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the tetr family of regulators.the most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a dna-binding domain. among the >20 classes of one-component systems, the tetr family of regulators (tfrs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. however, tfrs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and ma ...201324006471
cloning and characterization of ef-tu and ef-ts from pseudomonas aeruginosa.we have cloned genes encoding elongation factors ef-tu and ef-ts from pseudomonas aeruginosa and expressed and purified the proteins to greater than 95% homogeneity. sequence analysis indicated that p. aeruginosa ef-tu and ef-ts are 84% and 55% identical to e. coli counterparts, respectively. p. aeruginosa ef-tu was active when assayed in gdp exchange assays. kinetic parameters for the interaction of ef-tu with gdp in the absence of ef-ts were observed to be k m = 33 μm, k cat (obs) = 0.003 s(-1 ...201323984384
the glove-like structure of the conserved membrane protein tatc provides insight into signal sequence recognition in twin-arginine translocation.in bacteria, two signal-sequence-dependent secretion pathways translocate proteins across the cytoplasmic membrane. although the mechanism of the ubiquitous general secretory pathway is becoming well understood, that of the twin-arginine translocation pathway, responsible for translocation of folded proteins across the bilayer, is more mysterious. tatc, the largest and most conserved of three integral membrane components, provides the initial binding site of the signal sequence prior to pore ass ...201323583035
determination of the structure of the catabolic n-succinylornithine transaminase (astc) from escherichia coli.escherichia coli possesses two acyl ornithine aminotransferases, one catabolic (astc) and the other anabolic (argd), that participate in l-arginine metabolism. although only 58% identical, the enzymes have been shown to be functionally interchangeable. here we have purified astc and have obtained x-ray crystal structures of apo and holo-astc and of the enzyme complexed with its physiological substrate, succinylornithine. we compare the structures obtained in this study with those of argd from sa ...201323484010
shallow breathing: bacterial life at low o(2).competition for molecular oxygen (o(2)) among respiratory microorganisms is intense because o(2) is a potent electron acceptor. this competition leads to the formation of microoxic environments wherever microorganisms congregate in aquatic, terrestrial and host-associated communities. bacteria can harvest o(2) present at low, even nanomolar, concentrations using high-affinity terminal oxidases. here, we report the results of surveys searching for high-affinity terminal oxidase genes in sequenced ...201323411864
the variability of the 16s rrna gene in bacterial genomes and its consequences for bacterial community analyses.16s ribosomal rna currently represents the most important target of study in bacterial ecology. its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome. here we use the information from sequenced bacterial genomes to explore the variability of 16s rrna sequences and copy numbers at various taxonomic levels and apply it to estimate bacterial genome an ...201323460914
functional dissection of the multi-domain di-heme cytochrome c(550) from thermus thermophilus.in bacteria, oxidation of sulfite to sulfate, the most common strategy for sulfite detoxification, is mainly accomplished by the molybdenum-containing sulfite:acceptor oxidoreductases (sors). bacterial sors are very diverse proteins; they can exist as monomers or homodimers of their core subunit, as well as heterodimers with an additional cytochrome c subunit. we have previously described the homodimeric sor from thermus thermophilus hb8 (sor(tthb8)), identified its physiological electron accept ...201323383080
mechanism of tetracycline resistance by ribosomal protection protein tet(o).tetracycline resistance protein tet(o), which protects the bacterial ribosome from binding the antibiotic tetracycline, is a translational gtpase with significant similarity in both sequence and structure to the elongation factor ef-g. here, we present an atomic model of the tet(o)-bound 70s ribosome based on our cryo-electron microscopic reconstruction at 9.6-å resolution. this atomic model allowed us to identify the tet(o)-ribosome binding sites, which involve three characteristic loops in dom ...201323403578
type i pyridoxal 5'-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines.pyridoxal 5'-phosphate (plp)-dependent enzymes of fold type i, the most studied structural class of the plp-dependent enzyme superfamily, are known to exist as stand-alone homodimers or homotetramers. these enzymes have been found also embedded in multimodular and multidomain assembly lines involved in the biosynthesis of polyketides (pks) and nonribosomal peptides (nrps). the aim of this work is to provide a proteome-wide view of the distribution and characteristics of type i domains covalently ...201324148833
the active site of tthpolx is adapted to prevent 8-oxo-dgtp misincorporation.full genome sequencing of bacterial genomes has revealed the presence of numerous genes encoding family x dna polymerases. these enzymes play a variety of biological roles and, accordingly, display often striking functional differences. here we report that the polx from the heat-stable organism thermus thermophilus (tthpolx) inserts the four dntps with strong asymmetry. we demonstrate that this behaviour is related to the presence of a single divergent residue in the active site of tthpolx. muta ...201324084083
the active site of tthpolx is adapted to prevent 8-oxo-dgtp misincorporation.full genome sequencing of bacterial genomes has revealed the presence of numerous genes encoding family x dna polymerases. these enzymes play a variety of biological roles and, accordingly, display often striking functional differences. here we report that the polx from the heat-stable organism thermus thermophilus (tthpolx) inserts the four dntps with strong asymmetry. we demonstrate that this behaviour is related to the presence of a single divergent residue in the active site of tthpolx. muta ...201324084083
functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter.targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. the overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknow ...201324062736
veillonella, firmicutes: microbes disguised as gram negatives.the firmicutes represent a major component of the intestinal microflora. the intestinal firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. although most firmicutes are gram positive, members of the class negativicutes, including the genus veillonella, stain gram negative. veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerob ...201324976898
the crispr-associated gene cas2 of legionella pneumophila is required for intracellular infection of amoebae.recent studies have shown that the clustered regularly interspaced palindromic repeats (crispr) array and its associated (cas) genes can play a key role in bacterial immunity against phage and plasmids. upon analysis of the legionella pneumophila strain 130b chromosome, we detected a subtype ii-b crispr-cas locus that contains cas9, cas1, cas2, cas4, and an array with 60 repeats and 58 unique spacers. reverse transcription (rt)-pcr analysis demonstrated that the entire crispr-cas locus is expres ...201323481601
