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interaction of mycobacterium tuberculosis elongation factor tu with gtp is regulated by phosphorylation.during protein synthesis, translation elongation factor tu (ef-tu) is responsible for the selection and binding of the cognate aminoacyl-trna to the acceptor site on the ribosome. the activity of ef-tu is dependent on its interaction with gtp. post-translational modifications such as phosphorylation are known to regulate the activity of ef-tu in several prokaryotes. although, a study on mycobacterium tuberculosis phosphoproteome showed ef-tu to be phosphorylated, the role of phosphorylation in r ...201121803988
overexpression, crystallization, and preliminary x-ray crystallographic analysis of shikimate dehydrogenase from thermotoga maritima.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. previous structural studies showed that sdh exists in two conformations, an open form and a closed form, and it is believed that the conformational state is crucial to understanding a catalytic mechanism. to facilitate further structural comparisons among sdhs, structural analy ...201121795804
crystallization and preliminary x-ray analysis of 4-diphosphocytidyl-2-c-methyl-d-erythritol kinase (ispe) from mycobacterium tuberculosis.the 4-diphosphocytidyl-2-c-methyl-d-erythritol kinase (ispe) from mycobacterium tuberculosis, an enzyme from the 2-c-methyl-d-erythritol 4-phosphate (mep) pathway, is crucial and essential for the survival of this pathogenic bacterium. ispe catalyzes the conversion of 4-diphosphocytidyl-2-c-methyl-d-erythritol (cdp-me) to 4-diphosphocytidyl-2-c-methyl-d-erythritol 2-phosphate (cdp-me2p) in an atp-dependent manner. solving the crystal structure of m. tuberculosis ispe will shed light on its struc ...201121795803
expression, purification, crystallization and preliminary x-ray crystallographic analysis of the hyperthermophilic nucleotidyltransferase ttha1015 from thermus thermophilus hb8.the ttha1015 gene from thermus thermophilus hb8 encodes a hyperthermophilic nucleotidyltransferase. ttha1015 has high homology to proteins belonging to two related families: the nucleotidyltransferase-domain superfamily and the dna polymerase ß-like family. however, no crystal structures of these proteins have been reported. determination of the crystal structure of ttha1015 will help in elucidation of its function and will be useful for understanding the relationship between the structure and t ...201121795793
the role of smpb and the ribosomal decoding center in licensing tmrna entry into stalled ribosomes.in bacteria, stalled ribosomes are recycled by a hybrid transfer-messenger rna (tmrna). like trna, tmrna is aminoacylated with alanine and is delivered to the ribosome by ef-tu, where it reacts with the growing polypeptide chain. tmrna entry into stalled ribosomes poses a challenge to our understanding of ribosome function because it occurs in the absence of a codon-anticodon interaction. instead, tmrna entry is licensed by the binding of its protein partner, smpb, to the ribosomal decoding cent ...201121795410
catalytic and non-catalytic roles for the mono-adp-ribosyltransferase arr in the mycobacterial dna damage response.recent evidence indicates that the mycobacterial response to dna double strand breaks (dsbs) differs substantially from previously characterized bacteria. these differences include the use of three dsb repair pathways (hr, nhej, ssa), and the card pathway, which integrates dna damage with transcription. here we identify a role for the mono-adp-ribosyltransferase arr in the mycobacterial dna damage response. arr is transcriptionally induced following dna damage and cellular stress. although arr i ...201121789183
structural basis for the function of a small gtpase rsga on the 30s ribosomal subunit maturation revealed by cryoelectron microscopy.the bacterial rsga, a circularly permutated gtpase, whose gtpase activity is dependent on the 30s ribosomal subunit, is a late-stage ribosome biogenesis factor involved in the 30s subunit maturation. the role of rsga is to release another 30s biogenesis factor, rbfa, from the mature 30s subunit in a gtp-dependent manner. using cryoelectron microscopy, we have determined the structure of the 30s subunit bound with rsga in the presence of gmppnp at subnanometer resolution. in the structure, rsga b ...201121788480
