| overexpression of a cytosolic pyrophosphatase (tgppase) reveals a regulatory role of pyrophosphate in glycolysis for toxoplasma gondii. | pyrophosphate (ppi) is a critical element of cellular metabolism as both an energy donor and as an allosteric regulator of several metabolic pathways. the apicomplexan parasite, toxoplasma gondii, uses ppi in place of atp as an energy donor in at least two reactions: the glycolytic ppi-dependent phosphofructokinase (pfk), and the proton translocating vacuolar pyrophosphatase (v-h+-ppase). in the present work, we report the cloning, expression, and characterization of a cytosolic pyrophosphatase ... | 2011 | 21831041 |
| how are "atypical" sulfite dehydrogenases linked to cell metabolism? interactions between the sort sulfite dehydrogenase and small redox proteins. | sulfite dehydrogenases (sdhs) are enzymes that catalyze the oxidation of the toxic and mutagenic compound sulfite to sulfate, thereby protecting cells from adverse effects associated with sulfite exposure. while some bacterial sdhs that have been characterized to date are able to use cytochrome c as an electron acceptor, the majority of these enzymes prefer ferricyanide as an electron acceptor and have therefore been termed "atypical" sdhs. identifying the natural electron acceptor of these enzy ... | 2011 | 21833314 |
| crystallization and preliminary x-ray analysis of a cold-active +¦-galactosidase from the psychrotrophic and halotolerant planococcus sp. l4. | +¦-galactosidases catalyze the hydrolysis of a galactosyl moiety from the nonreducing termini of oligosaccharides or from glycosides. a novel gh family 42 cold-active +¦-galactosidase identified from the psychrotrophic and halotolerant planococcus sp. l4 (bgap) was crystallized and a complete data set was collected from a single frozen crystal on an in-house x-ray source. the crystal diffracted to 2.8ôçà+à resolution and belonged to space group p1, with unit-cell parameters a = 104.29, b = 118.1 ... | 2011 | 21821893 |
| sirna repositioning for guide strand selection by human dicer complexes. | the human ribonuclease dicer and its double-stranded rna (dsrna)-binding protein (dsrbp) partners trbp and pact play important roles in the biogenesis of regulatory rnas. following dicing, one dsrna product strand is preferentially assembled into an rna-induced silencing complex (risc). the mechanism of strand selection in humans and the possible role of dicer in this process remain unclear. here we demonstrate that dsrnas undergo significant repositioning within dicer complexes following dicing ... | 2011 | 21726814 |
| formation of m2g6 in methanocaldococcus jannaschii trna catalyzed by the novel methyltransferase trm14. | the modified nucleosides n(2)-methylguanosine and -dimethylguanosine in transfer rna occur at five positions in the d and anticodon arms, and at positions g6 and g7 in the acceptor stem. trm1 and trm11 enzymes are known to be responsible for several of the d/anticodon arm modifications, but methylases catalyzing post-transcriptional m(2)g synthesis in the acceptor stem are uncharacterized. here, we report that the mj0438 gene from methanocaldococcus jannaschii encodes a novel s-adenosylmethionin ... | 2011 | 21693558 |
| generation of targeted deletions in the genome of rhodothermus marinus. | the aim of this work was to develop an approach for chromosomal engineering of the thermophile rhodothermus marinus. a selection strategy for r. marinus had previously been developed; this strategy was based on complementing a restriction-negative trpb strain with the r. marinus trpb gene. the current work identified an additional selective marker, pura, which encodes adenylosuccinate synthase and confers adenine prototrophy. in a two-step procedure, the available trp(+) selection was used durin ... | 2011 | 21705543 |
| vma8p-gfp fusions can be functionally incorporated into v-atpase, suggesting structural flexibility at the top of v1. | the vacuolar atpase (v-atpase) complex of yeast (saccharomyces cerevisiae) is comprised of two sectors, v(1) (catalytic) and v(o) (proton transfer). the hexameric (a(3)b(3)) cylinder of v(1) has a central cavity that must accommodate at least part of the rotary stalk of v-atpase, a key component of which is subunit d (vma8p). recent electron microscopy (em) data for the prokaryote v-atpase complex (thermus thermophilus) suggest that subunit d penetrates deeply into the central cavity. the functi ... | 2011 | 21845105 |
| the dgt gene of escherichia coli facilitates thymine utilization in thymine-requiring strains. | the escherichia coli dgtp triphosphohydrolase (dgtpase) encoded by the dgt gene catalyses the hydrolysis of dgtp to deoxyguanosine and triphosphate. the recent discovery of a mutator effect associated with deletion of dgt indicated participation of the triphosphohydrolase in preventing mutagenesis. here, we have investigated the possible involvement of dgt in facilitating thymine utilization through its ability to provide intracellular deoxyguanosine, which is readily converted by the deod phosp ... | 2011 | 21736641 |
| phenylacetyl coenzyme a is an effector molecule of the tetr family transcriptional repressor paar from thermus thermophilushb8. | phenylacetic acid (paa) is a common intermediate in the catabolic pathways of several structurally related aromatic compounds. it is converted into phenylacetyl coenzyme a (pa-coa), which is degraded to general metabolites by a set of enzymes. within the genome of the extremely thermophilic bacterium thermus thermophilushb8, a cluster of genes, including a tetr family transcriptional regulator, may be involved in paa degradation. the gene product, which we named t. thermophiluspaar, negatively r ... | 2011 | 21725002 |
| characterization of two malaria parasite organelle translation elongation factor g proteins: the likely targets of the anti-malarial fusidic acid. | malaria parasites harbour two organelles with bacteria-like metabolic processes that are the targets of many anti-bacterial drugs. one such drug is fusidic acid, which inhibits the translation component elongation factor g. the response of p. falciparum to fusidic acid was characterised using extended sybr-green based drug trials. this revealed that fusidic acid kills in vitro cultured p. falciparum parasites by immediately blocking parasite development. two bacterial-type protein translation el ... | 2011 | 21695207 |
| structural contribution of the c-terminal segments of nuol (nd5) and nuom (nd4) subunits of complex i from e. coli. | the proton-translocating nadh-quinone oxidoreductase (complex i/ndh-1) is a multi-subunit enzymatic complex. it has a characteristic l-shaped form with two domains, a hydrophilic peripheral domain and a hydrophobic membrane domain. the membrane domain contains three antiporter-like subunits (nuol, nuom and nuon, escherichia coli naming) that are considered to be involved in the proton translocation. deletion of either nuol or nuom resulted in an incomplete assembly of ndh-1 and a total loss of t ... | 2011 | 21835926 |
| Biological significance of 5S rRNA import into human mitochondria: role of ribosomal protein MRP-L18. | 5S rRNA is an essential component of ribosomes of all living organisms, the only known exceptions being mitochondrial ribosomes of fungi, animals, and some protists. An intriguing situation distinguishes mammalian cells: Although the mitochondrial genome contains no 5S rRNA genes, abundant import of the nuclear DNA-encoded 5S rRNA into mitochondria was reported. Neither the detailed mechanism of this pathway nor its rationale was clarified to date. In this study, we describe an elegant molecular ... | 2011 | 21685364 |
