| multifrequency epr studies of manganese catalases provide a complete description of proteinaceous nitrogen coordination. | pulse electron paramagnetic resonance (epr) spectroscopy is employed at two very different excitation frequencies, 9.77 and 30.67 ghz, in the study of the nitrogen coordination environment of the mn(iii)mn(iv) state of the dimanganese-containing catalases from lactobacillus plantarum and thermus thermophilus. consistent with previous studies, the lower-frequency results reveal one unique histidine nitrogen-mn cluster interaction. for the first time, a second, more strongly hyperfine-coupled (14) ... | 2010 | 20055466 |
| structure and ligand binding properties of the epoxidase component of styrene monooxygenase . | styrene monooxygenase (smo) is a two-component flavoprotein monooxygenase that transforms styrene to styrene oxide in the first step of the styrene catabolic and detoxification pathway of pseudomonas putida s12. the crystal structure of the n-terminally histidine-tagged epoxidase component of this system, nsmoa, determined to 2.3 a resolution, indicates the enzyme exists as a homodimer in which each monomer forms two distinct domains. the overall architecture is most similar to that of p-hydroxy ... | 2010 | 20055497 |
| crystallization and preliminary x-ray crystallographic analysis of dna gyrase gyrb subunit from xanthomonas oryzae pv. oryzae. | dna gyrase is a type ii topoisomerase that is essential for chromosome segregation and cell division owing to its ability to modify the topological forms of bacterial dna. in this study, the n-terminal fragment of the gyrb subunit of dna gyrase from xanthomonas oryzae pv. oryzae was overexpressed in escherichia coli, purified and crystallized. diffraction data were collected to 2.10 a resolution using a synchrotron-radiation source. the crystal belonged to space group i4(1), with unit-cell param ... | 2010 | 20057069 |
| crystallization and preliminary x-ray crystallographic analysis of dna gyrase gyrb subunit from xanthomonas oryzae pv. oryzae. | dna gyrase is a type ii topoisomerase that is essential for chromosome segregation and cell division owing to its ability to modify the topological forms of bacterial dna. in this study, the n-terminal fragment of the gyrb subunit of dna gyrase from xanthomonas oryzae pv. oryzae was overexpressed in escherichia coli, purified and crystallized. diffraction data were collected to 2.10 a resolution using a synchrotron-radiation source. the crystal belonged to space group i4(1), with unit-cell param ... | 2010 | 20057069 |
| crystallization and preliminary x-ray crystallographic analysis of thermus thermophilus transcription elongation complex bound to gfh1. | rna polymerase (rnap) elongates rna by iterative nucleotide-addition cycles (nac). a specific structural state (or states) of rnap may be the target of transcription elongation factors. gfh1, a thermus thermophilus gre-family protein, inhibits nac. to elucidate which rnap structural state gfh1 associates with, the t. thermophilus rnap elongation complex (ec) was cocrystallized with gfh1. of the 70 dna/rna scaffolds tested, two (for ec1 and ec2) were successfully crystallized. in the presence of ... | 2010 | 20057074 |
| role of copper ion in regulating ligand binding in a myoglobin-based cytochrome c oxidase model. | cytochrome c oxidase (cco), the terminal enzyme in the mitochondrial respiratory chain, catalyzes the four-electron reduction of dioxygen to water in a binuclear center comprised of a high-spin heme (heme a(3)) and a copper atom (cu(b)) coordinated by three histidine residues. as a minimum model for cco, a mutant of sperm whale myoglobin, named cu(b)mb, has been engineered, in which a copper atom is held in the distal heme pocket by the native e7 histidine and two nonnative histidine residues. i ... | 2010 | 20070118 |
| an active dimanganese(iii)-tyrosyl radical cofactor in escherichia coli class ib ribonucleotide reductase. | escherichia coli class ib ribonucleotide reductase (rnr) converts nucleoside 5'-diphosphates to deoxynucleoside 5'-diphosphates and is expressed under iron-limited and oxidative stress conditions. this rnr is composed of two homodimeric subunits: alpha2 (nrde), where nucleotide reduction occurs, and beta2 (nrdf), which contains an unidentified metallocofactor that initiates nucleotide reduction. nrde and nrdf are found in an operon with nrdi, which encodes an unusual flavodoxin proposed to be in ... | 2010 | 20070127 |
| predicting the pathway involved in post-translational modification of elongation factor p in a subset of bacterial species. | background: the bacterial elongation factor p (ef-p) is strictly conserved in bacteria and essential for protein synthesis. it is homologous to the eukaryotic translation initiation factor 5a (eif5a). a highly conserved eif5a lysine is modified into an unusual amino acid derived from spermidine, hypusine. hypusine is absolutely required for eif5a's role in translation in saccharomyces cerevisiae. the homologous lysine of ef-p is also modified to a spermidine derivative in escherichia coli. howev ... | 2010 | 20070887 |
| telomere-centromere-driven genomic instability contributes to karyotype evolution in a mouse model of melanoma. | aneuploidy and chromosomal instability (cin) are hallmarks of most solid tumors. these alterations may result from inaccurate chromosomal segregation during mitosis, which can occur through several mechanisms including defective telomere metabolism, centrosome amplification, dysfunctional centromeres, and/or defective spindle checkpoint control. in this work, we used an in vitro murine melanoma model that uses a cellular adhesion blockade as a transforming factor to characterize telomeric and ce ... | 2010 | 20072649 |
| the nd2 subunit is labeled by a photoaffinity analogue of asimicin, a potent complex i inhibitor. | nadh:ubiquinone oxidoreductase (complex i) is the entry enzyme of mitochondrial oxidative phosphorylation. to obtain the structural information on inhibitor/quinone binding sites, we synthesized [3h]benzophenone-asimicin ([3h]bpa), a photoaffinity analogue of asimicin, which belongs to the acetogenin family known as the most potent complex i inhibitor. we found that [3h]bpa was photo-crosslinked to nd2, nd1 and nd5 subunits, by the three dimensional separation (blue-native/doubled sds-page) of [ ... | 2010 | 20074573 |
| unique features of animal mitochondrial translation systems. the non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases. | in animal mitochondria, several codons are non-universal and their meanings differ depending on the species. in addition, the trna structures that decipher codons are sometimes unusually truncated. these features seem to be related to the shortening of mitochondrial (mt) genomes, which occurred during the evolution of mitochondria. these organelles probably originated from the endosymbiosis of an aerobic eubacterium into an ancestral eukaryote. it is plausible that these events brought about the ... | 2010 | 20075606 |
| structure of intact thermus thermophilus v-atpase by cryo-em reveals organization of the membrane-bound v(o) motor. | the eubacterium thermus thermophilus uses a macromolecular assembly closely related to eukaryotic v-atpase to produce its supply of atp. this simplified v-atpase offers several advantages over eukaryotic v-atpases for structural analysis and investigation of the mechanism of the enzyme. here we report the structure of the complex at approximately 16 a resolution as determined by single particle electron cryomicroscopy (cryo-em). the resolution of the map and our use of cryo-em, rather than negat ... | 2010 | 20080582 |
| temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold. | a widely held hypothesis regarding the thermostability of thermophilic proteins states asserts that, at any given temperature, thermophilic proteins are more rigid than their mesophilic counterparts. many experimental and computational studies have addressed this question with conflicting results. here, we compare two homologous enzymes, one mesophilic (escherichia coli fmn-dependent nitroreductase; ntr) and one thermophilic (thermus thermophilus nadh oxidase; nox), by multiple molecular dynamic ... | 2010 | 20083491 |
| properties of escherichia coli ef-tu mutants designed for fluorescence resonance energy transfer from trna molecules. | here we describe the design, preparation and characterization of 10 ef-tu mutants of potential utility for the study of escherichia coli elongation factor tu (ef-tu) interaction with trna by a fluorescence resonance energy transfer assay. each mutant contains a single cysteine residue at positions in ef-tu that are proximal to trna sites within the aminoacyl-trna.ef-tu.gtp ternary complex that have previously been labeled with fluorophores. these positions fall in the 323-326 and 344-348 regions ... | 2010 | 20083494 |
| new, closely related haloarchaeal viral elements with different nucleic acid types. | during the search for haloarchaeal viruses, we isolated and characterized a new pleomorphic lipid-containing virus, haloarcula hispanica pleomorphic virus 1 (hhpv-1), that infects the halophilic archaeon haloarcula hispanica. the virus contains a circular double-stranded dna genome of 8,082 bp in size. the organization of the genome shows remarkable synteny and amino acid sequence similarity to the genome and predicted proteins of the halovirus hrpv-1, a pleomorphic single-stranded dna virus tha ... | 2010 | 20089654 |
| structural basis for l-lysine feedback inhibition of homocitrate synthase. | the alpha-aminoadipate pathway of lysine biosynthesis is modulated at the transcriptional and biochemical levels by feedback inhibition. the first enzyme in the alpha-aminoadipate pathway, homocitrate synthase (hcs), is the target of the feedback regulation and is strongly inhibited by l-lysine. here we report the structure of schizosaccharomyces pombe hcs (sphcs) in complex with l-lysine. the structure illustrates that the amino acid directly competes with the substrate 2-oxoglutarate for bindi ... | 2010 | 20089861 |
| a major role of the recfor pathway in dna double-strand-break repair through esdsa in deinococcus radiodurans. | in deinococcus radiodurans, the extreme resistance to dna-shattering treatments such as ionizing radiation or desiccation is correlated with its ability to reconstruct a functional genome from hundreds of chromosomal fragments. the rapid reconstitution of an intact genome is thought to occur through an extended synthesis-dependent strand annealing process (esdsa) followed by dna recombination. here, we investigated the role of key components of the recf pathway in esdsa in this organism naturall ... | 2010 | 20090937 |
| the regulatory protein rraa modulates rna-binding and helicase activities of the e. coli rna degradosome. | the escherichia coli endoribonuclease rnase e is an essential enzyme having key roles in mrna turnover and the processing of several structured rna precursors, and it provides the scaffold to assemble the multienzyme rna degradosome. the activity of rnase e is inhibited by the protein rraa, which can interact with the ribonuclease's degradosome-scaffolding domain. here, we report that rraa can bind to the rna helicase component of the degradosome (rhlb) and the two rna-binding sites in the degra ... | 2010 | 20106955 |
| improving small-angle x-ray scattering data for structural analyses of the rna world. | defining the shape, conformation, or assembly state of an rna in solution often requires multiple investigative tools ranging from nucleotide analog interference mapping to x-ray crystallography. a key addition to this toolbox is small-angle x-ray scattering (saxs). saxs provides direct structural information regarding the size, shape, and flexibility of the particle in solution and has proven powerful for analyses of rna structures with minimal requirements for sample concentration and volumes. ... | 2010 | 20106957 |
| crystal structure of the first eubacterial mre11 nuclease reveals novel features that may discriminate substrates during dna repair. | mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic dna double-strand breaks. as x-ray structural information has been available only for the pyrococcus furiosus enzyme (pfmre11), the conserved and variable features of this nuclease across the domains of life have not been experimentally defined. our crystal structure and biochemical studies demonstrate that tm1635 from thermotoga maritima, originally annotated as a putative nuclease, is an mre11 endo/exonuclease (tmmre1 ... | 2010 | 20122942 |
| crystallization and preliminary x-ray diffraction analyses of the homodimeric glycine decarboxylase (p-protein) from the cyanobacterium synechocystis sp. pcc 6803. | glycine decarboxylase, or p-protein, is a major enzyme that is involved in the c(1) metabolism of all organisms and in the photorespiratory pathway of plants and cyanobacteria. the protein from synechocystis sp. pcc 6803 is a homodimer with a mass of 215 kda. recombinant glycine decarboxylase was expressed in escherichia coli and purified by metal-affinity, ion-exchange and gel-filtration chromatography. crystals of p-protein that diffracted to a resolution of 2.1 a were obtained using the hangi ... | 2010 | 20124719 |
| identification of the tirandamycin biosynthetic gene cluster from streptomyces sp. 307-9. | the structurally intriguing bicyclic ketal moiety of tirandamycin is common to several acyl-tetramic acid antibiotics, and is a key determinant of biological activity. we have identified the tirandamycin biosynthetic gene cluster from the environmental marine isolate streptomyces sp. 307-9, thus providing the first genetic insight into the biosynthesis of this natural product scaffold. sequence analysis revealed a hybrid polyketide synthase-nonribosomal peptide synthetase gene cluster with a col ... | 2010 | 20127927 |
| structure of recj exonuclease defines its specificity for single-stranded dna. | recj is a single-stranded dna (ssdna)-specific 5'-3' exonuclease that plays an important role in dna repair and recombination. to elucidate how recj achieves its high specificity for ssdna, we determined the entire structures of recj both in a ligand-free form and in a complex with mn(2+) or mg(2+) by x-ray crystallography. the entire recj consists of four domains that form a molecule with an o-like structure. one of two newly identified domains had structural similarities to an oligonucleotide/ ... | 2010 | 20129927 |
| functional regions of the n-terminal domain of the antiterminator rfah. | rfah is a bacterial elongation factor that increases expression of distal genes in several long, horizontally acquired operons. rfah is recruited to the transcription complex during rna chain elongation through specific interactions with a dna element called ops. following recruitment, rfah remains bound to rna polymerase (rnap) and acts as an antiterminator by reducing rnap pausing and termination at some factor-independent and rho-dependent signals. rfah consists of two domains connected by a ... | 2010 | 20132437 |
