Publications

reconstitution of protein translation of mycobacterium reveals functional conservation and divergence with the gram-negative bacterium escherichia coli.	protein translation is essential for all bacteria pathogens. it has also been a major focus of structural and functional studies and an important target of antibiotics. here we report our attempts to biochemically reconstitute mycobacterial protein translation in vitro from purified components. this mycobacterial translation system consists of individually purified recombinant translation factors from mycobacterium tuberculosis (m. tuberculosis), purified trnas and ribosomes from mycobacterium s ...	2016	27564552
classification of the treble clef zinc finger: noteworthy lessons for structure and function evolution.	treble clef (tc) zinc fingers constitute a large fold-group of structural zinc-binding protein domains that mediate numerous cellular functions. we have analysed the sequence, structure, and function relationships among all tcs in the protein data bank. this led to the identification of novel tcs, such as lsr2, yggx and tfiiic τ 60 kda subunit, and prediction of a nuclease-like function for the duf1364 family. the structural malleability of tcs is evident from the many examples with variations t ...	2016	27562564
mitochondrial-nuclear interactions mediate sex-specific transcriptional profiles in drosophila.	the assembly and function of mitochondria require coordinated expression from two distinct genomes, the mitochondrial dna (mtdna) and nuclear dna (ndna). mutations in either genome can be a source of phenotypic variation, yet their coexpression has been largely overlooked as a source of variation, particularly in the emerging paradigm of mitochondrial replacement therapy. here we tested how the transcriptome responds to mtdna and ndna variation, along with mitonuclear interactions (mtdna × ndna) ...	2016	27558138
a mutagenic study identifying critical residues for the structure and function of rice manganese transporter osmtp8.1.	rice (oryza sativa) mtp8.1 (osmtp8.1) is a tonoplast-localized manganese transporter of the cation diffusion facilitator family. here we present a structure-function analysis of osmtp8.1 based on the site-directed and random mutagenesis and complementation assays in manganese hypersensitive yeast, in combination with three-dimensional (3d) structure modeling based on the crystal structure of the escherichia coli cdf family member, ecyiip. two metal-binding sites are conserved in osmtp8.1 with ec ...	2016	27555514
data for molecular dynamics simulations of b-type cytochrome c oxidase with the amber force field.	cytochrome c oxidase (cco) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. this article presents parameters for the cofactors of ba3-type cco that are compatible with the all-atom amber ff12sb and ff14sb force fields. specifically, parameters were developed for the cua pair, heme b, and the dinuclear center that consists of heme a3 and cub bridged by a hydroperoxo group. the data includes geometries in xy ...	2016	27547799
cryo-em studies of the structure and dynamics of vacuolar-type atpases.	electron cryomicroscopy (cryo-em) has significantly advanced our understanding of molecular structure in biology. recent innovations in both hardware and software have made cryo-em a viable alternative for targets that are not amenable to x-ray crystallography or nuclear magnetic resonance (nmr) spectroscopy. cryo-em has even become the method of choice in some situations where x-ray crystallography and nmr spectroscopy are possible but where cryo-em can determine structures at higher resolution ...	2016	27532044
characterization of outer membrane proteome of akkermansia muciniphila reveals sets of novel proteins exposed to the human intestine.	akkermansia muciniphila is a common member of the human gut microbiota and belongs to the planctomycetes-verrucomicrobia-chlamydiae superphylum. decreased levels of a. muciniphila have been associated with many diseases, and thus it is considered to be a beneficial resident of the intestinal mucus layer. surface-exposed molecules produced by this organism likely play important roles in colonization and communication with other microbes and the host, but the protein composition of the outer membr ...	2016	27507967
efficient crispr-mediated post-transcriptional gene silencing in a hyperthermophilic archaeon using multiplexed crrna expression.	crispr (clustered regularly interspaced short palindromic repeats)-mediated rna degradation is catalyzed by a type iii system in the hyperthermophilic archaeon sulfolobus solfataricus earlier work demonstrated that the system can be engineered to target specifically mrna of an endogenous host reporter gene, namely the β-galactosidase in s. solfataricus here, we investigated the effect of single and multiple spacers targeting the mrna of a second reporter gene, α-amylase, at the same, and at diff ...	2016	27507792
cold shock proteins: a minireview with special emphasis on csp-family of enteropathogenic yersinia.	bacteria have evolved a number of mechanisms for coping with stress and adapting to changing environmental conditions. many bacteria produce small cold shock proteins (csp) as a response to rapid temperature downshift (cold shock). during cold shock, the cell membrane fluidity and enzyme activity decrease, and the efficiency of transcription and translation is reduced due to stabilization of nucleic acid secondary structures. moreover, protein folding is inefficient and ribosome function is hamp ...	2016	27499753
cleavage of model substrates by arabidopsis thaliana prorp1 reveals new insights into its substrate requirements.	two broad classes of rnase p trim the 5' leader of precursor trnas (pre-trnas): ribonucleoprotein (rnp)- and proteinaceous (prorp)-variants. these two rnase p types, which use different scaffolds for catalysis, reflect independent evolutionary paths. while the catalytic rna-based rnp form is present in all three domains of life, the prorp family is restricted to eukaryotes. to obtain insights on substrate recognition by prorps, we examined the 5' processing ability of recombinant arabidopsis tha ...	2016	27494328
microbial rhodopsins: wide distribution, rich diversity and great potential.	one of the major topics in biophysics and physicobiology is to understand and utilize biological functions using various advanced techniques. taking advantage of the photoreactivity of the seven-transmembrane rhodopsin protein family has been actively investigated by a variety of methods. rhodopsins serve as models for membrane-embedded proteins, for photoactive proteins and as a fundamental tool for optogenetics, a new technology to control biological activity with light. in this review, we sum ...	2015	27493861
structural comparison between the open and closed forms of citrate synthase from thermus thermophilus hb8.	the crystal structures of citrate synthase from the thermophilic eubacteria thermus thermophilus hb8 (ttcs) were determined for an open form at 1.5 å resolution and for closed form at 2.3 å resolution, respectively. in the absence of ligands ttcs in the open form was crystalized into a tetragonal form with a single subunit in the asymmetric unit. ttcs was also co-crystallized with citrate and coenzyme-a to form an orthorhombic crystal with two homodimers in the asymmetric unit. citrate and coa a ...	2015	27493854