sulfolobus mutants, generated via pcr products, which lack putative enzymes of uv photoproduct repair.in order to determine the biological relevance of two s. acidocaldarius proteins to the repair of uv photoproducts, the corresponding genes (saci_1227 and saci_1096) were disrupted, and the phenotypes of the resulting mutants were examined by various genetic assays. the disruption used integration by homologous recombination of a functional but heterologous pyre gene, promoted by short sequences attached to both ends via pcr. the phenotypic analyses of the disruptants confirmed that orf saci_122 ...201121785574
identification and characterization of a re-citrate synthase in dehalococcoides strain cbdb1.the genome annotations of all sequenced dehalococcoides strains lack a citrate synthase although physiological experiments have indicated that such an activity should be encoded. we here report that a re-face specific citrate synthase is synthesized by dehalococcoides strain cbdb1 and that this function is encoded by the gene cbdba1708 (ncbi accession number cai83711), previously annotated as homocitrate synthase. gene cbdba1708 was heterologously expressed in e. coli and the recombinant enzyme ...201121784924
evidence for a thermodynamically distinct mg2+ ion associated with formation of an rna tertiary structure.a folding strategy adopted by some rnas is to chelate cations in pockets or cavities, where the ions neutralize charge from solvent-inaccessible phosphate. although such buried mg(2+)-rna chelates could be responsible for a significant fraction of the mg(2+)-dependent stabilization free energy of some rna tertiary structures, direct measurements have not been feasible because of the difficulty of finding conditions under which the free energy of mg(2+) chelation is uncoupled from rna folding and ...201121776997
structural and biochemical analysis of the nuclease domain of the clustered regularly interspaced short palindromic repeat (crispr) associated protein 3(cas3).rna transcribed from clustered regularly interspaced short palindromic repeats (crisprs) protects many prokaryotes from invasion by foreign dna such as viruses, conjugative plasmids and transposable elements. crispr-associated protein 3 (cas3) is essential for this crispr protection and is thought to mediate cleavage of the foreign dna through its n-terminal histidine-aspartate (hd) domain. we report here the 1.8 å crystal structure of the hd domain of cas3 from thermus thermophilus hb8. structu ...201121775431
role of trna amino acid-accepting end in aminoacylation and its quality control.aminoacyl-trna synthetases (aarss) are remarkable enzymes that are in charge of the accurate recognition and ligation of amino acids and trna molecules. the greatest difficulty in accurate aminoacylation appears to be in discriminating between highly similar amino acids. to reduce mischarging of trnas by non-cognate amino acids, aarss have evolved an editing activity in a second active site to cleave the incorrect aminoacyl-trnas. editing occurs after translocation of the aminoacyl-cca(76) end t ...201121775341
molecular basis for the selectivity of antituberculosis compounds capreomycin and viomycin.capreomycin and the structurally similar compound viomycin are cyclic peptide antibiotics which are particularly active against mycobacterium tuberculosis, including multi-drug resistant strains. both antibiotics bind across the ribosomal interface involving 23s rrna helix 69 (h69) and 16s rrna helix 44 (h44). the binding site of tuberactinomycins in h44 partially overlaps with that of aminoglycosides and they share with these drugs the side effect of irreversible hearing loss. here we studied t ...201121768509
diverse substrate recognition and hydrolysis mechanisms of human nudt5.human nudt5 (hnudt5) hydrolyzes various modified nucleoside diphosphates including 8-oxo-dgdp, 8-oxo-dadp and adp-ribose (adpr). however, the structural basis of the broad substrate specificity remains unknown. here, we report the crystal structures of hnudt5 complexed with 8-oxo-dgdp and 8-oxo-dadp. these structures reveal an unusually different substrate-binding mode. in particular, the positions of two phosphates (a and ß phosphates) of substrate in the 8-oxo-dgdp and 8-oxo-dadp complexes are ...201121768126