bacterial cell-envelope glycoconjugates.prokaryotic glycosylation fulfills an important role in maintaining and protecting the structural integrity and function of the bacterial cell wall, as well as serving as a flexible adaption mechanism to evade environmental and host-induced pressure. the scope of bacterial and archaeal protein glycosylation has considerably expanded over the past decade(s), with numerous examples covering the glycosylation of flagella, pili, glycosylated enzymes, as well as surface-layer proteins. this article a ...201324274370
phosphoproteomic analysis reveals the effects of pilf phosphorylation on type iv pilus and biofilm formation in thermus thermophilus hb27.thermus thermophilus hb27 is an extremely thermophilic eubacteria with a high frequency of natural competence. this organism is therefore often used as a thermophilic model to investigate the molecular basis of type iv pili-mediated functions, such as the uptake of free dna, adhesion, twitching motility, and biofilm formation, in hot environments. in this study, the phosphoproteome of t. thermophilus hb27 was analyzed via a shotgun approach and high-accuracy mass spectrometry. ninety-three uniqu ...201323828892
structure of the mtb card/rnap β-lobes complex reveals the molecular basis of interaction and presents a distinct dna-binding domain for mtb card.card from mycobacterium tuberculosis (mtb) is an essential protein shown to be involved in stringent response through downregulation of rrna and ribosomal protein genes. card interacts with the β-subunit of rnap and this interaction is vital for mtb's survival during the persistent infection state. we have determined the crystal structure of card in complex with the rnap β-subunit β1 and β2 domains at 2.1 å resolution. the structure reveals the molecular basis of card/rnap interaction, providing ...201324055315
crystallization and preliminary x-ray analysis of an alanine dehydrogenase from bacillus megaterium wsh-002.alanine dehydrogenase (l-aladh) from bacillus megaterium wsh-002 catalyses the nad⁺-dependent interconversion of l-alanine and pyruvate. the enzyme was expressed in escherichia coli bl21 (de3) cells and purified with a his6 tag by ni²⁺-chelating affinity chromatography for x-ray crystallographic analysis. crystals were grown in a solution consisting of 0.1 m hepes ph 8.0, 12%(w/v) polyethylene glycol 8000, 8%(v/v) ethylene glycol at a concentration of 15 mg ml⁻¹ purified protein. the crystal dif ...201323908047
type iv pilus proteins form an integrated structure extending from the cytoplasm to the outer membrane.the bacterial type iv pilus (t4p) is the strongest biological motor known to date as its retraction can generate forces well over 100 pn. myxococcus xanthus, a δ-proteobacterium, provides a good model for t4p investigations because its social (s) gliding motility is powered by t4p. in this study, the interactions among m. xanthus t4p proteins were investigated using genetics and the yeast two-hybrid (y2h) system. our genetic analysis suggests that there is an integrated t4p structure that crosse ...201323922942
structure and function of card, an essential mycobacterial transcription factor.card, an essential transcription regulator in mycobacterium tuberculosis, directly interacts with the rna polymerase (rnap). we used a combination of in vivo and in vitro approaches to establish that card is a global regulator that stimulates the formation of rnap-holoenzyme open promoter (rpo) complexes. we determined the x-ray crystal structure of thermus thermophilus card, allowing us to generate a structural model of the card/rpo complex. on the basis of our structural and functional analyse ...201323858468
activation and products of the cryptic secondary metabolite biosynthetic gene clusters by rifampin resistance (rpob) mutations in actinomycetes.a subset of rifampin resistance (rpob) mutations result in the overproduction of antibiotics in various actinomycetes, including streptomyces, saccharopolyspora, and amycolatopsis, with h437y and h437r rpob mutations effective most frequently. moreover, the rpob mutations markedly activate (up to 70-fold at the transcriptional level) the cryptic/silent secondary metabolite biosynthetic gene clusters of these actinomycetes, which are not activated under general stressful conditions, with the exce ...201323603745
peptidoglycan at its peaks: how chromatographic analyses can reveal bacterial cell wall structure and assembly.the peptidoglycan (pg) cell wall is a unique macromolecule responsible for both shape determination and cellular integrity under osmotic stress in virtually all bacteria. a quantitative understanding of the relationships between pg architecture, morphogenesis, immune system activation and pathogenesis can provide molecular-scale insights into the function of proteins involved in cell wall synthesis and cell growth. high-performance liquid chromatography (hplc) has played an important role in our ...201323679048
nusg-spt5 proteins-universal tools for transcription modification and communication. 201323638618
pilmnopq from the pseudomonas aeruginosa type iv pilus system form a transenvelope protein interaction network that interacts with pila.pseudomonas aeruginosa type iv pili (t4p) are virulence factors that promote infection of cystic fibrosis and immunosuppressed patients. as the absence of t4p impairs colonization, they are attractive targets for the development of novel therapeutics. genes in the pilmnopq operon are important for both t4p assembly and a form of bacterial movement, called twitching motility, that is required for pathogenicity. the type ii membrane proteins, piln and pilo, dimerize via their periplasmic domains a ...201323457250
biological diversity in the patent system.biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. to address this problem we text mined 11 million patent documents for 6 million latin species names from the global names index (gni) established by the global biodiversity information facility (gbif) and encyclopedia of life (eol). we identified 76,274 full latin species names from 23,882 genera in 767,955 patent documents. 2 ...201324265714
two homologous ef-g proteins from pseudomonas aeruginosa exhibit distinct functions.genes encoding two proteins corresponding to elongation factor g (ef-g) were cloned from pseudomonas aeruginosa. the proteins encoded by these genes are both members of the efg i subfamily. the gene encoding one of the forms of ef-g is located in the str operon and the resulting protein is referred to as ef-g1a while the gene encoding the other form of ef-g is located in another part of the genome and the resulting protein is referred to as ef-g1b. these proteins were expressed and purified to 9 ...201324260360
aggregate-reactivation activity of the molecular chaperone clpb from ehrlichia chaffeensis.rickettsiale diseases, including human monocytic ehrlichiosis caused by ehrlichia chaffeensis, are the second leading cause of the tick-borne infections in the usa and a growing health concern. little is known about how e. chaffeensis survives the host-induced stress in vertebrate and tick hosts. a molecular chaperone clpb from several microorganisms has been reported to reactivate aggregated proteins in cooperation with the co-chaperones dnak/dnaj/grpe (kje). in this study, we performed the fir ...201323667479