distinct conformation of atp molecule in solution and on protein.	adenosine triphosphate (atp) is a versatile molecule used mainly for energy and a phosphate source. the hydrolysis of γ phosphate initiates the reactions and these reactions almost always start when atp binds to protein. therefore, there should be a mechanism to prevent spontaneous hydrolysis reaction and a mechanism to lead atp to a pure energy source or to a phosphate source. to address these questions, we extensively analyzed the effect of protein to atp conformation based on the sampling of ...	2013	27493535
structures of torsina and its disease-mutant complexed with an activator reveal the molecular basis for primary dystonia.	the most common cause of early onset primary dystonia, a neuromuscular disease, is a glutamate deletion (δe) at position 302/303 of torsina, a aaa+ atpase that resides in the endoplasmic reticulum. while the function of torsina remains elusive, the δe mutation is known to diminish binding of two torsina atpase activators: lamina-associated protein 1 (lap1) and its paralog, luminal domain like lap1 (lull1). using a nanobody as a crystallization chaperone, we obtained a 1.4 å crystal structure of ...	2016	27490483
origins of tmrna: the missing link in the birth of protein synthesis?	the rna world hypothesis refers to the early period on earth in which rna was central in assuring both genetic continuity and catalysis. the end of this era coincided with the development of the genetic code and protein synthesis, symbolized by the apparition of the first non-random messenger rna (mrna). modern transfer-messenger rna (tmrna) is a unique hybrid molecule which has the properties of both mrna and transfer rna (trna). it acts as a key molecule during trans-translation, a major quali ...	2016	27484476
protein phosphorylation and its role in archaeal signal transduction.	reversible protein phosphorylation is the main mechanism of signal transduction that enables cells to rapidly respond to environmental changes by controlling the functional properties of proteins in response to external stimuli. however, whereas signal transduction is well studied in eukaryotes and bacteria, the knowledge in archaea is still rather scarce. archaea are special with regard to protein phosphorylation, due to the fact that the two best studied phyla, the euryarchaeota and crenarchae ...	2016	27476079
three-dimensional model of human nicotinamide nucleotide transhydrogenase (nnt) and sequence-structure analysis of its disease-causing variations.	defective mitochondrial proteins are emerging as major contributors to human disease. nicotinamide nucleotide transhydrogenase (nnt), a widely expressed mitochondrial protein, has a crucial role in the defence against oxidative stress. nnt variations have recently been reported in patients with familial glucocorticoid deficiency (fgd) and in patients with heart failure. moreover, knockout animal models suggest that nnt has a major role in diabetes mellitus and obesity. in this study, we used exp ...	2016	27459240
visualizing the phage t4 activated transcription complex of dna and e. coli rna polymerase.	the ability of rna polymerase (rnap) to select the right promoter sequence at the right time is fundamental to the control of gene expression in all organisms. however, there is only one crystallized structure of a complete activator/rnap/dna complex. in a process called σ appropriation, bacteriophage t4 activates a class of phage promoters using an activator (mota) and a co-activator (asia), which function through interactions with the σ(70) subunit of rnap. we have developed a holistic, struct ...	2016	27458207
driving apart and segregating genomes in archaea.	genome segregation is a fundamental biological process in organisms from all domains of life. how this stage of the cell cycle unfolds in eukarya has been clearly defined and considerable progress has been made to unravel chromosome partition in bacteria. the picture is still elusive in archaea. the lineages of this domain exhibit different cell-cycle lifestyles and wide-ranging chromosome copy numbers, fluctuating from 1 up to 55. this plurality of patterns suggests that a variety of mechanisms ...	2016	27450111
a bioinformatics analysis reveals a group of mocr bacterial transcriptional regulators linked to a family of genes coding for membrane proteins.	the mocr bacterial transcriptional regulators are characterized by an n-terminal domain, 60 residues long on average, possessing the winged-helix-turn-helix (whth) architecture responsible for dna recognition and binding, linked to a large c-terminal domain (350 residues on average) that is homologous to fold type-i pyridoxal 5'-phosphate (plp) dependent enzymes like aspartate aminotransferase (aat). these regulators are involved in the expression of genes taking part in several metabolic pathwa ...	2016	27446613
ribosomal frameshifting and transcriptional slippage: from genetic steganography and cryptography to adventitious use.	genetic decoding is not 'frozen' as was earlier thought, but dynamic. one facet of this is frameshifting that often results in synthesis of a c-terminal region encoded by a new frame. ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational 'correction' of problem or 'savior' indels. utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. one class of re ...	2016	27436286
cryptosporidium and toxoplasma parasites are inhibited by a benzoxaborole targeting leucyl-trna synthetase.	the apicomplexan parasites cryptosporidium and toxoplasma are serious threats to human health. cryptosporidiosis is a severe diarrheal disease in malnourished children and immunocompromised individuals, with the only fda-approved drug treatment currently being nitazoxanide. the existing therapies for toxoplasmosis, an important pathology in immunocompromised individuals and pregnant women, also have serious limitations. with the aim of developing alternative therapeutic options to address these ...	2016	27431220
identification of preferred dna-binding sites for the thermus thermophilus transcriptional regulator sbtr by the combinatorial approach repsa.	one of the first steps towards elucidating the biological function of a putative transcriptional regulator is to ascertain its preferred dna-binding sequences. this may be rapidly and effectively achieved through the application of a combinatorial approach, one involving very large numbers of randomized oligonucleotides and reiterative selection and amplification steps to enrich for high-affinity nucleic acid-binding sequences. previously, we had developed the novel combinatorial approach restri ...	2016	27428627
characterization of the nqo5 subunit of bacterial complex i in the isolated state.	the subunits that comprise bacterial complex i (nadh:ubiquinone oxidoreductase) are also found in more complicated mitochondrial enzymes in eukaryotic organisms. although the nqo5 subunit is one of these conserved components and important for the formation of complex, it has been little studied. here, we report structure analyses of isolated nqo5 from thermus thermophilus. biochemical studies indicated that the c-terminal region following the 30-kd subunit motif is disordered in the isolated sta ...	2016	27398308
a bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data.	metagenomics enables the analysis of bacterial population composition and the study of emergent population features, such as shared metabolic pathways. recently, we have shown that metagenomics datasets can be leveraged to characterize population-wide transcriptional regulatory networks, or meta-regulons, providing insights into how bacterial populations respond collectively to specific triggers. here we formalize a bayesian inference framework to analyze the composition of transcriptional regul ...	2016	27398089
sensitive proton-detected solid-state nmr spectroscopy of large proteins with selective ch3 labelling: application to the 50s ribosome subunit.	solid-state nmr spectroscopy allows the characterization of the structure, interactions and dynamics of insoluble and/or very large proteins. sensitivity and resolution are often major challenges for obtaining atomic-resolution information, in particular for very large protein complexes. here we show that the use of deuterated, specifically ch3-labelled proteins result in significant sensitivity gains compared to previously employed chd2 labelling, while line widths increase only marginally. we ...	2016	27385633
the mechanism of rna 5′ capping with nad+, nadh and desphospho-coa.	the chemical nature of the 5′ end of rna is a key determinant of rna stability, processing, localization and translation efficiency, and has been proposed to provide a layer of ‘epitranscriptomic’ gene regulation. recently it has been shown that some bacterial rna species carry a 5′-end structure reminiscent of the 5′ 7-methylguanylate ‘cap’ in eukaryotic rna. in particular, rna species containing a 5′-end nicotinamide adenine dinucleotide (nad+) or 3′-desphospho-coenzyme a (dpcoa) have been ide ...	2016	27383794
resistance mutations generate divergent antibiotic susceptibility profiles against translation inhibitors.	mutations conferring resistance to translation inhibitors often alter the structure of rrna. reduced susceptibility to distinct structural antibiotic classes may, therefore, emerge when a common ribosomal binding site is perturbed, which significantly reduces the clinical utility of these agents. the translation inhibitors negamycin and tetracycline interfere with trna binding to the aminoacyl-trna site on the small 30s ribosomal subunit. however, two negamycin resistance mutations display unexp ...	2016	27382179
a combined cryo-em and molecular dynamics approach reveals the mechanism of ermbl-mediated translation arrest.	nascent polypeptides can induce ribosome stalling, regulating downstream genes. stalling of ermbl peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in streptococcus sanguis. to reveal this stalling mechanism we obtained 3.6-å-resolution cryo-em structures of ermbl-stalled ribosomes with erythromycin. the nascent peptide adopts an unusual conformation with the c-terminal asp10 side chain in a previously unseen rotated position. together with molecula ...	2016	27380950
mechanism of endonuclease cleavage by the higb toxin.	bacteria encode multiple type ii toxin-antitoxin modules that cleave ribosome-bound mrnas in response to stress. all ribosome-dependent toxin family members structurally characterized to date adopt similar microbial rnase architectures despite possessing low sequence identities. therefore, determining which residues are catalytically important in this specialized rnase family has been a challenge in the field. structural studies of rele and yoeb toxins bound to the ribosome provided significant ...	2016	27378776
the sam68 nuclear body is composed of two rnase-sensitive substructures joined by the adaptor hnrnpl.	the mammalian cell nucleus contains membraneless suborganelles referred to as nuclear bodies (nbs). some nbs are formed with an architectural rna (arcrna) as the structural core. here, we searched for new nbs that are built on unidentified arcrnas by screening for ribonuclease (rnase)-sensitive nbs using 32,651 fluorescently tagged human cdna clones. we identified 32 tagged proteins that required rna for their localization in distinct nuclear foci. among them, seven rna-binding proteins commonly ...	2016	27377249
focal targeting of the bacterial envelope by antimicrobial peptides.	antimicrobial peptides (amps) are utilized by both eukaryotic and prokaryotic organisms. amps such as the human beta defensins, human neutrophil peptides, human cathelicidin, and many bacterial bacteriocins are cationic and capable of binding to anionic regions of the bacterial surface. cationic amps (camps) target anionic lipids [e.g., phosphatidylglycerol (pg) and cardiolipins (cl)] in the cell membrane and anionic components [e.g., lipopolysaccharide (lps) and lipoteichoic acid (lta)] of the ...	2016	27376064
structure and mechanism of a molecular rheostat, an rna thermometer that modulates immune evasion by neisseria meningitidis.	neisseria meningitidis causes bacterial meningitis and septicemia. it evades the host complement system by upregulating expression of immune evasion factors in response to changes in temperature. rna thermometers within mrnas control expression of bacterial immune evasion factors, including cssa, in the 5'-untranslated region of the operon for capsule biosynthesis. we dissect the molecular mechanisms of thermoregulation and report the structure of the cssa thermometer. we show that the rna therm ...	2016	27369378
hydrogen peroxide-resistant cota and yjqc of bacillus altitudinis spores are a promising biocatalyst for catalyzing reduction of sinapic acid and sinapine in rapeseed meal.	for the more efficient detoxification of phenolic compounds, a promising avenue would be to develop a multi-enzyme biocatalyst comprising peroxidase, laccase and other oxidases. however, the development of this multi-enzyme biocatalyst is limited by the vulnerability of fungal laccases and peroxidases to hydrogen peroxide (h2o2)-induced inactivation. therefore, h2o2-resistant peroxidase and laccase should be exploited. in this study, h2o2-stable cota and yjqc were isolated from the outer coat of ...	2016	27362423
structural insights into a novel class of aspartate aminotransferase from corynebacterium glutamicum.	aspartate aminotransferase from corynebacterium glutamicum (cgaspat) is a plp-dependent enzyme that catalyzes the production of l-aspartate and α-ketoglutarate from l-glutamate and oxaloacetate in l-lysine biosynthesis. in order to understand the molecular mechanism of cgaspat and compare it with those of other aspartate aminotransferases (aspats) from the aminotransferase class i, we determined the crystal structure of cgaspat. cgaspat functions as a dimer, and the cgaspat monomer consists of t ...	2016	27355211
the slicer activity of argonaute1 is required specifically for the phasing, not production, of trans-acting short interfering rnas in arabidopsis.	argonaute1 (ago1) mediates posttranscriptional silencing by micrornas (mirnas) and short interfering rnas (sirnas). ago1-catalyzed rna cleavage (slicing) represses mirna targets, but current models also highlight the roles of slicing in formation of sirnas and sirna-ago1 complexes. mirna-guided slicing is required for biogenesis of phased, trans-acting sirnas (tasirnas), whose cleaved precursor fragments are converted to double-stranded rna by rna-dependent rna polymerase 6 (rdr6). in addition, ...	2016	27354557