human fatty acid transport protein 2a/very long chain acyl coa synthetase 1 (fatp2a/acsvl1) has a preference in mediating the channeling of exogenous n-3 fatty acids into phosphatidylinositol.the trafficking of fatty acids across the membrane and into downstream metabolic pathways requires their activation to coa thioesters. members of the fatty acid transport protein/very long chain acyl coa synthetase (fatp/acsvl) family are emerging as key players in the trafficking of exogenous fatty acids into the cell and in intracellular fatty acid homeostasis. we have expressed two naturally occurring splice variants of fatp2 (acsvl1) in yeast and 293t-rex cells and addressed their roles in f ...201121768100
redox-coupled protonation of respiratory complex i: the hydrophilic domain.respiratory complex i, nadh:ubiquinone oxidoreductase, is a large and complex integral membrane enzyme found in respiring bacteria and mitochondria. it is responsible in part for generating the proton gradient necessary for atp production. complex i serves as both a proton pump and an entry point for electrons into the respiratory chain. although complex i is one of the most important of the respiratory complexes, it is also one of the least understood, with detailed structural information only ...201121767496
staphylococcus lugdunensis isdg liberates iron from host heme.staphylococcus lugdunensis is often found as part of the normal flora of human skin but has the potential to cause serious infections even in healthy individuals. it remains unclear what factors enable s. lugdunensis to transition from a skin commensal to an invasive pathogen. analysis of the complete genome reveals a putative iron-regulated surface determinant (isd) system encoded within s. lugdunensis. in other bacteria the isd system permits the utilization of host heme as a source of nutrien ...201121764939
a transcript cleavage factor of mycobacterium tuberculosis important for its survival.after initiation of transcription, a number of proteins participate during elongation and termination modifying the properties of the rna polymerase (rnap). gre factors are one such group conserved across bacteria. they regulate transcription by projecting their n-terminal coiled-coil domain into the active center of rnap through the secondary channel and stimulating hydrolysis of the newly synthesized rna in backtracked elongation complexes. rv1080c is a putative gre factor (mtbgre) in the geno ...201121760927
proline dehydrogenase is a positive regulator of cell death in different kingdoms.proline dehydrogenase (prodh) catalyzes the flavin-dependent oxidation of pro into δ1-pyrroline-5-carboxylate (p5c). this is the first of the two enzymatic reactions that convert proline (pro) into glutamic acid (glu). the p5c thus produced is non-enzymatically transformed into glutamate semialdehyde (gsa), which acts as a substrate of p5c dehydrogenase (p5cdh) to generate glu. activation of prodh can generate different effects depending on the behaviour of other enzymes of this metabolism. unde ...201121757996
probing the protonation/deprotonation of tyrosine residues in cytochrome ba3 oxidase from thermus thermophilus by time-resolved step-scan ftir spectroscopy.elucidating the properties of the heme fe-cu(b) binuclear center and the dynamics of the protein response in cytochrome c oxidase is crucial to understanding not only the dioxygen activation and bond cleavage by the enzyme, but also the events related with the release of the produced water molecules. the time-resolved step-scan ftir difference spectra show the ?7a(co) of the protonated form of y residues at 1247 cm(-1) and that of the deprotonated form at 1301 cm(-1). by monitoring the intensity ...201121757723
characterization of the deoxynucleotide triphosphate triphosphohydrolase (dntpase) activity of the ef1143 protein from enterococcus faecalis and crystal structure of the activator-substrate complex.the ef1143 protein from enterococcus faecalis is a distant homolog of deoxynucleotide triphosphate triphosphohydrolases (dntpases) from escherichia coli and thermus thermophilus. these dntpases are important components in the regulation of the dntp pool in bacteria. biochemical assays of the ef1143 dntpase activity demonstrated nonspecific hydrolysis of all canonical dntps in the presence of mn2+. in contrast, with mg2+ hydrolysis required the presence of dgtp as an effector, activating the degr ...201121757692
leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes.abstract: background: shine-dalgarno (sd) signal has long been viewed as the dominant translation initiation signal in prokaryotes. recently, leaderless genes, which lack 5'-untranslated regions (5'-utr) on their mrnas, have been shown abundant in archaea. however, current large-scale in silico analyses on initiation mechanisms in bacteria are mainly based on the sd-led initiation way, other than the leaderless one. the study of leaderless genes in bacteria remains open, which causes uncertain u ...201121749696