| crystal structures of trypanosomal histidyl-trna synthetase illuminate differences between eukaryotic and prokaryotic homologs. | crystal structures of histidyl-trna synthetase (hisrs) from the eukaryotic parasites trypanosoma brucei and trypanosoma cruzi provide a first structural view of a eukaryotic form of this enzyme and reveal differences from bacterial homologs. hisrss in general contain an extra domain inserted between conserved motifs 2 and 3 of the class ii aminoacyl-trna synthetase catalytic core. the current structures show that the three-dimensional topology of this domain is very different in bacterial and ar ... | 2010 | 20132829 |
| crystal structure of the bifunctional proline utilization a flavoenzyme from bradyrhizobium japonicum. | the bifunctional proline catabolic flavoenzyme, proline utilization a (puta), catalyzes the oxidation of proline to glutamate via the sequential activities of fad-dependent proline dehydrogenase (prodh) and nad(+)-dependent delta(1)-pyrroline-5-carboxylate dehydrogenase (p5cdh) domains. although structures for some of the domains of puta are known, a structure for the full-length protein has not previously been solved. here we report the 2.1 a resolution crystal structure of puta from bradyrhizo ... | 2010 | 20133651 |
| muts and mutl are dispensable for maintenance of the genomic mutation rate in the halophilic archaeon halobacterium salinarum nrc-1. | the genome of the halophilic archaeon halobacterium salinarum nrc-1 encodes for homologs of muts and mutl, which are key proteins of a dna mismatch repair pathway conserved in bacteria and eukarya. mismatch repair is essential for retaining the fidelity of genetic information and defects in this pathway result in the deleterious accumulation of mutations and in hereditary diseases in humans. | 2010 | 20140215 |
| homopolymeric tracts represent a general regulatory mechanism in prokaryotes. | while, traditionally, regulation of gene expression can be grouped into transcriptional, translational, and post-translational mechanisms, some mechanisms of rapid genetic variation can also contribute to regulation of gene expression, e.g., phase variation. | 2010 | 20144225 |
| plasticity of the rna kink turn structural motif. | the kink turn (k-turn) is an rna structural motif found in many biologically significant rnas. while most examples of the k-turn have a similar fold, the crystal structure of the azoarcus group i intron revealed a novel rna conformation, a reverse kink turn bent in the direction opposite that of a consensus k-turn. the reverse k-turn is bent toward the major grooves rather than the minor grooves of the flanking helices, yet the sequence differs from the k-turn consensus by only a single nucleoti ... | 2010 | 20145044 |
| kinetic and structural characterization of human mortalin. | human mortalin is an hsp70 chaperone that has been implicated in cancer, alzheimer's and parkinson's disease, and involvement has been suggested in cellular iron-sulfur cluster biosynthesis. however, study of this important human chaperone has been hampered by a lack of active material sufficient for biochemical characterization. herein, we report the successful purification and characterization of recombinant human mortalin in escherichia coli. the recombinant protein was expressed in the form ... | 2010 | 20152901 |
| organization of the electron transfer chain to oxygen in the obligate human pathogen neisseria gonorrhoeae: roles for cytochromes c4 and c5, but not cytochrome c2, in oxygen reduction. | although neisseria gonorrhoeae is a prolific source of eight c-type cytochromes, little is known about how its electron transfer pathways to oxygen are organized. in this study, the roles in the respiratory chain to oxygen of cytochromes c(2), c(4), and c(5), encoded by the genes ccca, cyca, and cycb, respectively, have been investigated. single mutations in genes for either cytochrome c(4) or c(5) resulted in an increased sensitivity to growth inhibition by excess oxygen and small decreases in ... | 2010 | 20154126 |
| the structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70s ribosome. | viomycin and capreomycin belong to the tuberactinomycin family of antibiotics, which are among the most effective antibiotics against multidrug-resistant tuberculosis. here we present two crystal structures of the 70s ribosome in complex with three trnas and bound to either viomycin or capreomycin at 3.3- and 3.5-a resolution, respectively. both antibiotics bind to the same site on the ribosome, which lies at the interface between helix 44 of the small ribosomal subunit and helix 69 of the large ... | 2010 | 20154709 |
| exit strategies for charged trna from glurs. | for several class i aminoacyl-trna synthetases (aarss), the rate-determining step in aminoacylation is the dissociation of charged trna from the enzyme. in this study, the following factors affecting the release of the charged trna from aarss are computationally explored: the protonation states of amino acids and substrates present in the active site, and the presence and the absence of amp and elongation factor tu. through molecular modeling, internal pk(a) calculations, and molecular dynamics ... | 2010 | 20156451 |
| multiple controls affect arsenite oxidase gene expression in herminiimonas arsenicoxydans. | both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. these transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of as(iii) to as(v) as a detoxification mechanism. | 2010 | 20167112 |
| increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function. | the process of translation can be affected by the use of rare versus common codons within the mrna transcript. | 2010 | 20167116 |
| characterization of endott, a novel single-stranded dna-specific endonuclease from thermoanaerobacter tengcongensis. | endott encoded by tte0829 of thermoanaerobacter tengcongensis binds and cleaves single-stranded (ss) and damaged double-stranded (ds) dna in vitro as well as binding dsdna. in the presence of a low concentration of nacl, endott cleaved ss regions of damaged dsdna efficiently but did not cleave dna that was entirely ss or ds. at high concentrations of nacl or mgcl(2) or atp, there was also specific cleavage of ssdna. this suggested a preference for ss/ds junctions to stimulate cleavage of the dna ... | 2010 | 20172959 |
| interaction of an essential escherichia coli gtpase, der, with the 50s ribosome via the kh-like domain. | der, an essential escherichia coli tandem gtpase, has been implicated in 50s subunit biogenesis. the rrmj gene encodes a methyltransferase that modifies the u2552 residue of 23s rrna, and its deletion causes a severe growth defect. peculiarly, overexpression of der suppresses growth impairment. in this study, using an rrmj-deletion strain, we demonstrated that two gtpase domains of der regulate its association with 50s subunit via the kh-like domain. we also identified a region of der that is cr ... | 2010 | 20172997 |
| the structure of the peripheral stalk of thermus thermophilus h+-atpase/synthase. | proton-translocating atpases are ubiquitous protein complexes that couple atp catalysis with proton translocation via a rotary catalytic mechanism. the peripheral stalks are essential components that counteract torque generated from proton translocation during atp synthesis or from atp hydrolysis during proton pumping. despite their essential role, the peripheral stalks are the least conserved component of the complexes, differing substantially between subtypes in composition and stoichiometry. ... | 2010 | 20173764 |