mechanistic and structural studies of protein-only rnase p compared to ribonucleoproteins reveal the two faces of the same enzymatic activity.	rnase p, the essential activity that performs the 5' maturation of trna precursors, can be achieved either by ribonucleoproteins containing a ribozyme present in the three domains of life or by protein-only enzymes called protein-only rnase p (prorp) that occur in eukaryote nuclei and organelles. a fast growing list of studies has investigated three-dimensional structures and mode of action of prorp proteins. results suggest that similar to ribozymes, prorp proteins have two main domains. a clea ...	2016	27348014
challenges with using names to link digital biodiversity information.		2016	27346955
translating the epitranscriptome.	rna modifications are indispensable for the translation machinery to provide accurate and efficient protein synthesis. whereas the importance of transfer rna (trna) and ribosomal rna (rrna) modifications has been well described and is unquestioned for decades, the significance of internal messenger rna (mrna) modifications has only recently been revealed. novel experimental methods have enabled the identification of thousands of modified sites within the untranslated and translated regions of mr ...	2016	27345446
translating the epitranscriptome.	rna modifications are indispensable for the translation machinery to provide accurate and efficient protein synthesis. whereas the importance of transfer rna (trna) and ribosomal rna (rrna) modifications has been well described and is unquestioned for decades, the significance of internal messenger rna (mrna) modifications has only recently been revealed. novel experimental methods have enabled the identification of thousands of modified sites within the untranslated and translated regions of mr ...	2016	27345446
detecting conformational differences between rna 3d structures.	a method is described for detecting local conformational differences between two 3d structures of the same rna molecule. these could be distinct 3d structures of the same molecule from the same organism, or homologous molecules from different organisms. in this approach, we detect the variability that exists among the relative translation and rotation operations that are needed to superimpose local neighborhoods after an initial rigid-body global superposition. each translation and rotation is r ...	2015	27330250
detecting conformational differences between rna 3d structures.	a method is described for detecting local conformational differences between two 3d structures of the same rna molecule. these could be distinct 3d structures of the same molecule from the same organism, or homologous molecules from different organisms. in this approach, we detect the variability that exists among the relative translation and rotation operations that are needed to superimpose local neighborhoods after an initial rigid-body global superposition. each translation and rotation is r ...	2015	27330250
structural basis for the recognition of guide rna and target dna heteroduplex by argonaute.	argonaute proteins are key players in the gene silencing mechanisms mediated by small nucleic acids in all domains of life from bacteria to eukaryotes. however, little is known about the argonaute protein that recognizes guide rna/target dna. here, we determine the 2 å crystal structure of rhodobacter sphaeroides argonaute (rsago) in a complex with 18-nucleotide guide rna and its complementary target dna. the heteroduplex maintains watson-crick base-pairing even in the 3'-region of the guide rna ...	2016	27325485
potential dna binding and nuclease functions of comec domains characterized in silico.	bacterial competence, which can be natural or induced, allows the uptake of exogenous double stranded dna (dsdna) into a competent bacterium. this process is known as transformation. a multiprotein assembly binds and processes the dsdna to import one strand and degrade another yet the underlying molecular mechanisms are relatively poorly understood. here distant relationships of domains in competence protein ec (comec) of bacillus subtilis (uniprot: p39695) were characterized. dna-protein intera ...	2016	27318187
monitoring tetracycline through a solid-state nanopore sensor.	antibiotics as emerging environmental contaminants, are widely used in both human and veterinary medicines. a solid-state nanopore sensing method is reported in this article to detect tetracycline, which is based on tet-off and tet-on systems. rtta (reverse tetracycline-controlled trans-activator) and tre (tetracycline responsive element) could bind each other under the action of tetracycline to form one complex. when the complex passes through nanopores with 8 ~ 9 nanometers in diameter, we cou ...	2016	27306259
crystal structure of glutamate-1-semialdehyde-2,1-aminomutase from arabidopsis thaliana.	glutamate-1-semialdehyde-2,1-aminomutase (gsam) catalyzes the isomerization of glutamate-1-semialdehyde (gsa) to 5-aminolevulinate (ala) and is distributed in archaea, most bacteria and plants. although structures of gsam from archaea and bacteria have been resolved, a gsam structure from a higher plant is not available, preventing further structure-function analysis. here, the structure of gsam from arabidopsis thaliana (atgsa1) obtained by x-ray crystallography is reported at 1.25 å resolution ...	2016	27303897
amicoumacin a induces cancer cell death by targeting the eukaryotic ribosome.	amicoumacin a is an antibiotic that was recently shown to target bacterial ribosomes. it affects translocation and provides an additional contact interface between the ribosomal rna and mrna. the binding site of amicoumacin a is formed by universally conserved nucleotides of rrna. in this work, we showed that amicoumacin a inhibits translation in yeast and mammalian systems by affecting translation elongation. we determined the structure of the amicoumacin a complex with yeast ribosomes at a res ...	2016	27296282
duf3380 domain from a salmonella phage endolysin shows potent n-acetylmuramidase activity.	bacteriophage-encoded endolysins are highly diverse enzymes that cleave the bacterial peptidoglycan layer. current research focuses on their potential applications in medicine, in food conservation, and as biotechnological tools. despite the wealth of applications relying on the use of endolysin, little is known about the enzymatic properties of these enzymes, especially in the case of endolysins of bacteriophages infecting gram-negative species. automated genome annotations therefore remain to ...	2016	27287318
structural basis of transcription activation.	class ii transcription activators function by binding to a dna site overlapping a core promoter and stimulating isomerization of an initial rna polymerase (rnap)-promoter closed complex into a catalytically competent rnap-promoter open complex. here, we report a 4.4 angstrom crystal structure of an intact bacterial class ii transcription activation complex. the structure comprises thermus thermophilus transcription activator protein tthb099 (tap) [homolog of escherichia coli catabolite activator ...	2016	27284196