| The structural biology of +¦-barrel membrane proteins: a summary of recent reports. | The outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts all contain transmembrane +¦-barrel proteins. These +¦-barrel proteins serve essential functions in cargo transport and signaling and are also vital for membrane biogenesis. They have also been adapted to perform a diverse set of important cellular functions including acting as porins, transporters, enzymes, virulence factors and receptors. Recent structures of transmembrane +¦-barrels include that of a full length aut ... | 2011 | 21719274 |
| The elusive third subunit IIa of the bacterial B-type oxidases: the enzyme from the hyperthermophile Aquifex aeolicus. | The reduction of molecular oxygen to water is catalyzed by complicated membrane-bound metallo-enzymes containing variable numbers of subunits, called cytochrome c oxidases or quinol oxidases. We previously described the cytochrome c oxidase II from the hyperthermophilic bacterium Aquifex aeolicus as a ba(3)-type two-subunit (subunits I and II) enzyme and showed that it is included in a supercomplex involved in the sulfide-oxygen respiration pathway. It belongs to the B-family of the heme-copper ... | 2011 | 21738733 |
| adaptation of aerobic respiration to low o2 environments. | aerobic respiration in bacteria, archaea, and mitochondria is performed by oxygen reductase members of the heme-copper oxidoreductase superfamily. these enzymes are redox-driven proton pumps which conserve part of the free energy released from oxygen reduction to generate a proton motive force. the oxygen reductases can be divided into three main families based on evolutionary and structural analyses (a-, b- and c-families), with the b- and c-families evolving after the a-family. the a-family ut ... | 2011 | 21844375 |
| the rela/spot homolog (rsh) superfamily: distribution and functional evolution of ppgpp synthetases and hydrolases across the tree of life. | rela/spot homologue (rsh) proteins, named for their sequence similarity to the rela and spot enzymes of escherichia coli, comprise a superfamily of enzymes that synthesize and/or hydrolyze the alarmone ppgpp, activator of the "stringent" response and regulator of cellular metabolism. the classical "long" rshs rel, rela and spot with the ppgpp hydrolase, synthetase, tgs and act domain architecture have been found across diverse bacteria and plant chloroplasts, while dedicated single domain ppgpp- ... | 2011 | 21858139 |
| structure of nitrilotriacetate monooxygenase component b from mycobacterium thermoresistibile. | mycobacterium tuberculosis belongs to a large family of soil bacteria which can degrade a remarkably broad range of organic compounds and utilize them as carbon, nitrogen and energy sources. it has been proposed that a variety of mycobacteria can subsist on alternative carbon sources during latency within an infected human host, with the help of enzymes such as nitrilotriacetate monooxygenase (nta-mo). nta-mo is a member of a class of enzymes which consist of two components: a and b. while compo ... | 2011 | 21904057 |
| francisella rna polymerase contains a heterodimer of non-identical alpha subunits. | abstract: background: all sequenced genomes of representatives of the francisella genus contain two rpoa genes, which encode non-identical rna polymerase (rnap) subunits, alpha1 and alpha2. in all other bacteria studied to date, a dimer of identical alpha subunits initiates the assembly of the catalytically proficient rnap core (subunit composition (alpha)2/beta/beta'). based on an observation that both alpha1 and alpha2 are incorporated into francisella rnap, charity et al. (2007) previously s ... | 2011 | 22108176 |
| sequence of the hyperplastic genome of the naturally competent thermus scotoductus sa-01. | many strains of thermus have been isolated from hot environments around the world. thermus scotoductus sa-01 was isolated from fissure water collected 3.2 km below surface in a south african gold mine. the isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. the genomes from two different thermus thermophilus strains have been com ... | 2011 | 22115438 |
| Alanyl-tRNA synthetase genes of Vanderwaltozyma polyspora arose from duplication of a dual-functional predecessor of mitochondrial origin. | In eukaryotes, the cytoplasmic and mitochondrial forms of a given aminoacyl-tRNA synthetase (aaRS) are typically encoded by two orthologous nuclear genes, one of eukaryotic origin and the other of mitochondrial origin. We herein report a novel scenario of aaRS evolution in yeast. While all other yeast species studied possess a single nuclear gene encoding both forms of alanyl-tRNA synthetase (AlaRS), Vanderwaltozyma polyspora, a yeast species descended from the same whole-genome duplication even ... | 2012 | 21908394 |
| Alanyl-tRNA synthetase genes of Vanderwaltozyma polyspora arose from duplication of a dual-functional predecessor of mitochondrial origin. | In eukaryotes, the cytoplasmic and mitochondrial forms of a given aminoacyl-tRNA synthetase (aaRS) are typically encoded by two orthologous nuclear genes, one of eukaryotic origin and the other of mitochondrial origin. We herein report a novel scenario of aaRS evolution in yeast. While all other yeast species studied possess a single nuclear gene encoding both forms of alanyl-tRNA synthetase (AlaRS), Vanderwaltozyma polyspora, a yeast species descended from the same whole-genome duplication even ... | 2012 | 21908394 |
| Genomic and proteomic characterization of the large Myoviridae bacteriophage ?TMA of the extreme thermophile Thermus thermophilus. | A lytic phage, designated as ?TMA, was isolated from a Japanese hot spring using Thermus thermophilus HB27 as an indicator strain. Electron microscopic examination showed that ?TMA had an icosahedral head and a contractile tail. The circular double-stranded DNA sequence of ?TMA was 151,483 bp in length, and its organization was essentially same as that of ?YS40 except that the ?TMA genome contained genes for a pair of transposase and resolvase, and a gene for a serine to asparagine substituted o ... | 2011 | 22164349 |
| evidence for atp-dependent structural rearrangement of nuclease catalytic site in dna mismatch repair endonuclease mutl. | dna mismatch repair (mmr) greatly contributes to genome integrity via the correction of mismatched bases that are mainly generated by replication errors. postreplicative mmr excises a relatively long tract of error-containing single-stranded dna. mutl is a widely conserved nicking endonuclease that directs the excision reaction to the error-containing strand of the duplex by specifically nicking the daughter strand. because mutl apparently exhibits nonspecific nicking endonuclease activity in vi ... | 2011 | 21953455 |
| comparison of two yeast mnsods: mitochondrial saccharomyces cerevisiae versus cytosolic candida albicans. | human mnsod is significantly more product-inhibited than bacterial mnsods at high concentrations of superoxide (o(2)(-)). this behavior limits the amount of h(2)o(2) produced at high [o(2)(-)]; its desirability can be explained by the multiple roles of h(2)o(2) in mammalian cells, particularly its role in signaling. to investigate the mechanism of product inhibition in mnsod, two yeast mnsods, one from saccharomyces cerevisiae mitochondria (scmnsod) and the other from candida albicans cytoso ... | 2011 | 22077216 |