| para2, a vibrio cholerae chromosome partitioning protein, forms left-handed helical filaments on dna. | most bacterial chromosomes contain homologs of plasmid partitioning (par) loci. these loci encode atpases called para that are thought to contribute to the mechanical force required for chromosome and plasmid segregation. in vibrio cholerae, the chromosome ii (chrii) par locus is essential for chrii segregation. here, we found that purified para2 had atpase activities comparable to other para homologs, but, unlike many other para homologs, did not form high molecular weight complexes in the pres ... | 2010 | 20176965 |
| deep phylogeny--how a tree can help characterize early life on earth. | the darwinian concept of biological evolution assumes that life on earth shares a common ancestor. the diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the tree of life. this article describes features of the tree of life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of ... | 2010 | 20182607 |
| structural and biochemical bases for the redox sensitivity of mycobacterium tuberculosis rsla. | an effective transcriptional response to redox stimuli is of particular importance for mycobacterium tuberculosis, as it adapts to the environment of host alveoli and macrophages. the m. tuberculosis sigma factor sigma(l) regulates the expression of genes involved in cell-wall and polyketide syntheses. sigma(l) interacts with the cytosolic anti-sigma domain of a membrane-associated protein, rsla. here we demonstrate that rsla binds zn(2+) and can sequester sigma(l) in a reducing environment. in ... | 2010 | 20184899 |
| a functional peptidyl-trna hydrolase, ict1, has been recruited into the human mitochondrial ribosome. | bioinformatic analysis classifies the human protein encoded by immature colon carcinoma transcript-1 (ict1) as one of a family of four putative mitochondrial translation release factors. however, this has not been supported by any experimental evidence. as only a single member of this family, mtrf1a, is required to terminate the synthesis of all 13 mitochondrially encoded polypeptides, the true physiological function of ict1 was unclear. here, we report that ict1 is an essential mitochondrial pr ... | 2010 | 20186120 |
| bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium deferribacter desulfuricans ssm1. | the complete genome sequence of the thermophilic sulphur-reducing bacterium, deferribacter desulfuricans smm1, isolated from a hydrothermal vent chimney has been determined. the genome comprises a single circular chromosome of 2,234,389 bp and a megaplasmid of 308,544 bp. many genes encoded in the genome are most similar to the genes of sulphur- or sulphate-reducing bacterial species within deltaproteobacteria. the reconstructed central metabolisms showed a heterotrophic lifestyle primarily driv ... | 2010 | 20189949 |
| partial steps of charge translocation in the nonpumping n139l mutant of rhodobacter sphaeroides cytochrome c oxidase with a blocked d-channel. | the n139l substitution in the d-channel of cytochrome oxidase from rhodobacter sphaeroides results in an approximately 15-fold decrease in the turnover number and a loss of proton pumping. time-resolved absorption and electrometric assays of the f --> o transition in the n139l mutant oxidase result in three major findings. (1) oxidation of the reduced enzyme by o(2) shows approximately 200-fold inhibition of the f --> o step (k approximately 2 s(-1) at ph 8) which is not compatible with enzyme t ... | 2010 | 20192226 |
| evolution and multifarious horizontal transfer of an alternative biosynthetic pathway for the alternative polyamine sym-homospermidine. | polyamines are small flexible organic polycations found in almost all cells. they likely existed in the last universal common ancestor of all extant life, and yet relatively little is understood about their biological function, especially in bacteria and archaea. unlike eukaryotes, where the predominant polyamine is spermidine, bacteria may contain instead an alternative polyamine, sym-homospermidine. we demonstrate that homospermidine synthase (hss) has evolved vertically, primarily in the alph ... | 2010 | 20194510 |
| the crystal structure of unmodified trnaphe from escherichia coli. | post-transcriptional nucleoside modifications fine-tune the biophysical and biochemical properties of transfer rna (trna) so that it is optimized for participation in cellular processes. here we report the crystal structure of unmodified trna(phe) from escherichia coli at a resolution of 3 a. we show that in the absence of modifications the overall fold of the trna is essentially the same as that of mature trna. however, there are a number of significant structural differences, such as rearrange ... | 2010 | 20203084 |
| the structure of dinb from geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily. | the crystal structure of the dinb gene product from geobacillus stearothermophilus (gsdinb) is reported at 2.5 a resolution. the dinb gene is one of the dna-damage-induced genes and the corresponding protein, dinb, is the founding member of a pfam family with no known function. the protein contains a four-helix up-down-down-up bundle that has previously been described in the literature in three disparate proteins: the enzyme mdmpi (mycothiol-dependent maleylpyruvate isomerase), yfit and ttha0303 ... | 2010 | 20208147 |
| crystallization and preliminary x-ray studies of ferredoxin-nadp+ oxidoreductase encoded by bacillus subtilis yumc. | ferredoxin-nadp(+) oxidoreductase encoded by bacillus subtilis yumc has been purified and successfully crystallized in complex with nadp(+) in two forms. diffraction data from crystals of these two forms were collected at resolutions of 1.8 and 1.9 a. the former belonged to space group p2(1)2(1)2, with unit-cell parameters a = 63.90, b = 135.72, c = 39.19 a, and the latter to space group c2, with unit-cell parameters a = 207.47, b = 64.85, c = 61.12 a, beta = 105.82 degrees. the initial structur ... | 2010 | 20208166 |
| crystallization and preliminary x-ray crystallographic study of phosphoglucose isomerase from plasmodium falciparum. | phosphoglucose isomerase (pgi) is a key enzyme in glycolysis and glycogenesis that catalyses the interconversion of glucose 6-phosphate (g6p) and fructose 6-phosphate (f6p). for crystallographic studies, pgi from the human malaria parasite plasmodium falciparum (pfpgi) was overproduced in escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. x-ray diffraction data to 1.5 a resolution were collected from an orthorhombic crystal form belonging to space group p ... | 2010 | 20208175 |
| isolation and purification of thermus thermophilus hpab by a crystallization approach. | the oxygenase hpab is a component of the 4-hydroxyphenylacetate 3-monooxygenase enzyme that is responsible for the hydroxylation of 4-hydroxyphenylacetate. it utilizes molecular oxygen and a reduced flavin, which is provided by hpac, the second component of the enzyme. while isolating integral membrane respiratory complexes from thermus thermophilus, microcrystals of hpab were formed. further purification of the enzyme was achieved by repetitive crystallization. subsequently, well shaped single ... | 2010 | 20208179 |