mass spectrometry analysis and transcriptome sequencing reveal glowing squid crystal proteins are in the same superfamily as firefly luciferase.	the japanese firefly squid hotaru-ika (watasenia scintillans) produces intense blue light from photophores at the tips of two arms. these photophores are densely packed with protein microcrystals that catalyse the bioluminescent reaction using atp and the substrate coelenterazine disulfate. the squid is the only organism known to produce light using protein crystals. we extracted microcrystals from arm tip photophores and identified the constituent proteins using mass spectrometry and transcript ...	2016	27279452
ribosome-dependent activation of stringent control.	in order to survive, bacteria continually sense, and respond to, environmental fluctuations. stringent control represents a key bacterial stress response to nutrient starvation that leads to rapid and comprehensive reprogramming of metabolic and transcriptional patterns. in general, transcription of genes for growth and proliferation is downregulated, while those important for survival and virulence are upregulated. amino acid starvation is sensed by depletion of the aminoacylated trna pools, an ...	2016	27279228
cloning and expression of dnak gene from bacillus pumilus of hot water spring origin.	a set of thermotolerant strains isolated from hot springs of manikaran and bakreshwar (india) were selected with an aim to isolate dnak gene which encodes dnak protein. the gene dnak along with its flanking region was successfully amplified from 5 different strains (4 from bakreshwar and one from manikaran). restriction fragment length polymorphism (rflp) revealed that amplicons were almost identical in sequence. the dnak gene from one representative, bacillus pumilus strain b3 isolated from bak ...	2013	27275408
cloning and expression of dnak gene from bacillus pumilus of hot water spring origin.	a set of thermotolerant strains isolated from hot springs of manikaran and bakreshwar (india) were selected with an aim to isolate dnak gene which encodes dnak protein. the gene dnak along with its flanking region was successfully amplified from 5 different strains (4 from bakreshwar and one from manikaran). restriction fragment length polymorphism (rflp) revealed that amplicons were almost identical in sequence. the dnak gene from one representative, bacillus pumilus strain b3 isolated from bak ...	2013	27275408
chloramphenicol derivatives as antibacterial and anticancer agents: historic problems and current solutions.	chloramphenicol (cam) is the d-threo isomer of a small molecule, consisting of a p-nitrobenzene ring connected to a dichloroacetyl tail through a 2-amino-1,3-propanediol moiety. cam displays a broad-spectrum bacteriostatic activity by specifically inhibiting the bacterial protein synthesis. in certain but important cases, it also exhibits bactericidal activity, namely against the three most common causes of meningitis, haemophilus influenzae, streptococcus pneumoniae and neisseria meningitidis. ...	2016	27271676
unusually situated binding sites for bacterial transcription factors can have hidden functionality.	a commonly accepted paradigm of molecular biology is that transcription factors control gene expression by binding sites at the 5' end of a gene. however, there is growing evidence that transcription factor targets can occur within genes or between convergent genes. in this work, we have investigated one such target for the cyclic amp receptor protein (crp) of enterotoxigenic escherichia coli. we show that crp binds between two convergent genes. when bound, crp regulates transcription of a small ...	2016	27258043
mechanism of b-box 2 domain-mediated higher-order assembly of the retroviral restriction factor trim5α.	restriction factors and pattern recognition receptors are important components of intrinsic cellular defenses against viral infection. mammalian trim5α proteins are restriction factors and receptors that target the capsid cores of retroviruses and activate ubiquitin-dependent antiviral responses upon capsid recognition. here, we report crystallographic and functional studies of the trim5α b-box 2 domain, which mediates higher-order assembly of trim5 proteins. the b-box can form both dimers and t ...	2016	27253059
expression and characterization of a novel glycerophosphodiester phosphodiesterase from pyrococcus furiosus dsm 3638 that possesses lysophospholipase d activity.	glycerophosphodiester phosphodiesterases (gdpd) are enzymes which degrade various glycerophosphodiesters to produce glycerol-3-phosphate and the corresponding alcohol moiety. apart from this, a very interesting finding is that this enzyme could be used in the degradation of toxic organophosphorus esters, which has resulted in much attention on the biochemical and application research of gdpds. in the present study, a novel gdpd from pyrococcus furiosus dsm 3638 (pfgdpd) was successfully expresse ...	2016	27248999
a mutation in the 16s rrna decoding region attenuates the virulence of mycobacterium tuberculosis.	mycobacterium tuberculosis contains a single rrna operon that encodes targets for antituberculosis agents, including kanamycin. to date, only four mutations in the kanamycin binding sites of 16s rrna have been reported in kanamycin-resistant clinical isolates. we hypothesized that another mutation(s) in the region may dramatically decrease m. tuberculosis viability and virulence. here, we describe an rrna mutation, u1406a, which was generated in vitro and confers resistance to kanamycin while hi ...	2016	27245411
a colorimetric microplate assay for dna-binding activity of his-tagged muts protein.	a simple microplate method was designed for rapid testing dna-binding activity of proteins. the principle of the assay involves binding of tested dna by his-tagged protein immobilized on a nickel-coated elisa plate, following colorimetric detection of biotinylated dna with avidin conjugated to horseradish peroxidase. the method was used to compare dna mismatch binding activities of muts proteins from three bacterial species. the assay required relatively low amounts of tested protein (approximat ...	2016	27241123
characterization of the atp-dependent lon-like protease in methanobrevibacter smithii.	the lon protease is highly evolutionarily conserved. however, little is known about lon in the context of gut microbial communities. a gene encoding a lon-like protease (lon-like-ms) was identified and characterized from methanobrevibacter smithii, the predominant archaeon in the human gut ecosystem. phylogenetic and sequence analyses showed that lon-like-ms and its homologs are newly identified members of the lon family. a recombinant form of the enzyme was purified by affinity chromatography, ...	2016	27239160
elongation factor tu prevents misediting of gly-trna(gly) caused by the design behind the chiral proofreading site of d-aminoacyl-trna deacylase.	d-aminoacyl-trna deacylase (dtd) removes d-amino acids mischarged on trnas and is thus implicated in enforcing homochirality in proteins. previously, we proposed that selective capture of d-aminoacyl-trna by dtd's invariant, cross-subunit gly-cispro motif forms the mechanistic basis for its enantioselectivity. we now show, using nuclear magnetic resonance (nmr) spectroscopy-based binding studies followed by biochemical assays with both bacterial and eukaryotic systems, that dtd effectively mised ...	2016	27224426