| Crystal structure of phosphopantetheine adenylyltransferase from Enterococcus faecalis in the ligand-unbound state and in complex with ATP and pantetheine. | Phosphopantetheine adenylyltransferase (PPAT) catalyzes the reversible transfer of an adenylyl group from ATP to 4'-phosphopantetheine (Ppant) to form dephospho-CoA (dPCoA) and pyrophosphate in the Coenzyme A (CoA) biosynthetic pathway. Importantly, PPATs are the potential target for developing antibiotics because bacterial and mammalian PPATs share little sequence homology. Previous structural studies revealed the mechanism of the recognizing substrates and products. The binding modes of ATP, A ... | 2011 | 21912874 |
| The rate-limiting step in O(2) reduction by cytochrome ba(3) from Thermus thermophilus. | Cytochrome ba(3) (ba(3)) of Thermus thermophilus (T. thermophilus) is a member of the heme-copper oxidase family, which has a binuclear catalytic center comprised of a heme (heme a(3)) and a copper (Cu(B)). The heme-copper oxidases generally catalyze the four electron reduction of molecular oxygen in a sequence involving several intermediates. We have investigated the reaction of the fully reduced ba(3) with O(2) using stopped-flow techniques. Transient visible absorption spectra indicated that ... | 2011 | 22138627 |
| binding and inhibition of human spermidine synthase by decarboxylated s-adenosylhomocysteine. | aminopropyltransferases are essential enzymes that form polyamines in eukaryotic and most prokaryotic cells. spermidine synthase (spds) is one of the most well-studied enzymes in this biosynthetic pathway. the enzyme uses decarboxylated s-adenosylmethionine and a short-chain polyamine (putrescine) to make a medium-chain polyamine (spermidine) and 5'-deoxy-5'-methylthioadenosine as a byproduct. here, we report a new spermidine synthase inhibitor, decarboxylated s-adenosylhomocysteine (dcsah). the ... | 2011 | 21898642 |
| Multifaceted SlyD from Helicobacter pylori: implication in [NiFe] hydrogenase maturation. | SlyD belongs to the FK506-binding protein (FKBP) family with both peptidylprolyl isomerase (PPIase) and chaperone activities, and is considered to be a ubiquitous cytosolic protein-folding facilitator in bacteria. It possesses a histidine- and cysteine-rich C-terminus binding to selected divalent metal ions (e.g., Ni(2+), Zn(2+)), which is important for its involvement in the maturation processes of metalloenzymes. We have determined the solution structure of C-terminus-truncated SlyD from Helic ... | 2011 | 22045417 |
| Multifaceted SlyD from Helicobacter pylori: implication in [NiFe] hydrogenase maturation. | SlyD belongs to the FK506-binding protein (FKBP) family with both peptidylprolyl isomerase (PPIase) and chaperone activities, and is considered to be a ubiquitous cytosolic protein-folding facilitator in bacteria. It possesses a histidine- and cysteine-rich C-terminus binding to selected divalent metal ions (e.g., Ni(2+), Zn(2+)), which is important for its involvement in the maturation processes of metalloenzymes. We have determined the solution structure of C-terminus-truncated SlyD from Helic ... | 2011 | 22045417 |
| 5' End-independent RNase J1 endonuclease cleavage of Bacillus subtilis model RNA. | Bacillus subtilis trp leader RNA is a small (140-nucleotide) RNA that results from attenuation of trp operon transcription upon binding of the regulatory TRAP complex. Previously, endonucleolytic cleavage by ribonuclease RNase J1 in a 3'-proximal, single-stranded region was shown to be critical for initiation of trp leader RNA decay. RNase J1 is a dual-specificity enzyme, with both 5' exonucleolytic and endonucleolytic activities. Here, we provide in vivo and in vitro evidence that RNase J1 acce ... | 2011 | 21862575 |
| new biotechnological perspectives of a nadh oxidase variant from thermus thermophilus hb27 as nad+-recycling enzyme. | the number of biotransformations that use nicotinamide recycling systems is exponentially growing. for this reason one of the current challenges in biocatalysis is to develop and optimize more simple and efficient cofactor recycling systems. one promising approach to regenerate nad+ pools is the use of nadh-oxidases that reduce oxygen to hydrogen peroxide while oxidizing nadh to nad+. this class of enzymes may be applied to asymmetric reduction of prochiral substrates in order to obtain enantiop ... | 2011 | 22053761 |
| inhibition of mycobacterium tuberculosis rna polymerase by binding of a gre factor homolog to secondary channel. | because of the essential nature, each step of transcription viz, initiation, elongation and termination is subjected to elaborate regulation. a number of transcription factors modulate the rates of transcription at these different steps in addition to several inhibitors which shut down the process. many modulators including small molecules and proteinaceous inhibitors bind rna polymerase (rnap) secondary channel to control transcription. we describe here the first small protein inhibitor of tran ... | 2011 | 22194445 |
| Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria. | Myxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2?m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this clus ... | 2011 | 22189493 |
| Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria. | Myxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2?m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this clus ... | 2011 | 22189493 |
| dehydratase mediated 1-propanol production in metabolically engineered escherichia coli. | with the increasing consumption of fossil fuels, the question of meeting the global energy demand is of great importance in the near future. as an effective solution, production of higher alcohols from renewable sources by microorganisms has been proposed to address both energy crisis and environmental concerns. higher alcohols contain more than two carbon atoms and have better physiochemical properties than ethanol as fuel substitutes. | 2011 | 22074179 |
| in vivo and in silico determination of essential genes of campylobacter jejuni. | in the united kingdom, the thermophilic campylobacter species c. jejuni and c. coli are the most frequent causes of food-borne gastroenteritis in humans. while campylobacteriosis is usually a relatively mild infection, it has a significant public health and economic impact, and possible complications include reactive arthritis and the autoimmune diseases guillain-barré syndrome. the rapid developments in "omics" technologies have resulted in the availability of diverse datasets allowing predicti ... | 2011 | 22044676 |
| Chloroplast RNase J compensates for inefficient transcription termination by removal of antisense RNA. | Ribonuclease J is an essential enzyme, and the Bacillus subtilis ortholog possesses both endoribonuclease and 5' ? 3' exoribonuclease activities. Chloroplasts also contain RNase J, which has been postulated to participate, as both an exo- and endonuclease, in the maturation of polycistronic mRNAs. Here we have examined recombinant Arabidopsis RNase J and found both 5' ? 3' exoribonuclease and endonucleolytic activities. Virus-induced gene silencing was used to reduce RNase J expression in Arabid ... | 2011 | 22033332 |
| proline utilization by bacillus subtilis: uptake and catabolism. | l-proline can be used by bacillus subtilis as a sole source of carbon or nitrogen. we traced l-proline utilization genetically to the putbcp (ycgmno) locus. the putbcp gene cluster encodes a high-affinity proline transporter (putp) and two enzymes, the proline dehydrogenase putb and the δ(1)-pyrroline-5-carboxylate dehydrogenase putc, which jointly catabolize l-proline to l-glutamate. northern blotting, primer extension, and putb-trea reporter gene fusion analysis showed that the putbcp locus is ... | 2011 | 22139509 |