| structural basis of o6-alkylguanine recognition by a bacterial alkyltransferase-like dna repair protein. | alkyltransferase-like proteins (atls) are a novel class of dna repair proteins related to o(6)-alkylguanine-dna alkyltransferases (agts) that tightly bind alkylated dna and shunt the damaged dna into the nucleotide excision repair pathway. here, we present the first structure of a bacterial atl, from vibrio parahaemolyticus (vpatl). we demonstrate that vpatl adopts an agt-like fold and that the protein is capable of tightly binding to o(6)-methylguanine-containing dna and disrupting its repair b ... | 2010 | 20212037 |
| dynamic effects of cofactors and dna on the oligomeric state of human mitochondrial dna helicase. | we examined the effects of cofactors and dna on the stability, oligomeric state and conformation of the human mitochondrial dna helicase. we demonstrate that low salt conditions result in protein aggregation that may cause dissociation of oligomeric structure. the low salt sensitivity of the mitochondrial dna helicase is mitigated by the presence of magnesium, nucleotide, and increased temperature. electron microscopic and glutaraldehyde cross-linking analyses provide the first evidence of a hep ... | 2010 | 20212038 |
| potassium-activated gtpase reaction in the g protein-coupled ferrous iron transporter b. | feob is a prokaryotic membrane protein responsible for the import of ferrous iron (fe(2+)). a defining feature of feob is that it includes an n-terminal 30-kda soluble domain with gtpase activity, which is required for iron transport. however, the low intrinsic gtp hydrolysis rate of this domain appears to be too slow for feob either to function as a channel or to possess an active fe(2+) membrane transport mechanism. here, we present crystal structures of the soluble domain of feob from strepto ... | 2010 | 20220129 |
| dewetting transitions in protein cavities. | in a previous analysis of the solvation of protein active sites, a drying transition was observed in the narrow hydrophobic binding cavity of cox-2. with the use of a crude metric that often seems able to discriminate those protein cavities that dry from those that do not, we made an extensive search of the pdb, and identified five other proteins that, in molecular dynamics simulations, undergo drying transitions in their active sites. because such cavities need not desolvate before binding hydr ... | 2010 | 20225258 |
| how to slice: snapshots of argonaute in action. | abstract: argonaute is the principal protein component of the mechanisms of rna silencing, providing anchor sites for the small guide rna strand and the 'slicer' activity for cleavage of target mrnas or short passenger rna strands. argonaute is the core constituent of the silencing effector complexes risc (rna-induced silencing complex) and the rits complex (rna-induced initiation of transcriptional gene silencing complex), interacting directly or indirectly with dicer proteins, r2d2/loquacious/ ... | 2010 | 20226069 |
| sesaw: balancing sequence and structural information in protein functional mapping. | motivation: functional similarity between proteins is evident at both the sequence and structure levels. sesaw is a web-based program for identifying functionally or evolutionarily conserved motifs in protein structures by locating sequence and structural similarities, and quantifying these at the level of individual residues. results can be visualized in 2d, as annotated alignments, or in 3d, as structural superpositions. an example is given for both an experimentally determined query structure ... | 2010 | 20299324 |
| crystal structure and functional insight of hp0420-homolog from helicobacter felis. | helicobacter pylori infect more than half of the world's population and are considered a cause of peptic ulcer disease and gastric cancer. recently, hypothetical gene hp0421 was identified in h. pylori as a cholesterol alpha-glucosyltransferase, which is required to synthesize cholesteryl glucosides, essential cell wall components of the bacteria. in the same gene-cluster, hp0420 was co-identified, whose function remains unknown. here we report the crystal structure of hp0420-homolog of h. felis ... | 2010 | 20302842 |
| blocking the k-pathway still allows rapid one-electron reduction of the binuclear center during the anaerobic reduction of the aa3-type cytochrome c oxidase from rhodobacter sphaeroides. | the k-pathway is one of the two proton-input channels required for function of cytochrome c oxidase. in the rhodobacter sphaeroides cytochrome c oxidase, the k-channel starts at glu101 in subunit ii, which is at the surface of the protein exposed to the cytoplasm, and runs to tyr288 at the heme a3/cub active site. mutations of conserved, polar residues within the k-channel block or inhibit steady state oxidase activity. a large body of research has demonstrated that the k-channel is required to ... | 2010 | 20307488 |
| disparate pathways for the biogenesis of cytochrome oxidases in bradyrhizobium japonicum. | this work addresses the biogenesis of heme-copper terminal oxidases in bradyrhizobium japonicum, the nitrogen-fixing root nodule symbiont of soybean. b. japonicum has four quinol oxidases and four cytochrome oxidases. the latter include the aa(3)- and cbb(3)-type oxidases. although both have a cu(b) center in subunit i, the subunit ii proteins differ in having either a cu(a) center (in aa(3)) or a covalently bound heme c (in cbb(3)). two biogenesis factors were genetically studied here, the peri ... | 2010 | 20335176 |
| conserved properties of polypeptide transport-associated (potra) domains derived from cyanobacterial omp85. | proteins of the omp85 family are conserved in all kingdoms of life. they mediate protein transport across or protein insertion into membranes and reside in the outer membranes of gram-negative bacteria, mitochondria, and chloroplasts. omp85 proteins contain a c-terminal transmembrane beta-barrel and a soluble n terminus with a varying number of polypeptide-transport-associated or potra domains. here we investigate omp85 from the cyanobacterium anabaena sp. pcc 7120. the crystallographic three-di ... | 2010 | 20348103 |
| a low affinity ground state conformation for the dynein microtubule binding domain. | dynein interacts with microtubules through a dedicated binding domain that is dynamically controlled to achieve high or low affinity, depending on the state of nucleotide bound in a distant catalytic pocket. the active sites for microtubule binding and atp hydrolysis communicate via conformational changes transduced through a approximately 10-nm length antiparallel coiled-coil stalk, which connects the binding domain to the roughly 300-kda motor core. recently, an x-ray structure of the murine c ... | 2010 | 20351100 |
| identification of a tsetse fly salivary protein with dual inhibitory action on human platelet aggregation. | tsetse flies (glossina sp.), the african trypanosome vectors, rely on anti-hemostatic compounds for efficient blood feeding. despite their medical importance, very few salivary proteins have been characterized and functionally annotated. | 2010 | 20351782 |
| structural analysis of thermus thermophilus hb27 mannosyl-3-phosphoglycerate synthase provides evidence for a second catalytic metal ion and new insight into the retaining mechanism of glycosyltransferases. | mannosyl-3-phosphoglycerate synthase is a glycosyltransferase involved in the two-step synthetic pathway of mannosylglycerate, a compatible solute that accumulates in response to salt and/or heat stresses in many microorganisms thriving in hot environments. the three-dimensional structure of mannosyl-3-phosphoglycerate synthase from thermus thermophilus hb27 in its binary complex form, with gdp-alpha-d-mannose and mg(2+), shows a second metal binding site, about 6 a away from the mannose moiety. ... | 2010 | 20356840 |