insight into centromere-binding properties of parb proteins: a secondary binding motif is essential for bacterial genome maintenance.parb proteins are one of the three essential components of partition systems that actively segregate bacterial chromosomes and plasmids. in binding to centromere sequences, parb assembles as nucleoprotein structures called partition complexes. these assemblies are the substrates for the partitioning process that ensures dna molecules are segregated to both sides of the cell. we recently identified the sopc centromere nucleotides required for binding to the parb homologue of plasmid f, sopb. this ...201323345617
redox specificity of 2-hydroxyacid-coupled nad(+)/nadh dehydrogenases: a study exploiting "reactive" arginine as a reporter of protein electrostatics.with "reactive" arginine as a kinetic reporter, 2-hydroxyacid dehydrogenases are assessed in basis of their specialization as nad(+)-reducing or nadh-oxidizing enzymes. specifically, m4 and h4 lactate dehydrogenases (ldhs) and cytoplasmic and mitochondrial malate dehydrogenases (mdhs) are compared to assess if their coenzyme specificity may involve electrostatics of cationic or neutral nicotinamide structure as the basis. the enzymes from diverse eukaryote and prokaryote sources thus are assesse ...201324391777
misfolding of amyloidogenic proteins and their interactions with membranes.in this paper, we discuss amyloidogenic proteins, their misfolding, resulting structures, and interactions with membranes, which lead to membrane damage and subsequent cell death. many of these proteins are implicated in serious illnesses such as alzheimer's disease and parkinson's disease. misfolding of amyloidogenic proteins leads to the formation of polymorphic oligomers and fibrils. oligomeric aggregates are widely thought to be the toxic species, however, fibrils also play a role in membran ...201324970204
misfolding of amyloidogenic proteins and their interactions with membranes.in this paper, we discuss amyloidogenic proteins, their misfolding, resulting structures, and interactions with membranes, which lead to membrane damage and subsequent cell death. many of these proteins are implicated in serious illnesses such as alzheimer's disease and parkinson's disease. misfolding of amyloidogenic proteins leads to the formation of polymorphic oligomers and fibrils. oligomeric aggregates are widely thought to be the toxic species, however, fibrils also play a role in membran ...201324970204
allosteric regulation in phosphofructokinase from the extreme thermophile thermus thermophilus.an investigation into the kinetics and regulatory properties of the type-1 phosphofructokinase (pfk) from the extreme thermophile thermus thermophilus (ttpfk) reveals an enzyme that is inhibited by pep and activated by adp by modifying the affinity exhibited for the substrate fructose 6-phosphate (fru-6-p) in a manner analogous to other prokaryotic pfks. however, ttpfk binds both of these allosteric ligands significantly more tightly than other bacterial pfks while effecting a substantially more ...201324328040
allosteric regulation in phosphofructokinase from the extreme thermophile thermus thermophilus.an investigation into the kinetics and regulatory properties of the type-1 phosphofructokinase (pfk) from the extreme thermophile thermus thermophilus (ttpfk) reveals an enzyme that is inhibited by pep and activated by adp by modifying the affinity exhibited for the substrate fructose 6-phosphate (fru-6-p) in a manner analogous to other prokaryotic pfks. however, ttpfk binds both of these allosteric ligands significantly more tightly than other bacterial pfks while effecting a substantially more ...201324328040
structure-based cleavage mechanism of thermus thermophilus argonaute dna guide strand-mediated dna target cleavage.we report on crystal structures of ternary thermus thermophilus argonaute (ttago) complexes with 5'-phosphorylated guide dna and a series of dna targets. these ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 å have provided molecular insights into the orchestrated positioning of catalytic residues, a pair of mg(2+) cations, and the putative water nucleophile positioned for in-line attack on the cleavable ph ...201324374628
structure-based cleavage mechanism of thermus thermophilus argonaute dna guide strand-mediated dna target cleavage.we report on crystal structures of ternary thermus thermophilus argonaute (ttago) complexes with 5'-phosphorylated guide dna and a series of dna targets. these ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 å have provided molecular insights into the orchestrated positioning of catalytic residues, a pair of mg(2+) cations, and the putative water nucleophile positioned for in-line attack on the cleavable ph ...201324374628
mutant lv(476-7)aa of a-subunit of enterococcus hirae v1-atpase: high affinity of a3b3 complex to df axis and low atpase activity.vacuolar atpase (v-atpase) of enterococcus hirae is composed of a soluble functional domain v1 (a3b3df) and an integral membrane domain vo (ac), where v1 and vo domains are connected by a central stalk, composed of d-, f-, and d-subunits; and two peripheral stalks (e- and g-subunits). we identified 120 interacting residues of a3b3 heterohexamer with d-subunit in df heterodimer in the crystal structures of a3b3 and a3b3df. in our previous study, we reported 10 mutants of e. hirae v1-atpase, which ...201324404436
distinct trna recognition strategies used by a homologous family of editing domains prevent mistranslation.errors in protein synthesis due to mispairing of amino acids with trnas jeopardize cell viability. several checkpoints to prevent formation of ala- and cys-trna(pro) have been described, including the ala-specific editing domain (ins) of most bacterial prolyl-trna synthetases (prorss) and an autonomous single-domain ins homolog, ybak, which clears cys-trna(pro) in trans. in many species where prors lacks an ins domain, proxp-ala, another single-domain ins-like protein, is responsible for editing ...201324371276
distinct trna recognition strategies used by a homologous family of editing domains prevent mistranslation.errors in protein synthesis due to mispairing of amino acids with trnas jeopardize cell viability. several checkpoints to prevent formation of ala- and cys-trna(pro) have been described, including the ala-specific editing domain (ins) of most bacterial prolyl-trna synthetases (prorss) and an autonomous single-domain ins homolog, ybak, which clears cys-trna(pro) in trans. in many species where prors lacks an ins domain, proxp-ala, another single-domain ins-like protein, is responsible for editing ...201324371276
active site plasticity enables metal-dependent tuning of cas5d nuclease activity in crispr-cas type i-c system.clustered regularly interspaced short palindromic repeat (crispr) in association with crispr-associated (cas) proteins constitutes a formidable defense system against mobile genetic elements in prokaryotes. in type i-c, the ribonucleoprotein surveillance complex comprises only three cas proteins, namely, cas5d, csd1 and csd2. unlike type i-e that uses cse3/case for metal-independent crispr rna maturation, type i-c that lacks this deputes cas5d to process the pre-crrna. here, we report the promis ...201324371266