| effects of pressure and temperature on the binding of reca protein to single-stranded dna. | the binding and polymerization of reca protein to dna is required for recombination, which is an essential function of life. we study the pressure and temperature dependence of reca binding to single-stranded dna in the presence of adenosine 5'-[γ-thio]triphosphate (atp[γ-s]), in a temperature regulated high pressure cell using fluorescence anisotropy. measurements were possible at temperatures between 5-60 °c and pressures up to 300 mpa. experiments were performed on escherichia coli reca and r ... | 2011 | 22123983 |
| arrangement of electron transport chain components in bovine mitochondrial supercomplex i1iii2iv1. | the respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for atp synthesis, and assemble into a supercomplex. a 19-å 3d map of the 1.7-mda amphipol-solubilized supercomplex i(1)iii(2)iv(1) from bovine heart obtained by single-particle electron cryo-microscopy reveals an amphipol belt replacing the membrane lipid bilayer. a precise fit of the x-ray structures of complex i, the complex iii dimer, and monomeric ... | 2011 | 21909073 |
| Crystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3. | Protein release factor 3 (RF3), a guanosine triphosphatase, binds to ribosome after release of the nascent peptide and promotes dissociation of the class I release factors during the termination of protein synthesis. Here we present the crystal structure of the 70S ribosome with RF3 in the presence of a nonhydrolyzable GTP analogue, guanosine 5'-ß,?-methylenetriphosphate (GDPCP), refined to 3.8 Å resolution. The structure shows that the subunits of the ribosome are rotated relative to each other ... | 2011 | 21903932 |
| Manganese superoxide dismutase is a mitochondrial fidelity protein that protects Pol? against UV-induced inactivation. | Manganese superoxide dismutase is a nuclear encoded primary antioxidant enzyme localized exclusively in the mitochondrial matrix. Genotoxic agents, such as ultraviolet (UV) radiation, generates oxidative stress and cause mitochondrial DNA (mtDNA) damage. The mtDNA polymerase (Pol?), a major constituent of nucleoids, is responsible for the replication and repair of the mitochondrial genome. Recent studies suggest that the mitochondria contain fidelity proteins and MnSOD constitutes an integral pa ... | 2011 | 21909133 |
| Manganese superoxide dismutase is a mitochondrial fidelity protein that protects Pol? against UV-induced inactivation. | Manganese superoxide dismutase is a nuclear encoded primary antioxidant enzyme localized exclusively in the mitochondrial matrix. Genotoxic agents, such as ultraviolet (UV) radiation, generates oxidative stress and cause mitochondrial DNA (mtDNA) damage. The mtDNA polymerase (Pol?), a major constituent of nucleoids, is responsible for the replication and repair of the mitochondrial genome. Recent studies suggest that the mitochondria contain fidelity proteins and MnSOD constitutes an integral pa ... | 2011 | 21909133 |
| a novel mechanism of sulfur transfer catalyzed by o-acetylhomoserine sulfhydrylase in the methionine-biosynthetic pathway of wolinella succinogenes. | o-acetylhomoserine sulfhydrylase (oahs) is a pyridoxal 5'-phosphate (plp) dependent sulfide-utilizing enzyme in the l-cysteine and l-methionine biosynthetic pathways of various enteric bacteria and fungi. oahs catalyzes the conversion of o-acetylhomoserine to homocysteine using sulfide in a process known as direct sulfhydrylation. however, the source of the sulfur has not been identified and no structures of oahs have been reported in the literature. here, the crystal structure of wolinella succ ... | 2011 | 21931214 |
| Characterization of benzoxaborole-based antifungal resistance mutations demonstrates that editing depends on electrostatic stabilization of the leucyl-tRNA synthetase editing cap. | The broad-spectrum benzoxaborole antifungal AN2690 blocks protein synthesis by inhibiting leucyl-tRNA synthetase (LeuRS) via a novel oxaborole tRNA trapping mechanism in the editing site. Herein, one set of resistance mutations is at Asp487 outside the LeuRS hydrolytic editing pocket, in a region of unknown function. It is located within a eukaryote/archaea specific insert I4, which forms part of a cap over a benzoxaborole-AMP that is bound in the LeuRS CP1 domain editing active site. Mutational ... | 2011 | 21856301 |
| Small-angle X-ray Scattering Studies of the Oligomeric State and Quaternary Structure of the Trifunctional Proline Utilization A (PutA) Flavoprotein from Escherichia coli. | The trifunctional flavoprotein proline utilization A (PutA) links metabolism and gene regulation in Gram-negative bacteria by catalyzing the two-step oxidation of proline to glutamate and repressing transcription of the proline utilization regulon. Small-angle x-ray scattering (SAXS) and domain deletion analysis were used to obtain solution structural information for the 1320-residue PutA from Escherichia coli. Shape reconstructions show that PutA is a symmetric V-shaped dimer having dimensions ... | 2011 | 22013066 |
| a temperature-dependent conformational change of nadh oxidase from thermus thermophilus hb8. | using molecular dynamics simulations and steady-state fluorescence spectroscopy, we have identified a conformational change in the active site of a thermophilic flavoenzyme, nadh oxidase from thermus thermophilus hb8 (nox). the enzyme's far-uv circular dichroism spectrum, intrinsic tryptophan fluorescence, and apparent molecular weight measured by dynamic light scattering varied little between 25 and 75°c. however, the fluorescence of the tightly bound fad cofactor increased approximately fourfo ... | 2011 | 22081476 |
| "stealth" melanoma cells in histology-negative sentinel lymph nodes. | a proportion of patients who develop regional and distant recurrences of melanoma after a pathologically negative sentinel lymph node (sn) biopsy are reported to have enhanced signals for melanoma-associated messenger ribonucleic acid (mrna) when sensitive molecular approaches such as reverse transcriptase polymerase chain reaction (rt-pcr) are used to evaluate their sn tissue. the significance of these findings remains controversial, because the cellular source of the augmented signals cannot b ... | 2011 | 21997686 |
| The structure and allosteric regulation of mammalian glutamate dehydrogenase. | Glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of l-glutamate to 2-oxoglutarate. Only in the animal kingdom is this enzyme heavily allosterically regulated by a wide array of metabolites. The major activators are ADP and leucine, while the most important inhibitors include GTP, palmitoyl CoA, and ATP. Recently, spontaneous mutations in the GTP inhibitory site that lead to the hyperinsulinism/hyperammonemia (HHS) syndrome have shed ligh ... | 2011 | 22079166 |
| The structure and allosteric regulation of mammalian glutamate dehydrogenase. | Glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of l-glutamate to 2-oxoglutarate. Only in the animal kingdom is this enzyme heavily allosterically regulated by a wide array of metabolites. The major activators are ADP and leucine, while the most important inhibitors include GTP, palmitoyl CoA, and ATP. Recently, spontaneous mutations in the GTP inhibitory site that lead to the hyperinsulinism/hyperammonemia (HHS) syndrome have shed ligh ... | 2011 | 22079166 |