| oligomeric interfaces under the lens: gemini. | the assembly of subunits in protein oligomers is an important topic to study as a vast number of proteins exists as stable or transient oligomer and because it is a mechanism used by some protein oligomers for killing cells (e.g., perforin from the human immune system, pore-forming toxins from bacteria, phage, amoeba, protein misfolding diseases, etc.). only a few of the amino acids that constitute a protein oligomer seem to regulate the capacity of the protein to assemble (to form interfaces), ... | 2010 | 20360856 |
| evaluation of lysine biosynthesis as an antifungal drug target: biochemical characterization of aspergillus fumigatus homocitrate synthase and virulence studies. | aspergillus fumigatus is the main cause of severe invasive aspergillosis. to combat this life-threatening infection, only limited numbers of antifungals are available. the fungal alpha-aminoadipate pathway, which is essential for lysine biosynthesis, has been suggested as a potential antifungal drug target. here we reanalyzed the role of this pathway for establishment of invasive aspergillosis in murine models. we selected the first pathway-specific enzyme, homocitrate synthase (hcsa), for bioch ... | 2010 | 20363898 |
| structural and functional characterization of an rnase hi domain from the bifunctional protein rv2228c from mycobacterium tuberculosis. | the open reading frame rv2228c from mycobacterium tuberculosis is predicted to encode a protein composed of two domains, each with individual functions, annotated through sequence similarity searches. the n-terminal domain is homologous with prokaryotic and eukaryotic rnase h domains and the c-terminal domain with alpha-ribazole phosphatase (cobc). the n-terminal domain of rv2228c (rv2228c/n) and the full-length protein were expressed as fusions with maltose binding protein (mbp). rv2228c/n was ... | 2010 | 20363939 |
| x-ray structure determination of the glycine cleavage system protein h of mycobacterium tuberculosis using an inverse compton synchrotron x-ray source. | structural genomics discovery projects require ready access to both x-ray diffraction and nmr spectroscopy which support the collection of experimental data needed to solve large numbers of novel protein structures. the most productive x-ray crystal structure determination laboratories make extensive use of tunable synchrotron x-ray light to solve novel structures by anomalous diffraction methods. this requires that frozen cryo-protected crystals be shipped to large multi acre synchrotron facili ... | 2010 | 20364333 |
| cdnl, a member of the large card-like family of bacterial proteins, is vital for myxococcus xanthus and differs functionally from the global transcriptional regulator card. | card, a global transcriptional regulator in myxococcus xanthus, interacts with carg via cardnter, its n-terminal domain, and with dna via a eukaryotic hmga-type c-terminal domain. genomic analysis reveals a large number of standalone proteins resembling cardnter. these constitute, together with the rna polymerase (rnap) interacting domain, rid, of transcription-repair coupling factors, the card_trcf protein family. we show that one such cardnter-like protein, m. xanthus cdnl, cannot functionally ... | 2010 | 20371514 |
| redox sensing by a rex-family repressor is involved in the regulation of anaerobic gene expression in staphylococcus aureus. | an alignment of upstream regions of anaerobically induced genes in staphylococcus aureus revealed the presence of an inverted repeat, corresponding to rex binding sites in streptomyces coelicolor. gel shift experiments of selected upstream regions demonstrated that the redox-sensing regulator rex of s. aureus binds to this inverted repeat. the binding sequence--ttgtgaaw(4)ttcacaa--is highly conserved in s. aureus. rex binding to this sequence leads to the repression of genes located downstream. ... | 2010 | 20374494 |
| euryarchaeal beta-casp proteins with homology to bacterial rnase j have 5'- to 3'-exoribonuclease activity. | in the archaea only a handful of ribonucleases involved in rna processing and degradation have been characterized. one potential group of archaeal ribonucleases are homologues of the bacterial rnase j family, which have a beta-casp metallo-beta-lactamase fold. here we show that beta-casp proteins encoded in the genomes of the hyperthermophilic euryarchaeota pyrococcus abyssi and thermococcus kodakaraensis are processive exoribonucleases with a 5' end dependence and a 5' to 3' directionality. we ... | 2010 | 20375016 |
| expression, purification and structural analysis of the pyrococcus abyssi rna binding protein pab1135. | abstract: | 2010 | 20380716 |
| ampn-ampg operon is essential for expression of l1 and l2 beta-lactamases in stenotrophomonas maltophilia. | ampg is an inner membrane permease which transports products of murein sacculus degradation from the periplasm into the cytosol in gram-negative bacteria. this process is linked to induction of the chromosomal ampc beta-lactamase gene in some members of the enterobacteriaceae and in pseudomonas aeruginosa. in this study, the ampg homologue of stenotrophomonas maltophilia kj was analyzed. the ampg homologue and its upstream ampn gene form an operon and are cotranscribed under the control of the p ... | 2010 | 20385866 |
| structure of a virulence regulatory factor cvfb reveals a novel winged helix rna binding module. | cvfb is a conserved regulatory protein important for the virulence of staphylococcus aureus. we show here that cvfb binds rna. the crystal structure of the cvfb ortholog from streptococcus pneumoniae at 1.4 a resolution reveals a unique rna binding protein that is formed from a concatenation of well-known structural modules that bind nucleic acids: three consecutive s1 rna binding domains and a winged helix (wh) domain. the third s1 and the wh domains are required for cooperative rna binding and ... | 2010 | 20399190 |
| a unique group of virus-related, genome-integrating elements found solely in the bacterial family thermaceae and the archaeal family halobacteriaceae. | viruses sh1 and p23-77, infecting archaeal haloarcula species and bacterial thermus species, respectively, were recently designated to form a novel viral lineage. in this study, the lineage is expanded to archaeal halomicrobium and bacterial meiothermus species by analysis of five genome-integrated elements that share the core genes with these viruses. | 2010 | 20400546 |
| cryoem structure of hsp104 and its mechanistic implication for protein disaggregation. | hsp104 is a ring-forming aaa+ machine that recognizes both aggregated proteins and prion-fibrils as substrates and, together with the hsp70 system, remodels substrates in an atp-dependent manner. whereas the ability to disaggregate proteins is dependent on the hsp104 m-domain, the location of the m-domain is controversial and its exact function remains unknown. here we present cryoem structures of two hsp104 variants in both crosslinked and noncrosslinked form, in addition to the structure of a ... | 2010 | 20404203 |
| a nonheme high-spin ferrous pool in mitochondria isolated from fermenting saccharomyces cerevisiae. | mössbauer spectroscopy was used to detect pools of fe in mitochondria from fermenting yeast cells, including those consisting of nonheme high-spin (hs) fe(ii) species, fe(iii) nanoparticles, and mononuclear hs fe(iii) species. at issue was whether these species were located within mitochondria or on their exterior. none could be removed by washing mitochondria extensively with ethylene glycol tetraacetic acid or bathophenanthroline sulfonate (bps), fe(ii) chelators that do not appear to penetrat ... | 2010 | 20408527 |