active site plasticity enables metal-dependent tuning of cas5d nuclease activity in crispr-cas type i-c system.clustered regularly interspaced short palindromic repeat (crispr) in association with crispr-associated (cas) proteins constitutes a formidable defense system against mobile genetic elements in prokaryotes. in type i-c, the ribonucleoprotein surveillance complex comprises only three cas proteins, namely, cas5d, csd1 and csd2. unlike type i-e that uses cse3/case for metal-independent crispr rna maturation, type i-c that lacks this deputes cas5d to process the pre-crrna. here, we report the promis ...201324371266
measurement of the intrinsic variability within protein crystals: implications for sample-evaluation and data-collection strategies.the advent of micro-focused x-ray beams has led to the development of a number of advanced methods of sample evaluation and data collection. in particular, multiple-position data-collection and helical oscillation strategies are now becoming commonplace in order to alleviate the problems associated with radiation damage. however, intra-crystal and inter-crystal variation means that it is not always obvious on which crystals or on which region or regions of a crystal these protocols should be per ...201324419635
measurement of the intrinsic variability within protein crystals: implications for sample-evaluation and data-collection strategies.the advent of micro-focused x-ray beams has led to the development of a number of advanced methods of sample evaluation and data collection. in particular, multiple-position data-collection and helical oscillation strategies are now becoming commonplace in order to alleviate the problems associated with radiation damage. however, intra-crystal and inter-crystal variation means that it is not always obvious on which crystals or on which region or regions of a crystal these protocols should be per ...201324419635
lysine carboxylation: unveiling a spontaneous post-translational modification.the carboxylation of lysine residues is a post-translational modification (ptm) that plays a critical role in the catalytic mechanisms of several important enzymes. it occurs spontaneously under certain physicochemical conditions, but is difficult to detect experimentally. its full impact is unknown. in this work, the signature microenvironment of lysine-carboxylation sites has been characterized. in addition, a computational method called predictor of lysine carboxylation (prelyscar) for the de ...201324419378
lysine carboxylation: unveiling a spontaneous post-translational modification.the carboxylation of lysine residues is a post-translational modification (ptm) that plays a critical role in the catalytic mechanisms of several important enzymes. it occurs spontaneously under certain physicochemical conditions, but is difficult to detect experimentally. its full impact is unknown. in this work, the signature microenvironment of lysine-carboxylation sites has been characterized. in addition, a computational method called predictor of lysine carboxylation (prelyscar) for the de ...201324419378
asymmetric chromosome segregation in xanthomonas citri ssp. citri.this study was intended to characterize the chromosome segregation process of xanthomonas citri ssp. citri (xac) by investigating the functionality of the parb factor encoded on its chromosome, and its requirement for cell viability and virulence. using tap tagging we show that parb is expressed in xac. disruption of parb increased the cell doubling time and precluded the ability of xac to colonize the host citrus. moreover, xac mutant cells expressing only truncated forms of parb exhibited the ...201324339434
asymmetric chromosome segregation in xanthomonas citri ssp. citri.this study was intended to characterize the chromosome segregation process of xanthomonas citri ssp. citri (xac) by investigating the functionality of the parb factor encoded on its chromosome, and its requirement for cell viability and virulence. using tap tagging we show that parb is expressed in xac. disruption of parb increased the cell doubling time and precluded the ability of xac to colonize the host citrus. moreover, xac mutant cells expressing only truncated forms of parb exhibited the ...201324339434
functional domains of the 50s subunit mature late in the assembly process.despite the identification of many factors that facilitate ribosome assembly, the molecular mechanisms by which they drive ribosome biogenesis are poorly understood. here, we analyze the late stages of assembly of the 50s subunit using bacillus subtilis cells depleted of rbga, a highly conserved gtpase. we found that rbga-depleted cells accumulate late assembly intermediates bearing sub-stoichiometric quantities of ribosomal proteins l16, l27, l28, l33a, l35 and l36. using a novel pulse labeling ...201324335279
functional domains of the 50s subunit mature late in the assembly process.despite the identification of many factors that facilitate ribosome assembly, the molecular mechanisms by which they drive ribosome biogenesis are poorly understood. here, we analyze the late stages of assembly of the 50s subunit using bacillus subtilis cells depleted of rbga, a highly conserved gtpase. we found that rbga-depleted cells accumulate late assembly intermediates bearing sub-stoichiometric quantities of ribosomal proteins l16, l27, l28, l33a, l35 and l36. using a novel pulse labeling ...201324335279
mechanisms of allosteric activation and inhibition of the deoxyribonucleoside triphosphate triphosphohydrolase from enterococcus faecalis.ef1143 from enterococcus faecalis, a life-threatening pathogen that is resistant to common antibiotics, is a homo-tetrameric deoxyribonucleoside triphosphate (dntp) triphosphohydrolase (dntpase), converting dntps into the deoxyribonucleosides and triphosphate. the dntpase activity of ef1143 is regulated by canonical dntps, which simultaneously act as substrates and activity modulators. previous crystal structures of apo-ef1143 and the protein bound to both dgtp and datp suggested allosteric regu ...201324338016
mechanisms of allosteric activation and inhibition of the deoxyribonucleoside triphosphate triphosphohydrolase from enterococcus faecalis.ef1143 from enterococcus faecalis, a life-threatening pathogen that is resistant to common antibiotics, is a homo-tetrameric deoxyribonucleoside triphosphate (dntp) triphosphohydrolase (dntpase), converting dntps into the deoxyribonucleosides and triphosphate. the dntpase activity of ef1143 is regulated by canonical dntps, which simultaneously act as substrates and activity modulators. previous crystal structures of apo-ef1143 and the protein bound to both dgtp and datp suggested allosteric regu ...201324338016
identification of a selective polymerase enables detection of n(6)-methyladenosine in rna.n(6)-methyladenosine (m(6)a) is the most abundant mrna modification and has important links to human health. while recent studies have successfully identified thousands of mammalian rna transcripts containing the modification, it is extremely difficult to identify the exact location of any specific m(6)a. here we have identified a polymerase with reverse transcriptase activity (from thermus thermophilus) that is selective by up to 18-fold for incorporation of thymidine opposite unmodified a over ...201324328136