| Trimming down a protein structure to its bare foldons: spatial organisation of the cooperative unit. | Folding of the ribosomal protein S6 is a malleable process controlled by two competing, and partly overlapping, folding nuclei. Together, these nuclei extend over most of the S6 structure, save the edge strand ß2, which is consistently missing in the folding transition states: despite being part of the S6 four-stranded sheet, ß2 seems not to be part of the protein's cooperative unit. The question is then if ß2 can be removed from the S6 structure without compromising folding cooperativity or ... | 2011 | 22117065 |
| Trimming down a protein structure to its bare foldons: spatial organisation of the cooperative unit. | Folding of the ribosomal protein S6 is a malleable process controlled by two competing, and partly overlapping, folding nuclei. Together, these nuclei extend over most of the S6 structure, save the edge strand ß2, which is consistently missing in the folding transition states: despite being part of the S6 four-stranded sheet, ß2 seems not to be part of the protein's cooperative unit. The question is then if ß2 can be removed from the S6 structure without compromising folding cooperativity or ... | 2011 | 22117065 |
| yeast cytochrome c oxidase: a model system to study mitochondrial forms of the haem-copper oxidase superfamily. | the known subunits of yeast mitochondrial cytochrome c oxidase are reviewed. the structures of all eleven of its subunits are explored by building homology models based on the published structures of the homologous bovine subunits and similarities and differences are highlighted, particularly of the core functional subunit i. yeast genetic techniques to enable introduction of mutations into the three core mitochondrially-encoded subunits are reviewed. this article is part of a special issue enti ... | 2011 | 21925484 |
| yeast cytochrome c oxidase: a model system to study mitochondrial forms of the haem-copper oxidase superfamily. | the known subunits of yeast mitochondrial cytochrome c oxidase are reviewed. the structures of all eleven of its subunits are explored by building homology models based on the published structures of the homologous bovine subunits and similarities and differences are highlighted, particularly of the core functional subunit i. yeast genetic techniques to enable introduction of mutations into the three core mitochondrially-encoded subunits are reviewed. this article is part of a special issue enti ... | 2011 | 21925484 |
| crystallization and preliminary crystallographic analysis of a putative glucokinase/hexokinase from thermus thermophilus. | glucokinase/hexokinase catalyzes the phosphorylation of glucose to glucose 6-phosphate, which is the first step of glycolysis. the open reading frame ttha0299 of the extreme thermophile thermus thermophilus encodes a putative glucokinase/hexokinase which contains the consensus sequence for proteins from the repressors, open reading frames and sugar kinases family. in this study, the glucokinase/hexokinase from t. thermophilus was purified and crystallized using polyethylene glycol 8000 as a prec ... | 2011 | 22139166 |
| High-resolution structure of shikimate dehydrogenase from Thermotoga maritima reveals a tightly closed conformation. | Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Structural analysis of a SDH from Thermotoga maritima encoded by the Tm0346 gene was performed to facilitate further structural comparisons between the various shikimate dehydrogenases. The crystal structure of SDH from T. maritima was determined at 1.45 SDH from T. maritima sh ... | 2011 | 22095087 |
| High-resolution structure of shikimate dehydrogenase from Thermotoga maritima reveals a tightly closed conformation. | Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Structural analysis of a SDH from Thermotoga maritima encoded by the Tm0346 gene was performed to facilitate further structural comparisons between the various shikimate dehydrogenases. The crystal structure of SDH from T. maritima was determined at 1.45 SDH from T. maritima sh ... | 2011 | 22095087 |
| functional genomic and advanced genetic studies reveal novel insights into the metabolism, regulation, and biology of haloferax volcanii. | the genome sequence of haloferax volcanii is available and several comparative genomic in silico studies were performed that yielded novel insight for example into protein export, rna modifications, small non-coding rnas, and ubiquitin-like small archaeal modifier proteins. the full range of functional genomic methods has been established and results from transcriptomic, proteomic and metabolomic studies are discussed. notably, hfx. volcanii is together with halobacterium salinarum the only prok ... | 2011 | 22190865 |
| structure and molecular evolution of cdgsh iron-sulfur domains. | the recently discovered cdgsh iron-sulfur domains (cisds) are classified into seven major types with a wide distribution throughout the three domains of life. the type 1 protein mitoneet has been shown to fold into a dimer with the signature cdgsh motif binding to a [2fe-2s] cluster. however, the structures of all other types of cisds were unknown. here we report the crystal structures of type 3, 4, and 6 cisds determined at 1.5 å, 1.8 å and 1.15 å resolution, respectively. the type 3 and 4 cisd ... | 2011 | 21949752 |
| orphan macrodomain protein (human c6orf130) is an o-acyl-adp-ribose deacylase: solution structure and catalytic properties. | post-translational modification of proteins/histones by lysine acylation has profound effects on the physiological function of modified proteins. deacylation by nad(+)-dependent sirtuin reactions yields as a product o-acyl-adp-ribose, which has been implicated as a signaling molecule in modulating cellular processes. macrodomain-containing proteins are reported to bind nad(+)-derived metabolites. here, we describe the structure and function of an orphan macrodomain protein, human c6orf130. this ... | 2011 | 21849506 |
| interaction of complexes i, iii, and iv within the bovine respirasome by single particle cryoelectron tomography. | the respirasome is a multisubunit supercomplex of the respiratory chain in mitochondria. here we report the 3d reconstruction of the bovine heart respirasome, composed of dimeric complex iii and single copies of complex i and iv, at about 2.2-nm resolution, determined by cryoelectron tomography and subvolume averaging. fitting of x-ray structures of single complexes i, iii(2), and iv with high fidelity allows interpretation of the model at the level of secondary structures and shows how the indi ... | 2011 | 21876144 |
| a mycobacterium leprae hsp65 mutant as a candidate for mitigating lupus aggravation in mice. | hsp60 is an abundant and highly conserved family of intracellular molecules. increased levels of this family of proteins have been observed in the extracellular compartment in chronic inflammation. administration of m. leprae hsp65 [wt] in [nzbxnzw]f(1) mice accelerates the systemic lupus erythematosus [sle] progression whereas the point mutated k(409)a hsp65 protein delays the disease. here, the biological effects of m. leprae hsp65 leader pep and k(409)a pep synthetic peptides, which cover res ... | 2011 | 21961033 |
| structural comparison of trna m1a58 methyltransferases revealed different molecular strategies to maintain their oligomeric architecture under extreme conditions. | abstract: background: trna m1a58 methyltransferases (trmi) catalyze the transfer of a methyl group from s-adenosyl-l-methionine to nitrogen 1 of adenine 58 in the t-loop of trnas from all three domains of life. the m1a58 modification has been shown to be essential for cell growth in yeast and for adaptation to high temperatures in thermophilic organisms. these enzymes were shown to be active as tetramers. the crystal structures of five trmis from hyperthermophilic archaea and thermophilic or me ... | 2011 | 22168821 |