| a bacterial antirepressor with sh3 domain topology mimics operator dna in sequestering the repressor dna recognition helix. | direct targeting of critical dna-binding elements of a repressor by its cognate antirepressor is an effective means to sequester the repressor and remove a transcription initiation block. structural descriptions for this, though often proposed for bacterial and phage repressor-antirepressor systems, are unavailable. here, we describe the structural and functional basis of how the myxococcus xanthus cars antirepressor recognizes and neutralizes its cognate repressors to turn on a photo-inducible ... | 2010 | 20410074 |
| helix-hairpin-helix protein mj1434 from methanocaldococcus jannaschii and endoiv homologue ttc0482 from thermus thermophilus hb27 do not process dna uracil residues. | the mutagenic threat of hydrolytic dna cytosine deamination is met mostly by uracil dna glycosylases (udg) initiating base excision repair. however, several sequenced genomes of archaeal organisms are devoid of genes coding for homologues of the otherwise ubiquitous udg superfamily of proteins. previously, two possible solutions to this problem were offered by (i) a report of a newly discovered family of uracil dna glycosylases exemplified by mj1434, a protein found in the hyperthermophilic arch ... | 2010 | 20410075 |
| a selection that reports on protein-protein interactions within a thermophilic bacterium. | many proteins can be split into fragments that exhibit enhanced function upon fusion to interacting proteins. while this strategy has been widely used to create protein-fragment complementation assays (pcas) for discovering protein-protein interactions within mesophilic organisms, similar assays have not yet been developed for studying natural and engineered protein complexes at the temperatures where thermophilic microbes grow. we describe the development of a selection for protein-protein inte ... | 2010 | 20418388 |
| methanococci use the diaminopimelate aminotransferase (dapl) pathway for lysine biosynthesis. | the pathway of lysine biosynthesis in the methanococci has not been identified previously. a variant of the diaminopimelic acid (dap) pathway uses diaminopimelate aminotransferase (dapl) to catalyze the direct conversion of tetrahydrodipicolinate (thdpa) to ll-dap. recently, the enzyme dapl (mth52) was identified in methanothermobacter thermautotrophicus and shown to belong to the dapl1 group. although the methanococcus maripaludis genome lacks a gene that can be unambiguously assigned a dapl fu ... | 2010 | 20418392 |
| diversity of 16s rrna genes within individual prokaryotic genomes. | analysis of intragenomic variation of 16s rrna genes is a unique approach to examining the concept of ribosomal constraints on rrna genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated human microbiome project (http://nihroadmap.nih.gov/hmp). the current genbank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16s ... | 2010 | 20418441 |
| bioinformatic, structural, and functional analyses support release factor-like mtrf1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria. | vertebrate mitochondria use stop codons uaa and uag decoded by the release factor (rf) mtrf1l and two reassigned arginine codons, aga and agg. a second highly conserved rf-like factor, mtrf1, which evolved from a gene duplication of an ancestral mitochondrial rf1 and not a rf2, is a good candidate for recognizing the nonstandard codons. mtrf1 differs from other rfs by having insertions in the two external loops important for stop codon recognition (tip of helix alpha5 and recognition loop) and b ... | 2010 | 20421313 |
| structure of the 70s ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release. | we report the crystal structure of release factor 2 bound to ribosome with an aminoacyl trna substrate analog at the ribosomal p site, at 3.1 a resolution. the structure shows that upon stop-codon recognition, the universally conserved ggq motif packs tightly into the peptidyl transferase center. nucleotide a2602 of 23s rrna, implicated in peptide release, packs with the ggq motif in release factor 2. the ribose of a76 of the peptidyl-trna adopts the c2'-endo conformation, and the 2' hydroxyl of ... | 2010 | 20421507 |
| the small subunit arob of arsenite oxidase: lessons on the [2fe-2s] rieske protein superfamily. | here, we describe the characterization of the [2fe-2s] clusters of arsenite oxidases from rhizobium sp. nt-26 and ralstonia sp. 22. both reduced rieske proteins feature epr signals similar to their homologs from rieske-cyt b complexes, with g values at 2.027, 1.88, and 1.77. redox titrations in a range of ph values showed that both [2fe-2s] centers have constant e(m) values up to ph 8 at approximately +210 mv. above this ph value, the e(m) values of both centers are ph-dependent, similar to what ... | 2010 | 20421651 |
| structural basis for the activity and substrate specificity of fluoroacetyl-coa thioesterase flk. | the thioesterase flk from the fluoroacetate-producing streptomyces cattleya catalyzes the hydrolysis of fluoroacetyl-coenzyme a. this provides an effective self-defense mechanism, preventing any fluoroacetyl-coenzyme a formed from being further metabolized to 4-hydroxy-trans-aconitate, a lethal inhibitor of the tricarboxylic acid cycle. remarkably, flk does not accept acetyl-coenzyme a as a substrate. crystal structure analysis shows that flk forms a dimer, in which each subunit adopts a hot dog ... | 2010 | 20430898 |
| molecular structure of wlbb, a bacterial n-acetyltransferase involved in the biosynthesis of 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid . | the pathogenic bacteria pseudomonas aeruginosa and bordetella pertussis contain in their outer membranes the rare sugar 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid. five enzymes are required for the biosynthesis of this sugar starting from udp-n-acetylglucosamine. one of these, referred to as wlbb, is an n-acetyltransferase that converts udp-2-acetamido-3-amino-2,3-dideoxy-d-glucuronic acid (udp-glcnac3na) to udp-2,3-diacetamido-2,3-dideoxy-d-glucuronic acid (udp-glcnac3naca). here we report t ... | 2010 | 20433200 |
| analysis of the functional consequences of lethal mutations in mitochondrial translational elongation factors. | mammalian mitochondria synthesize a set of thirteen proteins that are essential for energy generation via oxidative phosphorylation. the genes for all of the factors required for synthesis of the mitochondrially encoded proteins are located in the nuclear genome. a number of disease-causing mutations have been identified in these genes. in this manuscript, we have elucidated the mechanisms of translational failure for two disease states characterized by lethal mutations in mitochondrial elongati ... | 2010 | 20435138 |
| an unconventional copper protein required for cytochrome c oxidase respiratory function under extreme acidic conditions. | very little is known about the processes used by acidophile organisms to preserve stability and function of respiratory pathways. here, we reveal a potential strategy of these organisms for protecting and keeping functional key enzymes under extreme conditions. using acidithiobacillus ferrooxidans, we have identified a protein belonging to a new cupredoxin subfamily, acop, for "acidophile cco partner," which is required for the cytochrome c oxidase (cco) function. we show that it is a multifunct ... | 2010 | 20442397 |