abundance and temperature dependency of protein-protein interaction revealed by interface structure analysis and stability evolution.	protein complexes are major forms of protein-protein interactions and implement essential biological functions. the subunit interface in a protein complex is related to its thermostability. though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. in the present work, we studied this relationship and found a positive correlation in thermophiles ...	2016	27220911
wake me when it's over - bacterial toxin-antitoxin proteins and induced dormancy.	toxin-antitoxin systems are encoded by bacteria and archaea to enable an immediate response to environmental stresses, including antibiotics and the host immune response. during normal conditions, the antitoxin components prevent toxins from interfering with metabolism and arresting growth; however, toxin activation enables microbes to remain dormant through unfavorable conditions that might continue over millions of years. intense investigations have revealed a multitude of mechanisms for both ...	2016	27216598
essential structural elements in trna(pro) for ef-p-mediated alleviation of translation stalling.	the ribosome stalls on translation of polyproline sequences due to inefficient peptide bond formation between consecutive prolines. the translation factor ef-p is able to alleviate this stalling by accelerating pro-pro formation. however, the mechanism by which ef-p recognizes the stalled complexes and accelerates peptide bond formation is not known. here, we use genetic code reprogramming through a flexible in-vitro translation (fit) system to investigate how mutations in trna(pro) affect ef-p ...	2016	27216360
the pilin n-terminal domain maintains neisseria gonorrhoeae transformation competence during pilus phase variation.	the obligate human pathogen neisseria gonorrhoeae is the sole aetiologic agent of the sexually transmitted infection, gonorrhea. required for gonococcal infection, type iv pili (tfp) mediate many functions including adherence, twitching motility, defense against neutrophil killing, and natural transformation. critical for immune escape, the gonococcal tfp undergoes antigenic variation, a recombination event at the pile locus that varies the surface exposed residues of the major pilus subunit pil ...	2016	27213957
functional characterization of the subunits n, h, j, and o of the nad(p)h dehydrogenase complexes in synechocystis sp. strain pcc 6803.	the cyanobacterial nad(p)h dehydrogenase (ndh-1) complexes play crucial roles in variety of bioenergetic reactions such as respiration, co2 uptake, and cyclic electron transport around psi. recently, substantial progress has been made in identifying the composition of subunits of ndh-1 complexes. however, the localization and the physiological roles of several subunits in cyanobacteria are not fully understood. here, by constructing fully segregated ndhn, ndho, ndhh, and ndhj null mutants in syn ...	2016	27208236
implications of limited thermophilicity of nitrite reduction for control of sulfide production in oil reservoirs.	nitrate reduction to nitrite in oil fields appears to be more thermophilic than the subsequent reduction of nitrite. concentrated microbial consortia from oil fields reduced both nitrate and nitrite at 40 and 45°c but only nitrate at and above 50°c. the abundance of the nirs gene correlated with mesophilic nitrite reduction activity. thauera and pseudomonas were the dominant mesophilic nitrate-reducing bacteria (mnrb), whereas petrobacter and geobacillus were the dominant thermophilic nrb (tnrb) ...	2016	27208132
a highly thermostable kanamycin resistance marker expands the tool kit for genetic manipulation of caldicellulosiruptor bescii.	caldicellulosiruptor bescii, an anaerobic gram-positive bacterium with an optimal growth temperature of 78°c, is the most thermophilic cellulose degrader known. it is of great biotechnological interest, as it efficiently deconstructs nonpretreated lignocellulosic plant biomass. currently, its genetic manipulation relies on a mutant uracil auxotrophic background strain that contains a random deletion in the pyrf genome region. the pyrf gene serves as a genetic marker to select for uracil prototro ...	2016	27208106
structure of human cdc45 and implications for cmg helicase function.	cell division cycle protein 45 (cdc45) is required for dna synthesis during genome duplication, as a component of the cdc45-mcm-gins (cmg) helicase. despite its essential biological function, its biochemical role in dna replication has remained elusive. here we report the 2.1-å crystal structure of human cdc45, which confirms its evolutionary link with the bacterial recj nuclease and reveals several unexpected features that underpin its function in eukaryotic dna replication. these include a lon ...	2016	27189187
the diversity of ribonuclease p: protein and rna catalysts with analogous biological functions.	ribonuclease p (rnase p) is an essential endonuclease responsible for catalyzing 5' end maturation in precursor transfer rnas. since its discovery in the 1970s, rnase p enzymes have been identified and studied throughout the three domains of life. interestingly, rnase p is either rna-based, with a catalytic rna subunit, or a protein-only (prorp) enzyme with differential evolutionary distribution. the available structural data, including the active site data, provides insight into catalysis and s ...	2016	27187488
anatomy of risc: how do small rnas and chaperones activate argonaute proteins?	rna silencing is a eukaryote-specific phenomenon in which micrornas and small interfering rnas degrade messenger rnas containing a complementary sequence. to this end, these small rnas need to be loaded onto an argonaute protein (ago protein) to form the effector complex referred to as rna-induced silencing complex (risc). risc assembly undergoes multiple and sequential steps with the aid of hsc70/hsp90 chaperone machinery. the molecular mechanisms for this assembly process remain unclear, despi ...	2016	27184117
cyclic amp receptor protein acts as a transcription regulator in response to stresses in deinococcus radiodurans.	the cyclic amp receptor protein family of transcription factors regulates various metabolic pathways in bacteria, and also play roles in response to environmental changes. here, we identify four homologs of the crp family in deinococcus radiodurans, one of which tolerates extremely high levels of oxidative stress and dna-damaging reagents. transcriptional levels of crp were increased under hydrogen peroxide (h2o2) treatment during the stationary growth phase, indicating that crps function in res ...	2016	27182600
global quantitative proteomics reveal up-regulation of endoplasmic reticulum stress response proteins upon depletion of eif5a in hela cells.	the eukaryotic translation factor, eif5a, is a translation factor essential for protein synthesis, cell growth and animal development. by use of a adenoviral eif5a shrna, we have achieved an effective depletion of eif5a in hela cells and undertook in vivo comprehensive proteomic analyses to examine the effects of eif5a depletion on the total proteome and to identify cellular pathways influenced by eif5a. the proteome of hela cells transduced with eif5a shrna was compared with that of scramble sh ...	2016	27180817