| cloning, expression, and homology modeling of groel protein from leptospira interrogans serovar autumnalis strain n2. | leptospirosis is an infectious bacterial disease caused by leptospira species. in this study, we cloned and sequenced the gene encoding the immunodominant protein groel from l. interrogans serovar autumnalis strain n2, which was isolated from the urine of a patient during an outbreak of leptospirosis in chennai, india. this groel gene encodes a protein of 60 kda with a high degree of homology (99% similarity) to those of other leptospiral serovars. recombinant groel was overexpressed in escheric ... | 2011 | 22196358 |
| a novel metagenomic short-chain dehydrogenase/reductase attenuates pseudomonas aeruginosa biofilm formation and virulence on caenorhabditis elegans. | in pseudomonas aeruginosa, the expression of a number of virulence factors, as well as biofilm formation, are controlled by quorum sensing (qs). n-acylhomoserine lactones (ahls) are an important class of signaling molecules involved in bacterial qs and in many pathogenic bacteria infection and host colonization are ahl-dependent. the ahl signaling molecules are subject to inactivation mainly by hydrolases (enzyme commission class number ec 3) (i.e. n-acyl-homoserine lactonases and n-acyl-homoser ... | 2011 | 22046268 |
| rational design of an evolutionary precursor of glutaminyl-trna synthetase. | the specificity of most aminoacyl-trna synthetases for an amino acid and cognate trna pair evolved before the divergence of the three domains of life. glutaminyl-trna synthetase (glnrs) evolved later and is derived from the archaeal-type nondiscriminating glutamyl-trna synthetase (glurs), an enzyme with relaxed trna specificity capable of forming both glu-trna(glu) and glu-trna(gln). the archaea lack glnrs and use a specialized amidotransferase to convert glu-trna(gln) to gln-trna(gln) needed fo ... | 2011 | 22158897 |
| membrane proteins in four acts: function precedes structure determination. | studies on four membrane protein systems, which combine information derived from crystal structures and biophysical studies have emphasized, as a precursor to crystallization, demonstration of functional activity. these assays have relied on sensitive spectrophotometric, electrophysiological, and microbiological assays of activity to select purification procedures that lead to functional complexes and with greater likelihood to successful crystallization: (i), hetero-oligomeric proteins involved ... | 2011 | 22079407 |
| mass spectrometry-based quantification of pseudouridine in rna. | direct detection of pseudouridine (ψ), an isomer of uridine, in rna is challenging. the most popular method requires chemical derivatization using n-cyclohexyl-n'-β-(4-methylmorpholinum ethyl) carbodiimide p-tosylate (cmct) followed by radiolabeled primer extension mediated by reverse transcriptase. more recently, mass spectrometry (ms)-based approaches for sequence placement of pseudouridine in rna have been developed. nearly all of these approaches, however, only yield qualitative information ... | 2011 | 21953190 |
| tagetitoxin inhibits rna polymerase through trapping of the trigger loop. | tagetitoxin (tgt) inhibits multisubunit chloroplast, bacterial, and some eukaryotic rna polymerases (rnaps). a crystallographic structure of tgt bound to bacterial rnap apoenzyme shows that tgt binds near the active site but does not explain why tgt acts only at certain sites. to understand the tgt mechanism, we constructed a structural model of tgt bound to the transcription elongation complex. in this model, tgt interacts with the β' subunit trigger loop (tl), stabilizing it in an inactive con ... | 2011 | 21976682 |
| massive multiplication of genome and ribosomes in dormant cells (akinetes) of aphanizomenon ovalisporum (cyanobacteria). | akinetes are dormancy cells commonly found among filamentous cyanobacteria, many of which are toxic and/or nuisance, bloom-forming species. development of akinetes from vegetative cells is a process that involves morphological and biochemical modifications. here, we applied a single-cell approach to quantify genome and ribosome content of akinetes and vegetative cells in aphanizomenon ovalisporum (cyanobacteria). vegetative cells of a. ovalisporum were naturally polyploid and contained, on avera ... | 2011 | 21975597 |
| massive multiplication of genome and ribosomes in dormant cells (akinetes) of aphanizomenon ovalisporum (cyanobacteria). | akinetes are dormancy cells commonly found among filamentous cyanobacteria, many of which are toxic and/or nuisance, bloom-forming species. development of akinetes from vegetative cells is a process that involves morphological and biochemical modifications. here, we applied a single-cell approach to quantify genome and ribosome content of akinetes and vegetative cells in aphanizomenon ovalisporum (cyanobacteria). vegetative cells of a. ovalisporum were naturally polyploid and contained, on avera ... | 2011 | 21975597 |
| structural and functional insights into the dna replication factor cdc45 reveal an evolutionary relationship to the dhh family of phosphoesterases. | cdc45 is an essential protein conserved in all eukaryotes and is involved both in the initiation of dna replication, as well as the progression of the replication fork. with gins, cdc45 is an essential co-factor of the mcm2-7 replicative helicase complex. despite its importance, no detailed information is available on either the structure or the biochemistry of the protein. intriguingly, whereas homologues of both gins and mcm proteins have been described in archaea, no counterpart for cdc45 is ... | 2011 | 22147708 |
| structural and functional insights into the dna replication factor cdc45 reveal an evolutionary relationship to the dhh family of phosphoesterases. | cdc45 is an essential protein conserved in all eukaryotes and is involved both in the initiation of dna replication, as well as the progression of the replication fork. with gins, cdc45 is an essential co-factor of the mcm2-7 replicative helicase complex. despite its importance, no detailed information is available on either the structure or the biochemistry of the protein. intriguingly, whereas homologues of both gins and mcm proteins have been described in archaea, no counterpart for cdc45 is ... | 2011 | 22147708 |
| crystal structure of human β-galactosidase: the structural basis of gm1 gangliosidosis and morquio b diseases. | gm1 gangliosidosis and morquio b are autosomal recessive lysosomal storage diseases associated with a neurodegenerative disorder or dwarfism and skeletal abnormalities, respectively. these diseases are caused by deficiencies in the lysosomal enzyme β-d-galactosidase (β-gal), which lead to accumulations of the β-gal substrates, gm1 ganglioside and keratan sulfate. β-gal is an exoglycosidase that catalyzes the hydrolysis of terminal β-linked galactose residues. the present study shows the crystal ... | 2011 | 22128166 |
| crystal structure of human β-galactosidase: the structural basis of gm1 gangliosidosis and morquio b diseases. | gm1 gangliosidosis and morquio b are autosomal recessive lysosomal storage diseases associated with a neurodegenerative disorder or dwarfism and skeletal abnormalities, respectively. these diseases are caused by deficiencies in the lysosomal enzyme β-d-galactosidase (β-gal), which lead to accumulations of the β-gal substrates, gm1 ganglioside and keratan sulfate. β-gal is an exoglycosidase that catalyzes the hydrolysis of terminal β-linked galactose residues. the present study shows the crystal ... | 2011 | 22128166 |