characterization of the mitochondrial atp synthase from yeast saccharomyces cerevisae.the mitochondrial atp synthase from yeast s. cerevisiae has been genetically modified, purified in a functional form, and characterized with regard to lipid requirement, compatibility with a variety of detergents, and the steric limit with rotation of the central stalk has been assessed. the atp synthase has been modified on the n-terminus of the ß-subunit to include a his(6) tag for ni-chelate affinity purification. the enzyme is purified by a two-step procedure from submitochondrial particles ...201121748405
crystallizing membrane proteins in lipidic mesophases. a host lipid screen.the default lipid for the bulk of the crystallogenesis studies performed to date using the cubic mesophase method is monoolein. there is no good reason however, why this 18-carbon, cis-monounsaturated monoacylglycerol should be the preferred lipid for all target membrane proteins. the latter come from an array of biomembrane types with varying properties that include hydrophobic thickness, intrinsic curvature, lateral pressure profile, lipid and protein makeup, and compositional asymmetry. thus, ...201121743796
rna transcript 3'-proximal sequence affects translocation bias of rna polymerase.translocation of rna polymerase on dna is thought to involve oscillations between pretranslocated and posttranslocated states that are rectified by nucleotide addition or pyrophosphorolysis. the pretranslocated register is also a precursor to transcriptional pause states that mediate regulation of transcript elongation. however, the determinants of bias between the pretranslocated and posttranslocated states are incompletely understood. to investigate translocation bias in multisubunit rna polym ...201121739957
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 ...201121738733
towards a rigorous network of protein-protein interactions of the model sulfate reducer desulfovibrio vulgaris hildenborough.protein-protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. the aforementioned tools have been extensively applied to study escherichia coli and other aerobes and more recently to study the stress response behavior of desulfovibrio vulgaris hildenborough, a model obligate anaerobe and sulfate reducer and the subject of this study. here we carried out affinity purification follow ...201121738675
clpxp, an atp-powered unfolding and protein-degradation machine.clpxp is a aaa+ protease that uses the energy of atp binding and hydrolysis to perform mechanical work during targeted protein degradation within cells. clpxp consists of hexamers of a aaa+ atpase (clpx) and a tetradecameric peptidase (clpp). asymmetric clpx hexamers bind unstructured peptide tags in protein substrates, unfold stable tertiary structure in the substrate, and then translocate the unfolded polypeptide chain into an internal proteolytic compartment in clpp. here, we review our prese ...201121736903
clpxp, an atp-powered unfolding and protein-degradation machine.clpxp is a aaa+ protease that uses the energy of atp binding and hydrolysis to perform mechanical work during targeted protein degradation within cells. clpxp consists of hexamers of a aaa+ atpase (clpx) and a tetradecameric peptidase (clpp). asymmetric clpx hexamers bind unstructured peptide tags in protein substrates, unfold stable tertiary structure in the substrate, and then translocate the unfolded polypeptide chain into an internal proteolytic compartment in clpp. here, we review our prese ...201121736903
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 ...201121736641
kinetic and chemical mechanisms of homocitrate synthase from thermus thermophilus.the homocitrate synthase from thermus thermophilus (tthcs) is a metal-activated enzyme with either mg(2+) or mn(2+) capable of serving as the divalent cation. the enzyme exhibits a sequential kinetic mechanism. the mechanism is steady state ordered with +¦-ketoglutarate (+¦-kg) binding prior to acetyl-coa (accoa) with mn(2+), whereas it is steady state random with mg(2+), suggesting a difference in the competence of the e-àmn-à+¦-kg-àaccoa and e-àmg-à+¦-kg-àaccoa complexes. the mechanism is supp ...201121733842