measuring the shapes of macromolecules - and why it matters.the molecular basis of life rests on the activity of biological macromolecules, mostly nucleic acids and proteins. a perhaps surprising finding that crystallized over the last handful of decades is that geometric reasoning plays a major role in our attempt to understand these activities. in this paper, we address this connection between geometry and biology, focusing on methods for measuring and characterizing the shapes of macromolecules. we briefly review existing numerical and analytical appr ...201324688748
identification of residues required for stalled-ribosome rescue in the codon-independent release factor yaej.the yaej protein is a codon-independent release factor with peptidyl-trna hydrolysis (pth) activity, and functions as a stalled-ribosome rescue factor in escherichia coli. to identify residues required for yaej function, we performed mutational analysis for in vitro pth activity towards rescue of ribosomes stalled on a non-stop mrna, and for ribosome-binding efficiency. we focused on residues conserved among bacterial yaej proteins. additionally, we determined the solution structure of the ggq d ...201324322300
identification of residues required for stalled-ribosome rescue in the codon-independent release factor yaej.the yaej protein is a codon-independent release factor with peptidyl-trna hydrolysis (pth) activity, and functions as a stalled-ribosome rescue factor in escherichia coli. to identify residues required for yaej function, we performed mutational analysis for in vitro pth activity towards rescue of ribosomes stalled on a non-stop mrna, and for ribosome-binding efficiency. we focused on residues conserved among bacterial yaej proteins. additionally, we determined the solution structure of the ggq d ...201324322300
the mononuclear metal center of type-i dihydroorotase from aquifex aeolicus.dihydroorotase (dho) is a zinc metalloenzyme, although the number of active site zinc ions has been controversial. e. coli dho was initially thought to have a mononuclear metal center, but the subsequent x-ray structure clearly showed two zinc ions, α and β, at the catalytic site. aquifex aeolicus dho, is a dodecamer comprised of six dho and six aspartate transcarbamoylase (atc) subunits. the isolated dho monomer, which lacks catalytic activity, has an intact α-site and conserved β-site ligands, ...201324314009
structure of the ribosome with elongation factor g trapped in the pretranslocation state.during protein synthesis, trnas and their associated mrna codons move sequentially on the ribosome from the a (aminoacyl) site to the p (peptidyl) site to the e (exit) site in a process catalyzed by a universally conserved ribosome-dependent gtpase [elongation factor g (ef-g) in prokaryotes and elongation factor 2 (ef-2) in eukaryotes]. although the high-resolution structure of ef-g bound to the posttranslocation ribosome has been determined, the pretranslocation conformation of the ribosome bou ...201324324137
posttranscriptional rna modifications: playing metabolic games in a cell's chemical legoland.nature combines existing biochemical building blocks, at times with subtlety of purpose. rna modifications are a prime example of this, where standard rna nucleosides are decorated with chemical groups and building blocks that we recall from our basic biochemistry lectures. the result: a wealth of chemical diversity whose full biological relevance has remained elusive despite being public knowledge for some time. here, we highlight several modifications that, because of their chemical intricacy, ...201324315934
posttranscriptional rna modifications: playing metabolic games in a cell's chemical legoland.nature combines existing biochemical building blocks, at times with subtlety of purpose. rna modifications are a prime example of this, where standard rna nucleosides are decorated with chemical groups and building blocks that we recall from our basic biochemistry lectures. the result: a wealth of chemical diversity whose full biological relevance has remained elusive despite being public knowledge for some time. here, we highlight several modifications that, because of their chemical intricacy, ...201324315934
structure-function features of a mycoplasma glycolipid synthase derived from structural data integration, molecular simulations, and mutational analysis.glycoglycerolipids are structural components of mycoplasma membranes with a fundamental role in membrane properties and stability. their biosynthesis is mediated by glycosyltransferases (gt) that catalyze the transfer of glycosyl units from a sugar nucleotide donor to diacylglycerol. the essential function of glycolipid synthases in mycoplasma viability, and the absence of glycoglycerolipids in animal host cells make these gt enzymes a target for drug discovery by designing specific inhibitors. ...201324312618
flexibility within the rotor and stators of the vacuolar h+-atpase.the v-atpase is a membrane-bound protein complex which pumps protons across the membrane to generate a large proton motive force through the coupling of an atp-driven 3-stroke rotary motor (v1) to a multistroke proton pump (vo). this is done with near 100% efficiency, which is achieved in part by flexibility within the central rotor axle and stator connections, allowing the system to flex to minimise the free energy loss of conformational changes during catalysis. we have used electron microscop ...201324312643
visualization of the joining of ribosomal subunits reveals the presence of 80s ribosomes in the nucleus.in eukaryotes the 40s and 60s ribosomal subunits are assembled in the nucleolus, but there appear to be mechanisms preventing mrna binding, 80s formation, and initiation of translation in the nucleus. to visualize association between ribosomal subunits, we tagged pairs of drosophila ribosomal proteins (rps) located in different subunits with mutually complementing halves of fluorescent proteins. pairs of tagged rps expected to interact, or be adjacent in the 80s structure, showed strong fluoresc ...201324129492
the central role of protein s12 in organizing the structure of the decoding site of the ribosome.the ribosome decodes mrna by monitoring the geometry of codon-anticodon base-pairing using a set of universally conserved 16s rrna nucleotides within the conformationally dynamic decoding site. by applying single-molecule fret and x-ray crystallography, we have determined that conditional-lethal, streptomycin-dependence mutations in ribosomal protein s12 interfere with trna selection by allowing conformational distortions of the decoding site that impair gtpase activation of ef-tu during the trn ...201324152548
intra- and intermolecular regulatory interactions in upf1, the rna helicase central to nonsense-mediated mrna decay in yeast.rna helicases are involved in almost every aspect of rna metabolism, yet very little is known about the regulation of this class of enzymes. in saccharomyces cerevisiae, the stability and translational fidelity of nonsense-containing mrnas are controlled by the group i rna helicase upf1 and the proteins it interacts with, upf2 and upf3. combining the yeast two-hybrid system with genetic analysis, we show here that the cysteine- and histidine-rich (ch) domain and the rna helicase domain of yeast ...201324100012