| regulation and isoform function of the v-atpases. | the vacuolar (h(+))-atpases are atp-dependent proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane of eukaryotic cells. intracellular v-atpases play an important role in normal physiological processes such as receptor-mediated endocytosis, intracellular membrane trafficking, pro-hormone processing, protein degradation, and the coupled uptake of small molecules, such as neurotransmitters. they also function in the entry of various p ... | 2010 | 20450191 |
| purification and characterization of put1p from saccharomyces cerevisiae. | in saccharomyces cerevisiae, the put1 and put2 genes are required for the conversion of proline to glutamate. the put1 gene encodes put1p, a proline dehydrogenase (prodh) enzyme localized in the mitochondrion. put1p was expressed and purified from escherichia coli and shown to have a uv-visible absorption spectrum that is typical of a bound flavin cofactor. a k(m) value of 36 mm proline and a k(cat)=27 s(-1) were determined for put1p using an artificial electron acceptor. put1p also exhibited hi ... | 2010 | 20450881 |
| identification of a novel arsenite oxidase gene, arxa, in the haloalkaliphilic, arsenite-oxidizing bacterium alkalilimnicola ehrlichii strain mlhe-1. | although arsenic is highly toxic to most organisms, certain prokaryotes are known to grow on and respire toxic metalloids of arsenic (i.e., arsenate and arsenite). two enzymes are known to be required for this arsenic-based metabolism: (i) the arsenate respiratory reductase (arra) and (ii) arsenite oxidase (aoxb). both catalytic enzymes contain molybdopterin cofactors and form distinct phylogenetic clades (arra and aoxb) within the dimethyl sulfoxide (dmso) reductase family of enzymes. here we r ... | 2010 | 20453090 |
| the hyperthermophilic euryarchaeon archaeoglobus fulgidus repairs uracil by single-nucleotide replacement. | hydrolytic deamination of cytosine to uracil in cellular dna is a major source of c-to-t transition mutations if uracil is not repaired by the dna base excision repair (ber) pathway. since deamination increases rapidly with temperature, hyperthermophiles, in particular, are expected to succumb to such damage. there has been only one report of crenarchaeotic ber showing strong similarities to that in most eukaryotes and bacteria for hyperthermophilic archaea. here we report a different type of be ... | 2010 | 20453094 |
| cracking pre-40s ribosomal subunit structure by systematic analyses of rna-protein cross-linking. | understanding of eukaryotic ribosome synthesis has been slowed by a lack of structural data for the pre-ribosomal particles. we report rrna-binding sites for six late-acting 40s ribosome synthesis factors, three of which cluster around the 3' end of the 18s rrna in model 3d structures. enp1 and ltv1 were previously implicated in 'beak' structure formation during 40s maturation--and their binding sites indicate direct functions. the kinase rio2, putative gtpase tsr1 and dimethylase dim1 bind sequ ... | 2010 | 20453830 |
| mechanisms of the hsp70 chaperone system. | molecular chaperones of the hsp70 family have diverse functions in cells. they assist the folding of newly synthesized and stress-denatured proteins, as well as the import of proteins into organelles, and the dissociation of aggregated proteins. the well-conserved hsp70 chaperones are atp dependent: binding and hydrolysis of atp regulates their interactions with unfolded polypeptide substrates, and atpase cycling is necessary for their function. all cellular functions of hsp70 chaperones use the ... | 2010 | 20453930 |
| a novel single-stranded dna-specific 3'-5' exonuclease, thermus thermophilus exonuclease i, is involved in several dna repair pathways. | single-stranded dna (ssdna)-specific exonucleases (ssexos) are expected to be involved in a variety of dna repair pathways corresponding to their cleavage polarities; however, the relationship between the cleavage polarity and the respective dna repair pathways is only partially understood. to understand the cellular function of ssexos in dna repair better, genes encoding ssexos were disrupted in thermus thermophilus hb8 that seems to have only a single set of 5'-3' and 3'-5' ssexos unlike other ... | 2010 | 20457749 |
| multiple roles of the rna polymerase {beta}' sw2 region in transcription initiation, promoter escape, and rna elongation. | interactions of rna polymerase (rnap) with nucleic acids must be tightly controlled to ensure precise and processive rna synthesis. the rnap β'-subunit switch-2 (sw2) region is part of a protein network that connects the clamp domain with the rnap body and mediates opening and closing of the active center cleft. sw2 interacts with the template dna near the rnap active center and is a target for antibiotics that block dna melting during initiation. here, we show that substitutions of a conserved ... | 2010 | 20457751 |
| the archaeal transamidosome for rna-dependent glutamine biosynthesis. | archaea make glutaminyl-trna (gln-trna(gln)) in a two-step process; a non-discriminating glutamyl-trna synthetase (nd-glurs) forms glu-trna(gln), while the heterodimeric amidotransferase gatde converts this mischarged trna to gln-trna(gln). many prokaryotes synthesize asparaginyl-trna (asn-trna(asn)) in a similar manner using a non-discriminating aspartyl-trna synthetase (nd-asprs) and the heterotrimeric amidotransferase gatcab. the transamidosome, a complex of trna synthetase, amidotransferase ... | 2010 | 20457752 |
| kinetic and structural characterization of a heterohexamer 4-oxalocrotonate tautomerase from chloroflexus aurantiacus j-10-fl: implications for functional and structural diversity in the tautomerase superfamily . | 4-oxalocrotonate tautomerase (4-ot) isozymes play prominent roles in the bacterial utilization of aromatic hydrocarbons as sole carbon sources. these enzymes catalyze the conversion of 2-hydroxy-2,4-hexadienedioate (or 2-hydroxymuconate) to 2-oxo-3-hexenedioate, where pro-1 functions as a general base and shuttles a proton from the 2-hydroxyl group of the substrate to the c-5 position of the product. 4-ot, a homohexamer from pseudomonas putida mt-2, is the most extensively studied 4-ot isozyme a ... | 2010 | 20465238 |
| mass spectrometry defines the stoichiometry of ribosomal stalk complexes across the phylogenetic tree. | the ribosomal stalk complex plays a crucial role in delivering translation factors to the catalytic site of the ribosome. it has a very similar architecture in all cells, although the protein components in bacteria are unrelated to those in archaea and eukaryotes. here we used mass spectrometry to investigate ribosomal stalk complexes from bacteria, eukaryotes, and archaea in situ on the ribosome. specifically we targeted ribosomes with different optimal growth temperatures. our results showed t ... | 2010 | 20467040 |
| natural competence in thermoanaerobacter and thermoanaerobacterium species. | low-g+c thermophilic obligate anaerobes in the class clostridia are considered among the bacteria most resistant to genetic engineering due to the difficulty of introducing foreign dna, thus limiting the ability to study and exploit their native hydrolytic and fermentative capabilities. here, we report evidence of natural genetic competence in 13 thermoanaerobacter and thermoanaerobacterium strains previously believed to be difficult to transform or genetically recalcitrant. in thermoanaerobacte ... | 2010 | 20472726 |