characterization of the flexibility of the peripheral stalk of prokaryotic rotary a-atpases by atomistic simulations.	rotary atpases are involved in numerous physiological processes, with the three distinct types (f/a/v-atpases) sharing functional properties and structural features. the basic mechanism involves the counter rotation of two motors, a soluble atp hydrolyzing/synthesizing domain and a membrane-embedded ion pump connected through a central rotor axle and a stator complex. within the a/v-atpase family conformational flexibility of the eg stators has been shown to accommodate catalytic cycling and is ...	2016	27177595
a water-forming nadh oxidase regulates metabolism in anaerobic fermentation.	water-forming nadh oxidase can oxidize cytosolic nadh to nad(+), thus relieving cytosolic nadh accumulation in saccharomyces cerevisiae. previous studies of the enzyme were conducted under aerobic conditions, as o2 is the recognized electron acceptor of the enzyme. in order to extend its use in industrial production and to study its effect on anaerobes, the effects of overexpression of this oxidase in s. cerevisiae by4741 and clostridium acetobutylicum 428 (cac-428) under anaerobic conditions we ...	2016	27175216
the crispr rna-guided surveillance complex in escherichia coli accommodates extended rna spacers.	bacteria and archaea acquire resistance to foreign genetic elements by integrating fragments of foreign dna into crispr (clustered regularly interspaced short palindromic repeats) loci. in escherichia coli, crispr-derived rnas (crrnas) assemble with cas proteins into a multi-subunit surveillance complex called cascade (crispr-associated complex for antiviral defense). cascade recognizes dna targets via protein-mediated recognition of a protospacer adjacent motif and complementary base pairing be ...	2016	27174938
zinc coordination is essential for the function and activity of the type ii secretion atpase epse.	the type ii secretion system eps in vibrio cholerae promotes the extracellular transport of cholera toxin and several hydrolytic enzymes and is a major virulence system in many gram-negative pathogens which is structurally related to the type iv pilus system. the cytoplasmic atpase epse provides the energy for exoprotein secretion through atp hydrolysis. epse contains a unique metal-binding domain that coordinates zinc through a tetracysteine motif (cxxcx29 cxxc), which is also present in type i ...	2016	27168165
comparative transcriptomics across the prokaryotic tree of life.	whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding rnas, cis-antisense transcription and regulatory untranslated regions (utrs). understanding the functional relevance of the plethora of non-coding rnas in a given organism is challenging, especially since some of these rnas were attributed to 'transcriptional noise'. to allow the search for conserved transcriptomic elements we produce ...	2016	27154273
independent evolution of six families of halogenating enzymes.	halogenated natural products are widespread in the environment, and the halogen atoms are typically vital to their bioactivities. thus far, six families of halogenating enzymes have been identified: cofactor-free haloperoxidases (hpo), vanadium-dependent haloperoxidases (v-hpo), heme iron-dependent haloperoxidases (hi-hpo), non-heme iron-dependent halogenases (ni-hg), flavin-dependent halogenases (f-hg), and s-adenosyl-l-methionine (sam)-dependent halogenases (s-hg). however, these halogenating ...	2016	27153321
evidence for fast electron transfer between the high-spin haems in cytochrome bd-i from escherichia coli.	cytochrome bd-i is one of the three proton motive force-generating quinol oxidases in the o2-dependent respiratory chain of escherichia coli. it contains one low-spin haem (b558) and the two high-spin haems (b595 and d) as the redox-active cofactors. in order to examine the flash-induced intraprotein reverse electron transfer (the so-called ''electron backflow''), co was photolyzed from the ferrous haem d in one-electron reduced (b5583+b5953+d2+-co) cytochrome bd-i, and the fully reduced (b5582+ ...	2016	27152644
bioprospecting sponge-associated microbes for antimicrobial compounds.	sponges are the most prolific marine organisms with respect to their arsenal of bioactive compounds including antimicrobials. however, the majority of these substances are probably not produced by the sponge itself, but rather by bacteria or fungi that are associated with their host. this review for the first time provides a comprehensive overview of antimicrobial compounds that are known to be produced by sponge-associated microbes. we discuss the current state-of-the-art by grouping the bioact ...	2016	27144573
transcription regulation in archaea.	the known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. archaea are reliant on a single rna polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcripti ...	2016	27137495
life without complex i: proteome analyses of an arabidopsis mutant lacking the mitochondrial nadh dehydrogenase complex.	the mitochondrial nadh dehydrogenase complex (complex i) is of particular importance for the respiratory chain in mitochondria. it is the major electron entry site for the mitochondrial electron transport chain (metc) and therefore of great significance for mitochondrial atp generation. we recently described an arabidopsis thaliana double-mutant lacking the genes encoding the carbonic anhydrases ca1 and ca2, which both form part of a plant-specific 'carbonic anhydrase domain' of mitochondrial co ...	2016	27122571
structural dynamics of human argonaute2 and its interaction with sirnas designed to target mutant tdp43.	the human argonaute2 protein (ago2) is a key player in rna interference pathway and small rna recognition by ago2 is the crucial step in sirna mediated gene silencing mechanism. the present study highlights the structural and functional dynamics of human ago2 and the interaction mechanism of ago2 with a set of seven sirnas for the first time. the human ago2 protein adopts two conformations such as "open" and "close" during the simulation of 25 ns. one of the domains named as paz, which is respon ...	2016	27110240
engineering a d-lactate dehydrogenase that can super-efficiently utilize nadph and nadh as cofactors.	engineering the cofactor specificity of a natural enzyme often results in a significant decrease in its activity on original cofactor. here we report that a nadh-dependent dehydrogenase (d-ldh) from lactobacillus delbrueckii 11842 can be rationally engineered to efficiently use both nadh and nadph as cofactors. point mutations on three amino acids (d176s, i177r, f178t) predicted by computational analysis resulted in a modified enzyme designated as d-ldh. the kcat/km of the purified d-ldh on na ...	2016	27109778
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