membrane chaperone secdf plays a role in the secretion of listeria monocytogenes major virulence factors.listeria monocytogenes is a gram-positive human intracellular pathogen that infects diverse mammalian cells. upon invasion, l. monocytogenes secretes multiple virulence factors that target host cellular processes and promote infection. it has been presumed, but was not empirically established, that the sec translocation system is the primary mediator of this secretion. here, we validate an important role for secdf, a component of the sec system, in the secretion of several critical l. monocytoge ...201324056100
functional role of methylation of g518 of the 16s rrna 530 loop by gidb in mycobacterium tuberculosis.posttranscriptional modifications of bacterial rrna serve a variety of purposes, from stabilizing ribosome structure to preserving its functional integrity. here, we investigated the functional role of one rrna modification in particular-the methylation of guanosine at position 518 (g518) of the 16s rrna in mycobacterium tuberculosis. based on previously reported evidence that g518 is located 5 å; from proline 44 of ribosomal protein s12, which interacts directly with the mrna wobble position of ...201324100503
tools for characterizing bacterial protein synthesis inhibitors.many antibiotics inhibit the growth of sensitive bacteria by interfering with ribosome function. however, discovery of new protein synthesis inhibitors is curbed by the lack of facile techniques capable of readily identifying antibiotic target sites and modes of action. furthermore, the frequent rediscovery of known antibiotic scaffolds, especially in natural product extracts, is time-consuming and expensive and diverts resources that could be used toward the isolation of novel lead molecules. i ...201324041905
cloning, expression, purification, crystallization and preliminary x-ray studies of argininosuccinate lyase (rv1659) from mycobacterium tuberculosis.the last enzyme in the arginine-biosynthesis pathway, argininosuccinate lyase, from mycobacterium tuberculosis has been cloned, expressed, purified and crystallized, and preliminary x-ray studies have been carried out on the crystals. the his-tagged tetrameric enzyme with a subunit molecular weight of 50.9 kda crystallized with two tetramers in the asymmetric unit of the orthorhombic unit cell, space group p2(1)2(1)2(1). molecular-replacement calculations and self-rotation calculations confirmed ...201324316845
dna binding properties of human cdc45 suggest a function as molecular wedge for dna unwinding.the cell division cycle protein 45 (cdc45) represents an essential replication factor that, together with the mcm2-7 complex and the four subunits of gins, forms the replicative dna helicase in eukaryotes. recombinant human cdc45 (hcdc45) was structurally characterized and its dna-binding properties were determined. synchrotron radiation circular dichroism spectroscopy, dynamic light scattering, small-angle x-ray scattering and atomic force microscopy revealed that hcdc45 exists as an alpha-heli ...201324293646
dna binding properties of human cdc45 suggest a function as molecular wedge for dna unwinding.the cell division cycle protein 45 (cdc45) represents an essential replication factor that, together with the mcm2-7 complex and the four subunits of gins, forms the replicative dna helicase in eukaryotes. recombinant human cdc45 (hcdc45) was structurally characterized and its dna-binding properties were determined. synchrotron radiation circular dichroism spectroscopy, dynamic light scattering, small-angle x-ray scattering and atomic force microscopy revealed that hcdc45 exists as an alpha-heli ...201324293646
purification, crystallization and preliminary x-ray studies of mbtn (rv1346) from mycobacterium tuberculosis.in mycobacterium tuberculosis, the protein mbtn (rv1346) catalyzes the formation of a double bond in the fatty-acyl moiety of the siderophore mycobactin, which is used by this organism to acquire essential iron. mbtn is homologous to acyl-coa dehydrogenases, whose general role is to catalyze the α,β-dehydrogenation of fatty-acyl-coa conjugates. mycobactins, however, contain a long unsaturated fatty-acid chain with an unusual cis double bond conjugated to the carbonyl group of the mycobactin core ...201324316828
conserved distal loop residues in the hsp104 and clpb middle domain contact nucleotide-binding domain 2 and enable hsp70-dependent protein disaggregation.the homologous hexameric aaa(+) proteins, hsp104 from yeast and clpb from bacteria, collaborate with hsp70 to dissolve disordered protein aggregates but employ distinct mechanisms of intersubunit collaboration. how hsp104 and clpb coordinate polypeptide handover with hsp70 is not understood. here, we define conserved distal loop residues between middle domain (md) helix 1 and 2 that are unexpectedly critical for hsp104 and clpb collaboration with hsp70. surprisingly, the hsp104 and clpb md dista ...201324280225
conserved distal loop residues in the hsp104 and clpb middle domain contact nucleotide-binding domain 2 and enable hsp70-dependent protein disaggregation.the homologous hexameric aaa(+) proteins, hsp104 from yeast and clpb from bacteria, collaborate with hsp70 to dissolve disordered protein aggregates but employ distinct mechanisms of intersubunit collaboration. how hsp104 and clpb coordinate polypeptide handover with hsp70 is not understood. here, we define conserved distal loop residues between middle domain (md) helix 1 and 2 that are unexpectedly critical for hsp104 and clpb collaboration with hsp70. surprisingly, the hsp104 and clpb md dista ...201324280225
structural and physiological analyses of the alkanesulphonate-binding protein (ssua) of the citrus pathogen xanthomonas citri.the uptake of sulphur-containing compounds plays a pivotal role in the physiology of bacteria that live in aerobic soils where organosulfur compounds such as sulphonates and sulphate esters represent more than 95% of the available sulphur. until now, no information has been available on the uptake of sulphonates by bacterial plant pathogens, particularly those of the xanthomonas genus, which encompasses several pathogenic species. in the present study, we characterised the alkanesulphonate uptak ...201324282519
redox regulation of the calvin-benson cycle: something old, something new.reversible redox post-translational modifications such as oxido-reduction of disulfide bonds, s-nitrosylation, and s-glutathionylation, play a prominent role in the regulation of cell metabolism and signaling in all organisms. these modifications are mainly controlled by members of the thioredoxin and glutaredoxin families. early studies in photosynthetic organisms have identified the calvin-benson cycle, the photosynthetic pathway responsible for carbon assimilation, as a redox regulated proces ...201324324475
structure of the proteus vulgaris higb-(higa)2-higb toxin-antitoxin complex.bacterial toxin-antitoxin (ta) systems regulate key cellular processes to promote cell survival during periods of stress. during steady-state cell growth, antitoxins typically interact with their cognate toxins to inhibit activity presumably by preventing substrate recognition. we solved two x-ray crystal structures of the proteus vulgaris tetrameric higb-(higa)2-higb ta complex and found that, unlike most other ta systems, the antitoxin higa makes minimal interactions with toxin higb. higb adop ...201324257752
