, membrane-bound enzyme of the respiratory chain. the energy from nadh oxidation in the peripheral region of the enzyme is used to drive proton translocation across the membrane. one of the integral membrane subunits, nuol in escherichia coli, has an unusual lateral helix of ∼75 residues that lies parallel to the membrane surface and has been proposed to play a mechanical role as a piston during proton translocation (efremov, r. g., bar ...	2015	26134569
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
structural mapping of the clpb atpases of plasmodium falciparum: targeting protein folding and secretion for antimalarial drug design.	caseinolytic chaperones and proteases (clp) belong to the aaa+ protein superfamily and are part of the protein quality control machinery in cells. the eukaryotic parasite plasmodium falciparum, the causative agent of malaria, has evolved an elaborate network of clp proteins including two distinct clpb atpases. clpb1 and clpb2 are involved in different aspects of parasitic proteostasis. clpb1 is present in the apicoplast, a parasite-specific and plastid-like organelle hosting various metabolic pa ...	2015	26130467
implication from the predicted docked interaction of sigma h and exploration of its interaction with rna polymerase in mycobacterium tuberculosis.	m. tuberculosis is adapted to remain active in the extreme environmental condition due to the presence of atypical sigma factors commonly called extra cytoplasmic function (ecf) sigma factors. among the 13 sigma factors of m. tuberculosis, 10 are regarded as the ecf sigma factor that exerts their attributes in various stress response. therefore it is of interest to describe the structural prediction of one of the ecf sigma factors, sigma h (sigh), involved in oxidative and heat stress having int ...	2015	26229290
from bacterial to human dihydrouridine synthase: automated structure determination.	the reduction of uridine to dihydrouridine at specific positions in trna is catalysed by dihydrouridine synthase (dus) enzymes. increased expression of human dihydrouridine synthase 2 (hdus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. here, the x-ray crystal structure of a construct of hdus2 encompassing the catalytic and trna-recognition domains (residues 1 ...	2015	26143927
enhancement of e. coli acyl-coa synthetase fadd activity on medium chain fatty acids.	fadd catalyses the first step in e. coli beta-oxidation, the activation of free fatty acids into acyl-coa thioesters. this activation makes fatty acids competent for catabolism and reduction into derivatives like alcohols and alkanes. alcohols and alkanes derived from medium chain fatty acids (mcfas, 6-12 carbons) are potential biofuels; however, fadd has low activity on mcfas. herein, we generate mutations in fadd that enhance its acyl-coa synthetase activity on mcfas. homology modeling reveals ...	2015	26157619
identifying novel sequence variants of rna 3d motifs.	predicting rna 3d structure from sequence is a major challenge in biophysics. an important sub-goal is accurately identifying recurrent 3d motifs from rna internal and hairpin loop sequences extracted from secondary structure (2d) diagrams. we have developed and validated new probabilistic models for 3d motif sequences based on hybrid stochastic context-free grammars and markov random fields (scfg/mrf). the scfg/mrf models are constructed using atomic-resolution rna 3d structures. to parameteriz ...	2015	26130723
expression, purification, crystallization and crystallographic study of lutzomyia longipalpis ljl143.	leishmaniasis is a neglected vector-borne disease with a global prevalence of over 12 million cases and 59,000 annual deaths. transmission of the parasite requires salivary proteins, including ljl143 from the new world sandfly lutzomyia longipalpis. ljl143 is a known marker of sandfly exposure in zoonotic hosts. ljl143 was crystallized from soluble protein expressed using pichia pastoris. x-ray data were collected to 2.6 å resolution from orthorhombic crystals belonging to space group p2(1)2(1)2 ...	2015	26144240
identification of chemical compounds that inhibit the function of glutamyl-trna synthetase from pseudomonas aeruginosa.	pseudomonas aeruginosa glutamyl-trna synthetase (glurs) was overexpressed in escherichia coli. sequence analysis indicated that p. aeruginosa glurs is a discriminating glurs and, similar to other glurs proteins, requires the presence of trna(glu) to produce a glutamyl-amp intermediate. kinetic parameters for interaction with trna were determined and the k(cat) and km were 0.8 s(-1) and 0.68 µm, respectively, resulting in a k(cat)/km of 1.18 s(-1) µm(-1). a robust aminoacylation-based scintillati ...	2015	26116192
specificity and catalysis hardwired at the rna-protein interface in a translational proofreading enzyme.	proofreading modules of aminoacyl-trna synthetases are responsible for enforcing a high fidelity during translation of the genetic code. they use strategically positioned side chains for specifically targeting incorrect aminoacyl-trnas. here, we show that a unique proofreading module possessing a d-aminoacyl-trna deacylase fold does not use side chains for imparting specificity or for catalysis, the two hallmark activities of enzymes. we show, using three distinct archaea, that a side-chain-stri ...	2015	26113036