nucleoside modifications in the regulation of gene expression: focus on trna.	both, dna and rna nucleoside modifications contribute to the complex multi-level regulation of gene expression. modified bases in trnas modulate protein translation rates in a highly dynamic manner. synonymous codons, which differ by the third nucleoside in the triplet but code for the same amino acid, may be utilized at different rates according to codon-anticodon affinity. nucleoside modifications in the trna anticodon loop can favor the interaction with selected codons by stabilizing specific ...	2016	27094388
the ancient evolutionary history of polyomaviruses.	polyomaviruses are a family of dna tumor viruses that are known to infect mammals and birds. to investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billi ...	2016	27093155
elongation factor 4 remodels the a-site trna on the ribosome.	during translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. many of those factors are guanosine triphosphatases (gtpases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (gtp) to promote conformational changes. despite numerous studies, the function of elongation factor 4 (ef-4/lepa), a highly conserved translational gtpase, has remained elusive. here, we present the crystal structure at 2.6-å resolution of the thermus thermophilus 7 ...	2016	27092003
evolutionary relationships between heme-binding ferredoxin α + β barrels.	the α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. the barrel architecture of these proteins is formed by either homo-/hetero-dimerization or duplication and fusion of ferredoxin-like domains. several members of this superfamily bind heme in order to carry out their functions.	2016	27089923
crystal structures of apo and liganded 4-oxalocrotonate decarboxylase uncover a structural basis for the metal-assisted decarboxylation of a vinylogous β-keto acid.	the enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. in a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria pseudomonas putida g7. in this organism, the 83 kb nah7 plasmid carries several genes involved in this biotransformation process. one enzyme in this route, nahk, ...	2016	27082660
insights into rna binding by the anticancer drug cisplatin from the crystal structure of cisplatin-modified ribosome.	cisplatin is a widely prescribed anticancer drug, which triggers cell death by covalent binding to a broad range of biological molecules. among cisplatin targets, cellular rnas remain the most poorly characterized molecules. although cisplatin was shown to inactivate essential rnas, including ribosomal, spliceosomal and telomeric rnas, cisplatin binding sites in most rna molecules are unknown, and therefore it remains challenging to study how modifications of rna by cisplatin contributes to its ...	2016	27079977
inhibition of translation initiation complex formation by ge81112 unravels a 16s rrna structural switch involved in p-site decoding.	in prokaryotic systems, the initiation phase of protein synthesis is governed by the presence of initiation factors that guide the transition of the small ribosomal subunit (30s) from an unlocked preinitiation complex (30s preic) to a locked initiation complex (30sic) upon the formation of a correct codon-anticodon interaction in the peptidyl (p) site. biochemical and structural characterization of ge81112, a translational inhibitor specific for the initiation phase, indicates that the main mech ...	2016	27071098
global association between thermophilicity and vancomycin susceptibility in bacteria.	exploration of the aquatic microbiota of several circum-neutral (6.0-8.5 ph) mid-temperature (55-85°c) springs revealed rich diversities of phylogenetic relatives of mesophilic bacteria, which surpassed the diversity of the truly-thermophilic taxa. to gain insight into the potentially-thermophilic adaptations of the phylogenetic relatives of gram-negative mesophilic bacteria detected in culture-independent investigations we attempted pure-culture isolation by supplementing the enrichment media w ...	2016	27065976
the chthonomonas calidirosea genome is highly conserved across geographic locations and distinct chemical and microbial environments in new zealand's taupō volcanic zone.	chthonomonas calidirosea t49(t) is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. we hypothesized that the c. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. we tested this hypothesis by sequencing the genomes of four c. calidirosea isolates obtained from four separate geoth ...	2016	27060125
structural basis for dna 5´-end resection by recj.	the resection of dna strand with a 5´ end at double-strand breaks is an essential step in recombinational dna repair. recj, a member of dhh family proteins, is the only 5´ nuclease involved in the recf recombination pathway. here, we report the crystal structures of deinococcus radiodurans recj in complex with deoxythymidine monophosphate (dtmp), ssdna, the c-terminal region of single-stranded dna-binding protein (ssb-ct) and a mechanistic insight into the recf pathway. a terminal 5´-phosphate-b ...	2016	27058167
escherichia coli dnae polymerase couples pyrophosphatase activity to dna replication.	dna polymerases generate pyrophosphate every time they catalyze a step of dna elongation. this elongation reaction is generally believed as thermodynamically favoured by the hydrolysis of pyrophosphate, catalyzed by inorganic pyrophosphatases. however, the specific action of inorganic pyrophosphatases coupled to dna replication in vivo was never demonstrated. here we show that the polymerase-histidinol-phosphatase (php) domain of escherichia coli dna polymerase iii α subunit features pyrophospha ...	2016	27050298
crystal structure of cota laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site.	the cota laccase from bacillus subtilis is an abundant component of the spore outer coat and has been characterized as a typical laccase. the crystal structure of cota complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (abts) in a hole motif has been solved. the novel binding site was about 26 å away from the t1 binding pocket. comparison with known structures of other laccases revealed that the hole is a specific feature of cota. the key residues arg476 and ser360 were directly bo ...	2016	27050268
a bacterial argonaute with noncanonical guide rna specificity.	eukaryotic argonaute proteins induce gene silencing by small rna-guided recognition and cleavage of mrna targets. although structural similarities between human and prokaryotic argonautes are consistent with shared mechanistic properties, sequence and structure-based alignments suggested that argonautes encoded within crispr-cas [clustered regularly interspaced short palindromic repeats (crispr)-associated] bacterial immunity operons have divergent activities. we show here that the crispr-associ ...	2016	27035975
structures of e. coli σs-transcription initiation complexes provide new insights into polymerase mechanism.	in bacteria, multiple σ factors compete to associate with the rna polymerase (rnap) core enzyme to form a holoenzyme that is required for promoter recognition. during transcription initiation rnap remains associated with the upstream promoter dna via sequence-specific interactions between the σ factor and the promoter dna while moving downstream for rna synthesis. as rna polymerase repetitively adds nucleotides to the 3'-end of the rna, a pyrophosphate ion is generated after each nucleotide inco ...	2016	27035955