structure of the proteus vulgaris higb-(higa)2-higb toxin-antitoxin complex.bacterial toxin-antitoxin (ta) systems regulate key cellular processes to promote cell survival during periods of stress. during steady-state cell growth, antitoxins typically interact with their cognate toxins to inhibit activity presumably by preventing substrate recognition. we solved two x-ray crystal structures of the proteus vulgaris tetrameric higb-(higa)2-higb ta complex and found that, unlike most other ta systems, the antitoxin higa makes minimal interactions with toxin higb. higb adop ...201324257752
crystal structure of the γ-hydroxymuconic semialdehyde dehydrogenase from pseudomonas sp. strainwbc-3, a key enzyme involved in para-nitrophenol degradation.para-nitrophenol (pnp) is a highly toxic compound with threats to mammalian health. the pnpe-encoded γ-hydroxymuconic semialdehyde dehydrogenase catalyzes the reduction of γ-hydroxymuconic semialdehyde to maleylacetate in pseudomonas sp. strain wbc-3, playing a key role in the catabolism of pnp to krebs cycle intermediates. however, the catalyzing mechanism by pnpe has not been well understood.201324252642
dynamic dna underpins chromosome dynamics.a recent article by meyer and co-workers provides a detailed description of the dynamics of base-step conformational transitions and of the first steps to the basepair opening. these results underpin the essential role that dna dynamics place in the dna structural transitions that accompany the active processes of transcription, replication, and recombination in bacterial and eukaryotic chromatin.201324268134
molecular basis of adp inhibition of vacuolar (v)-type atpase/synthase.reduction of atp hydrolysis activity of vacuolar-type atpase/synthase (v0v1) as a result of adp inhibition occurs as part of the normal mechanism of v0v1 of thermus thermophilus but not v0v1 of enterococcus hirae or eukaryotes. to investigate the molecular basis for this difference, domain-swapped chimeric v1 consisting of both t. thermophilus and e. hirae enzymes were generated, and their function was analyzed. the data showed that the interaction between the nucleotide binding and c-terminal d ...201324247239
molecular basis of adp inhibition of vacuolar (v)-type atpase/synthase.reduction of atp hydrolysis activity of vacuolar-type atpase/synthase (v0v1) as a result of adp inhibition occurs as part of the normal mechanism of v0v1 of thermus thermophilus but not v0v1 of enterococcus hirae or eukaryotes. to investigate the molecular basis for this difference, domain-swapped chimeric v1 consisting of both t. thermophilus and e. hirae enzymes were generated, and their function was analyzed. the data showed that the interaction between the nucleotide binding and c-terminal d ...201324247239
analysis of the mechanism of nucleosome survival during transcription.maintenance of nucleosomal structure in the cell nuclei is essential for cell viability, regulation of gene expression and normal aging. our previous data identified a key intermediate (a small intranucleosomal dna loop, ø-loop) that is likely required for nucleosome survival during transcription by rna polymerase ii (pol ii) through chromatin, and suggested that strong nucleosomal pausing guarantees efficient nucleosome survival. to evaluate these predictions, we analysed transcription through ...201324234452
analysis of the mechanism of nucleosome survival during transcription.maintenance of nucleosomal structure in the cell nuclei is essential for cell viability, regulation of gene expression and normal aging. our previous data identified a key intermediate (a small intranucleosomal dna loop, ø-loop) that is likely required for nucleosome survival during transcription by rna polymerase ii (pol ii) through chromatin, and suggested that strong nucleosomal pausing guarantees efficient nucleosome survival. to evaluate these predictions, we analysed transcription through ...201324234452
comparative xylose metabolism among the ascomycetes c. albicans, s. stipitis and s. cerevisiae.the ascomycetes candida albicans, saccharomyces cerevisiae and scheffersomyces stipitis metabolize the pentose sugar xylose very differently. s. cerevisiae fails to grow on xylose, while c. albicans can grow, and s. stipitis can both grow and ferment xylose to ethanol. however, all three species contain highly similar genes that encode potential xylose reductases and xylitol dehydrogenases required to convert xylose to xylulose, and xylulose supports the growth of all three fungi. we have create ...201324236198
overexpression, purification, and enthalpy of unfolding of ferricytochrome c552 from a psychrophilic microorganism.the psychrophilic, hydrocarbonoclastic microorganism colwellia psychrerythraea is important in global nutrient cycling and bioremediation. in order to investigate how this organism can live so efficiently at low temperatures (~4°c), thermal denaturation studies of a small electron transfer protein from colwellia were performed. colwellia cytochrome c552 was overexpressed in escherichia coli, isolated, purified, and characterized by uv-visible absorption spectroscopy. the melting temperature (tm) ...201324275750
overexpression, purification, and enthalpy of unfolding of ferricytochrome c552 from a psychrophilic microorganism.the psychrophilic, hydrocarbonoclastic microorganism colwellia psychrerythraea is important in global nutrient cycling and bioremediation. in order to investigate how this organism can live so efficiently at low temperatures (~4°c), thermal denaturation studies of a small electron transfer protein from colwellia were performed. colwellia cytochrome c552 was overexpressed in escherichia coli, isolated, purified, and characterized by uv-visible absorption spectroscopy. the melting temperature (tm) ...201324275750
biosynthesis of rare hexoses using microorganisms and related enzymes.rare sugars, referred to as monosaccharides and their derivatives that rarely exist in nature, can be applied in many areas ranging from foodstuffs to pharmaceutical and nutrition industry, or as starting materials for various natural products and drug candidates. unfortunately, an important factor restricting the utilization of rare sugars is their limited availability, resulting from limited synthetic methods. nowadays, microbial and enzymatic transformations have become a very powerful tool i ...201324367410
structure and assembly of an inner membrane platform for initiation of type iv pilus biogenesis.type iv pili are long fibers that are assembled by polymerization of a major pilin protein in the periplasm of a wide range of bacteria and archaea. they play crucial roles in pathogenesis, dna transformation, and motility, and are capable of rapid retraction, generating powerful motor forces. piln and pilo are integral inner membrane proteins that are essential for type iv pilus formation. here, we show that piln and pilo from thermus thermophilus can be isolated as a complex with pilm, a cytop ...201324218553