cautions about the reliability of pairwise gene correlations based on expression data.	rapid growth in the availability of genome-wide transcript abundance levels through gene expression microarrays and rnaseq promises to provide deep biological insights into the complex, genome-wide transcriptional behavior of single-celled organisms. however, this promise has not yet been fully realized.	2015	26167162
transcriptional slippage in the positive-sense rna virus family potyviridae.	the family potyviridae encompasses ~30% of plant viruses and is responsible for significant economic losses worldwide. recently, a small overlapping coding sequence, termed pipo, was found to be conserved in the genomes of all potyvirids. pipo is expressed as part of a frameshift protein, p3n-pipo, which is essential for virus cell-to-cell movement. however, the frameshift expression mechanism has hitherto remained unknown. here, we demonstrate that transcriptional slippage, specific to the vira ...	2015	26113364
identification of determinants for trna substrate recognition by escherichia coli c/u34 2'-o-methyltransferase.	post-transcriptional modifications bring chemical diversity to trnas, especially at positions 34 and 37 of the anticodon stem-loop (asl). trml is the prokaryotic methyltransferase that catalyzes the transfer of the methyl group from s-adenosyl-l-methionine to the wobble base of trna(leu)caa and trna(leu)uaa isoacceptors. this cm34/um34 modification affects codon-anticodon interactions and is essential for translational fidelity. trml-catalyzed 2'-o-methylation requires its homodimerization; howe ...	2015	26106808
developmentally regulated heart stopper, a mitochondrially targeted l18 ribosomal protein gene, is required for cell division, differentiation, and seed development in arabidopsis.	evidence is presented for the role of a mitochondrial ribosomal (mitoribosomal) l18 protein in cell division, differentiation, and seed development after the characterization of a recessive mutant, heart stopper (hes). the hes mutant produced uncellularized endosperm and embryos arrested at the late globular stage. the mutant embryos differentiated partially on rescue medium with some forming callus. hes (at1g08845) encodes a mitochondrially targeted member of a highly diverged l18 ribosomal pro ...	2015	26105995
mechanism of protective immunity by vaccination with recombinant echinococcus granulosus glutathione s-transferase (chinese strain) in mice.	the aim of this study was to investigate the immunoprotective effects of recombinant echinococcus granulosus glutathione s-transferase (reggst) against the development of protoscolices (pscs), and to determine the mechanisms underlying this protection. icr mice were subcutaneously immunized three times with reggst at weeks 0, 2 and 4, followed by the intraperitoneal administration of e. granulosus pscs at week 10. six mice in each group were sacrificed at 0, 2, 4, 6, 10, 18 and 30 weeks followin ...	2015	26622451
co-chaperone specificity in gating of the polypeptide conducting channel in the membrane of the human endoplasmic reticulum.	in mammalian cells, signal peptide-dependent protein transport into the endoplasmic reticulum (er) is mediated by a dynamic polypeptide-conducting channel, the heterotrimeric sec61 complex. previous work has characterized the sec61 complex as a potential er ca(2+) leak channel in hela cells and identified er lumenal molecular chaperone immunoglobulin heavy-chain-binding protein (bip) as limiting ca(2+) leakage via the open sec61 channel by facilitating channel closing. this bip activity involves ...	2015	26085089
structural organization of enzymes of the phenylacetate catabolic hybrid pathway.	aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. they are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. in bacterial genomes, the phenylacetate (pa) utilization pathway is abundant and represents the central route for degradation of a variety of organic compound ...	2015	26075354
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
halophiles and their enzymes: negativity put to good use.	halophilic microorganisms possess stable enzymes that function in very high salinity, an extreme condition that leads to denaturation, aggregation, and precipitation of most other proteins. genomic and structural analyses have established that the enzymes of halophilic archaea and many halophilic bacteria are negatively charged due to an excess of acidic over basic residues, and altered hydrophobicity, which enhance solubility and promote function in low water activity conditions. here, we provi ...	2015	26066288
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
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
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
a replisome's journey through the bacterial chromosome.	genome duplication requires the coordinated activity of a multi-component machine, the replisome. in contrast to the background of metabolic diversity across the bacterial domain, the composition and architecture of the bacterial replisome seem to have suffered few changes during evolution. this immutability underlines the replisome's efficiency in copying the genome. it also highlights the success of various strategies inherent to the replisome for responding to stress and avoiding problems dur ...	2015	26097470
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
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 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
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