| peptides from aminoacyl-trna synthetases can cure the defects due to mutations in mt trna genes. | recent results from several laboratories have confirmed that human and yeast leucyl- and valyl-trna synthetases can rescue the respiratory defects due to mutations in mitochondrial trna genes. in this report we show that this effect cannot be ascribed to the catalytic activity per se and that isolated domains of aminoacyl-trna synthetases and even short peptides thereof have suppressing effects. | 2011 | 21903180 |
| characterization of family iv udg from aeropyrum pernix and its application in hot-start pcr by family b dna polymerase. | recombinant uracil-dna glycosylase (udg) from aeropyrum pernix (a. pernix) was expressed in e. coli. the biochemical characteristics of a. pernix udg (apeudg) were studied using oligonucleotides carrying a deoxyuracil (du) base. the optimal temperature range and ph value for du removal by apeudg were 55-65°c and ph 9.0, respectively. the removal of du was inhibited by the divalent ions of zn, cu, co, ni, and mn, as well as a high concentration of nacl. the opposite base in the complementary stra ... | 2011 | 22087273 |
| catalytic properties of the isolated diaphorase fragment of the nad-reducing [nife]-hydrogenase from ralstonia eutropha. | the nad+-reducing soluble hydrogenase (sh) from ralstonia eutropha h16 catalyzes the h₂-driven reduction of nad+, as well as reverse electron transfer from nadh to h+, in the presence of o₂. it comprises six subunits, hoxhyfui₂, and incorporates a [nife] h+/h₂ cycling catalytic centre, two non-covalently bound flavin mononucleotide (fmn) groups and an iron-sulfur cluster relay for electron transfer. this study provides the first characterization of the diaphorase sub-complex made up of hoxf and ... | 2011 | 22016788 |
| structures of the rna-guided surveillance complex from a bacterial immune system. | bacteria and archaea acquire resistance to viruses and plasmids by integrating short fragments of foreign dna into clustered regularly interspaced short palindromic repeats (crisprs). these repetitive loci maintain a genetic record of all prior encounters with foreign transgressors. crisprs are transcribed and the long primary transcript is processed into a library of short crispr-derived rnas (crrnas) that contain a unique sequence complementary to a foreign nucleic-acid challenger. in escheric ... | 2011 | 21938068 |
| recent progress in bacillus subtilis sporulation. | the gram-positive bacterium bacillus subtilis can initiate the process of sporulation under conditions of nutrient limitation. here, we review some of the last 5 years of work in this area, with a particular focus on the decision to initiate sporulation, dna translocation, cell-cell communication, protein localization and spore morphogenesis. the progress we describe has implications not only just for the study of sporulation but also for other biological systems where homologs of sporulation-sp ... | 2012 | 22091839 |
| recent progress in bacillus subtilis sporulation. | the gram-positive bacterium bacillus subtilis can initiate the process of sporulation under conditions of nutrient limitation. here, we review some of the last 5 years of work in this area, with a particular focus on the decision to initiate sporulation, dna translocation, cell-cell communication, protein localization and spore morphogenesis. the progress we describe has implications not only just for the study of sporulation but also for other biological systems where homologs of sporulation-sp ... | 2012 | 22091839 |
| substrate specificity of bacterial prolyl-trna synthetase editing domain is controlled by a tunable hydrophobic pocket. | aminoacyl-trna synthetases catalyze the covalent attachment of amino acids onto their cognate trnas. high fidelity in this reaction is crucial to the accurate decoding of genetic information and is ensured, in part, by proofreading of the newly synthesized aminoacyl-trnas. prolyl-trna synthetases (prors) mischarge trna(pro) with alanine or cysteine due to their smaller or similar sizes relative to cognate proline. mischarged ala-trna(pro) is hydrolyzed by an editing domain (ins) present in most ... | 2011 | 22128149 |
| substrate specificity of bacterial prolyl-trna synthetase editing domain is controlled by a tunable hydrophobic pocket. | aminoacyl-trna synthetases catalyze the covalent attachment of amino acids onto their cognate trnas. high fidelity in this reaction is crucial to the accurate decoding of genetic information and is ensured, in part, by proofreading of the newly synthesized aminoacyl-trnas. prolyl-trna synthetases (prors) mischarge trna(pro) with alanine or cysteine due to their smaller or similar sizes relative to cognate proline. mischarged ala-trna(pro) is hydrolyzed by an editing domain (ins) present in most ... | 2011 | 22128149 |
| thermostable multicopper oxidase from thermus thermophilus hb27: crystallization and preliminary x-ray diffraction analysis of apo and holo forms. | a thermostable multicopper oxidase from thermus thermophilus hb27 (tth-mco) was successfully crystallized using the sitting-drop and hanging-drop vapour-diffusion methods. crystallization conditions and preliminary x-ray diffraction data to 1.5 å resolution obtained using synchrotron radiation at 100 k are reported. the crystals belonged to space group c222(1), with unit-cell parameters a = 93.6, b = 110.3, c = 96.3 å. a monomer in the asymmetric unit yielded a matthews coefficient (v(m)) of 2.6 ... | 2011 | 22139175 |
| Unique structural features and sequence motifs of proline utilization A (PutA). | Proline utilization A proteins (PutAs) are bifunctional enzymes that catalyze the oxidation of proline to glutamate using spatially separated proline dehydrogenase and pyrroline-5-carboxylate dehydrogenase active sites. Here we use the crystal structure of the minimalist PutA from Bradyrhizobium japonicum (BjPutA) along with sequence analysis to identify unique structural features of PutAs. This analysis shows that PutAs have secondary structural elements and domains not found in the related mon ... | 2012 | 22201760 |
| in vivo, in vitro, and x-ray crystallographic analyses suggest the involvement of an uncharacterized triose-phosphate isomerase (tim) barrel protein in protection against oxidative stress. | accumulating genome sequences have revealed the existence of a large number of conserved hypothetical proteins. characterization of these proteins is considered essential in the elucidation of intracellular biological pathways. our previous transcriptomic analysis suggested that, in thermus thermophilus hb8, loss of an oxidized dna-repairing activity leads to the up-regulation of a function-unknown gene, tthb071, which is conserved in a wide range of bacteria. interestingly, the tthb071 gene pro ... | 2011 | 21984829 |
| structural and mutational studies of a hyperthermophilic intein from dna polymerase ii of pyrococcus abyssi. | protein splicing is a precise self-catalyzed process in which an intein excises itself from a precursor with the concomitant ligation of the flanking polypeptides (exteins). protein splicing proceeds through a four-step reaction but the catalytic mechanism is not fully understood at the atomic level. we report the solution nmr structures of the hyperthermophilic pyrococcus abyssi polii intein, which has a noncanonical c-terminal glutamine instead of an asparagine. the nmr structures were determi ... | 2011 | 21914805 |
| Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy. | The comparison of a pair of electron microscope images recorded at different specimen tilt angles provides a powerful approach for evaluating the quality of images, image-processing procedures, or three-dimensional structures. Here, we analyze tilt-pair images recorded from a range of specimens with different symmetries and molecular masses and show how the analysis can produce valuable information not easily obtained otherwise. We show that the accuracy of orientation determination of individua ... | 2011 | 21939668 |
| isolation and characterization of the prochlorococcus carboxysome reveal the presence of the novel shell protein csos1d. | cyanobacteria, including members of the genus prochlorococcus, contain icosahedral protein microcompartments known as carboxysomes that encapsulate multiple copies of the co(2)-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) in a thin protein shell that enhances the catalytic performance of the enzyme in part through the action of a shell-associated carbonic anhydrase. however, the exact mechanism by which compartmentation provides a catalytic advantage to the enzyme is n ... | 2011 | 22155772 |
| bacteriophage t4 mota activator and the β-flap tip of rna polymerase target the same set of σ70 carboxyl-terminal residues. | sigma factors, the specificity subunits of rna polymerase, are involved in interactions with promoter dna, the core subunits of rna polymerase, and transcription factors. the bacteriophage t4-encoded activator, mota, is one such factor, which engages the c terminus of the escherichia coli housekeeping sigma factor, σ(70). mota functions in concert with a phage-encoded co-activator, asia, as a molecular switch. this process, termed sigma appropriation, inhibits host transcription while activating ... | 2011 | 21911499 |
| crystal structure of the bacteriophage t4 late-transcription coactivator gp33 with the β-subunit flap domain of escherichia coli rna polymerase. | activated transcription of the bacteriophage t4 late genes, which is coupled to concurrent dna replication, is accomplished by an initiation complex containing the host rna polymerase associated with two phage-encoded proteins, gp55 (the basal promoter specificity factor) and gp33 (the coactivator), as well as the dna-mounted sliding-clamp processivity factor of the phage t4 replisome (gp45, the activator). we have determined the 3.0 å-resolution x-ray crystal structure of gp33 complexed with it ... | 2011 | 22135460 |
| An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase. | Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and Northern Australia. Burkholderia is responsible for melioidosis, a serious infection of the skin. The enzyme 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (PGAM) catalyzes the interconversion of 3-phosphoglycerate and 2-phosphoglycerate, a key step in the glycolytic pathway. As such it is an extensively studied enzyme and X-ray crystal structures of PGAM enzymes from multiple species have been elucid ... | 2011 | 21904048 |
| identification of human fumarylacetoacetate hydrolase domain-containing protein 1 (fahd1) as a novel mitochondrial acylpyruvase. | the human fumarylacetoacetate hydrolase (fah) domain-containing protein 1 (fahd1) is part of the fah protein superfamily, but its enzymatic function is unknown. in the quest for a putative enzymatic function of fahd1, we found that fahd1 exhibits acylpyruvase activity, demonstrated by the hydrolysis of acetylpyruvate and fumarylpyruvate in vitro, whereas several structurally related compounds were not hydrolyzed as efficiently. conserved amino acids asp-102 and arg-106 of fahd1 were found import ... | 2011 | 21878618 |
| protective role of catechin on d-galactosamine induced hepatotoxicity through a p53 dependent pathway. | objective of this study was to obtain a better understanding of the mechanism responsible for the d-galactosamine (d-galn) induced hepatotoxicity and to study the effect of catechin against d-galn induced hepatotoxicity. catechin 50 and 100 mg/kg b.wt was administered for 1 week by oral route. liver damage was induced by intra-peritoneal administration of 400 mg/kg b.wt d-galactosamine on the last day of catechin treatment. at the end of treatment all animals were killed and liver enzyme levels ... | 2010 | 21966103 |
| transcriptional regulation of central carbon and energy metabolism in bacteria by redox responsive repressor rex. | redox-sensing repressor rex was previously implicated in the control of anaerobic respiration in response to the cellular nadh/nad(+) levels in gram-positive bacteria. we utilized the comparative genomics approach to infer candidate rex-binding dna motifs and assess the rex regulon content in 119 genomes from 11 taxonomic groups. both dna-binding and nad-sensing domains are broadly conserved in rex orthologs identified in the phyla firmicutes, thermotogales, actinobacteria, chloroflexi, deinococ ... | 2011 | 22210771 |
| Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids. | The Mre11/Rad50 complex and the homologous SbcD/SbcC complex in bacteria play crucial roles in the metabolism of DNA double-strand breaks, including DNA repair, genome replication, homologous recombination and non-homologous end-joining in cellular life forms and viruses. Here we investigated the amino acid sequence of the Mimivirus R555 gene product, originally annotated as a Rad50 homolog, and later shown to have close homologs in marine microbial metagenomes. | 2011 | 21899737 |
| Post-translational modification by ß-lysylation is required for the activity of E. coli Elongation Factor P (EF-P). | Bacterial elongation factor P (EF-P) is the ortholog of archaeal and eukaryotic initiation factor 5A (aIF5A and eIF5A). EF-P shares sequence homology and crystal structure with eIF5A, but unlike eIF5A, EF-P does not undergo hypusine modification. Recently, two bacterial genes, yjeA and yjeK, encoding truncated homologs of class II lysyl-tRNA synthetase and of lysine-2,3-aminomutase, respectively, have been implicated in the modification of EF-P to convert a specific lysine to a hypothetical ß- ... | 2011 | 22128152 |
| Post-translational modification by ß-lysylation is required for the activity of E. coli Elongation Factor P (EF-P). | Bacterial elongation factor P (EF-P) is the ortholog of archaeal and eukaryotic initiation factor 5A (aIF5A and eIF5A). EF-P shares sequence homology and crystal structure with eIF5A, but unlike eIF5A, EF-P does not undergo hypusine modification. Recently, two bacterial genes, yjeA and yjeK, encoding truncated homologs of class II lysyl-tRNA synthetase and of lysine-2,3-aminomutase, respectively, have been implicated in the modification of EF-P to convert a specific lysine to a hypothetical ß- ... | 2011 | 22128152 |
| genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. | prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet earth with human beings (among others). however, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. an understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. the vast majorit ... | 2011 | 22126996 |
| estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. | for many research questions in modern molecular and systems biology information about absolute protein quantities is imperative. these include, for example, kinetic modeling of processes, protein turnover determinations, stoichiometric investigations of protein complexes or quantitative comparisons of different proteins within one or across samples. to date, the vast majority of proteomic studies are limited to providing relative quantitative comparisons of protein levels between limited numbers ... | 2011 | 22101334 |