a structured-based model for the decreased activity of ala222val and glu429ala methylenetetrahydrofolate reductase (mthfr) mutants.the structure of human methylenetetrahydrofolate reductase (mthfr) is not known either by nmr or by x-ray methods. phosphorylation seems to play an important role in the functioning of this flavoprotein. mthfr catalyzes an irreversible reaction in homocysteine metabolism. phosphorylation decreases the activity of mthfr by enhancing the sensitivity of the enzyme to sadenosylmethione. two common polymorphisms in mthfr, ala222val and glu429ala, can result in a number of vascular diseases. effects o ...201324307772
architecture and gene repertoire of the flexible genome of the extreme acidophile acidithiobacillus caldus.acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the acidithiobacillales. as such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. in this study, we explore the genomic diversity of a. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome.201324250794
niche specialization of novel thaumarchaeota to oxic and hypoxic acidic geothermal springs of yellowstone national park.novel lineages of the phylum thaumarchaeota are endemic to thermal habitats, and may exhibit physiological capabilities that are not yet observed in members of this phylum. the primary goals of this study were to conduct detailed phylogenetic and functional analyses of metagenome sequence assemblies of two different thaumarchaeal populations found in high-temperature (65-72 °c), acidic (ph~3) iron oxide and sulfur sediment environments of yellowstone national park (ynp). metabolic reconstruction ...201324196321
niche specialization of novel thaumarchaeota to oxic and hypoxic acidic geothermal springs of yellowstone national park.novel lineages of the phylum thaumarchaeota are endemic to thermal habitats, and may exhibit physiological capabilities that are not yet observed in members of this phylum. the primary goals of this study were to conduct detailed phylogenetic and functional analyses of metagenome sequence assemblies of two different thaumarchaeal populations found in high-temperature (65-72 °c), acidic (ph~3) iron oxide and sulfur sediment environments of yellowstone national park (ynp). metabolic reconstruction ...201324196321
aminoacylation of plasmodium falciparum trna(asn) and insights in the synthesis of asparagine repeats.genome sequencing revealed an extreme at-rich genome and a profusion of asparagine repeats associated with low complexity regions (lcrs) in proteins of the malarial parasite plasmodium falciparum. despite their abundance, the function of these lcrs remains unclear. because they occur in almost all families of plasmodial proteins, the occurrence of lcrs cannot be associated with any specific metabolic pathway; yet their accumulation must have given selective advantages to the parasite. translatio ...201324196969
in silico insights of l-glutamate: structural features in vacuum and in complex with its receptor.structural properties of the glutamate in vacuum and in complex with its receptor were analyzed. the analysis was focused on global properties, attempting to characterize features such as overall flexibility and common trends in the conformation set. the glutamate, as other ligands in complex with the receptor, adopts a spatial conformation that corresponds to one of the possible molecular equilibrium states in physiological conditions. the glutamate forms an extended structure for all cases, bu ...201324307941
correlation between supercoiling and conformational motions of the bacterial flagellar filament.the bacterial flagellar filament is a very large macromolecular assembly of a single protein, flagellin. various supercoiled states of the filament exist, which are formed by two structurally different conformations of flagellin in different ratios. we investigated the correlation between supercoiling of the protofilaments and molecular dynamics in the flagellar filament using quasielastic and elastic incoherent neutron scattering on the picosecond and nanosecond timescales. thermal fluctuations ...201324209861
rigidity analysis of protein biological assemblies and periodic crystal structures.we initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. the goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. we use experimental x-ray crystallography data from the protein data bank (pdb). the analysis relies on an effcient graph-based algorithm. computational experiments were performed using new protein rigidity analysis tools av ...201324564201
mechanisms of copper homeostasis in bacteria.copper is an important micronutrient required as a redox co-factor in the catalytic centers of enzymes. however, free copper is a potential hazard because of its high chemical reactivity. consequently, organisms exert a tight control on cu(+) transport (entry-exit) and traffic through different compartments, ensuring the homeostasis required for cuproprotein synthesis and prevention of toxic effects. recent studies based on biochemical, bioinformatics, and metalloproteomics approaches, reveal a ...201324205499
sequence, structure, and stacking: specifics of trna anchoring to the t box riboswitch.the term riboswitch usually refers to small molecule sensing regulatory modules in the 5' untranslated regions of a mrna. they are typically comprised of separate ligand binding and regulatory domains. the t box riboswitch is unique from other identified riboswitches because its effector is an essential macromolecule, trna. it senses the aminoacylation state of trna to regulate genes involved in a variety of functions relating to amino acid metabolism and trna aminoacylation. t box riboswitches ...201324356646
insights into protein allostery in the csor/rcnr family of transcriptional repressors.csor/rcnr transcriptional repressors adopt a disc-shaped, all α-helical dimer of dimers tetrameric architecture, with a four-helix bundle the key structural feature of the dimer. individual members of this large family of repressors coordinate cu(i) or ni(ii)/co(ii) or perform cysteine sulfur chemistry in mitigating the effects of metal or metabolite toxicity, respectively. here we highlight recent insights into the functional diversity of this fascinating family of repressors.201324695963
insights into protein allostery in the csor/rcnr family of transcriptional repressors.csor/rcnr transcriptional repressors adopt a disc-shaped, all α-helical dimer of dimers tetrameric architecture, with a four-helix bundle the key structural feature of the dimer. individual members of this large family of repressors coordinate cu(i) or ni(ii)/co(ii) or perform cysteine sulfur chemistry in mitigating the effects of metal or metabolite toxicity, respectively. here we highlight recent insights into the functional diversity of this fascinating family of repressors.201324695963
purification, crystallization and preliminary crystallographic analysis of katb, a manganese catalase from anabaena pcc 7120.catalases are enzymes that play an important role in the detoxification of hydrogen peroxide (h2o2) in aerobic organisms. among catalases, haem-containing catalases are ubiquitously distributed and their enzymatic mechanism is very well understood. on the other hand, manganese catalases that contain a bimanganese core in the active site have been less well characterized and their mode of action is not fully understood. the genome of anabaena pcc 7120 does not show the presence of a haem catalase ...201324192374
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