phylogenetic sequence variations in bacterial rrna affect species-specific susceptibility to drugs targeting protein synthesis.antibiotics targeting the bacterial ribosome typically bind to highly conserved rrna regions with only minor phylogenetic sequence variations. it is unclear whether these sequence variations affect antibiotic susceptibility or resistance development. to address this question, we have investigated the drug binding pockets of aminoglycosides and macrolides/ketolides. the binding site of aminoglycosides is located within helix 44 of the 16s rrna (a site); macrolides/ketolides bind to domain v of th ...201121730122
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 ...201121726814
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 ...201121725002
glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass.industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. compost-derived microbial consortia were adapted to switchgrass at 60-¦c to develop thermophilic biomass-degrading consortia for detailed studies. microbial community analysis using small-subunit rrna gene am ...201121724886
new structural and functional contexts of the dx[dn]xdg linear motif: insights into evolution of calcium-binding proteins.binding of calcium ions (ca²⁺) to proteins can have profound effects on their structure and function. common roles of calcium binding include structure stabilization and regulation of activity. it is known that diverse families--ef-hands being one of at least twelve--use a dx[dn]xdg linear motif to bind calcium in near-identical fashion. here, four novel structural contexts for the motif are described. existing experimental data for one of them, a thermophilic archaeal subtilisin, demonstrate fo ...201121720552
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 ...201121719274
allosteric drugs: the interaction of antitumor compound mkt-077 with human hsp70 chaperones.hsp70 (heat shock protein 70-ákda) chaperones are key to cellular protein homeostasis. however, they also have the ability to inhibit tumor apoptosis and contribute to aberrant accumulation of hyperphosphorylated tau in neuronal cells affected by tauopathies, including alzheimer's disease. hence, hsp70 chaperones are increasingly becoming identified as targets for therapeutic intervention in these widely abundant diseases. hsp70 proteins are allosteric machines and offer, besides classical activ ...201121708173
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 ...201121705543
difference in the distribution pattern of substrate enzymes in the metabolic network of escherichia coli, according to chaperonin requirement.abstract:201121702926
structural aspects of translation termination on the ribosome.translation of genetic information encoded in messenger rnas into polypeptide sequences is carried out by ribosomes in all organisms. when a full protein is synthesized, a stop codon positioned in the ribosomal a site signals termination of translation and protein release. translation termination depends on class i release factors. recently, atomic-resolution crystal structures were determined for bacterial 70s ribosome termination complexes bound with release factors rf1 or rf2. in combination ...201121700725
community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential.phototrophic microbial mat communities from 60-¦c and 65-¦c regions in the effluent channels of mushroom and octopus springs (yellowstone national park, wy, usa) were investigated by shotgun metagenomic sequencing. analyses of assembled metagenomic sequences resolved six dominant chlorophototrophic populations and permitted the discovery and characterization of undescribed but predominant community members and their physiological potential. linkage of phylogenetic marker genes and functional gen ...201121697961
dynamics of gene duplication in the genomes of chlorophyll d-producing cyanobacteria: implications for the ecological niche.gene duplication may be an important mechanism for the evolution of new functions and for the adaptive modulation of gene expression via dosage effects. here, we analyzed the fate of gene duplicates for two strains of a novel group of cyanobacteria (genus acaryochloris) that produces the far-red light absorbing chlorophyll d as its main photosynthetic pigment. the genomes of both strains contain an unusually high number of gene duplicates for bacteria. as has been observed for eukaryotic genomes ...201121697100
structural and functional evolution of isopropylmalate dehydrogenases in the leucine and glucosinolate pathways of arabidopsis thaliana.the methionine chain-elongation pathway is required for aliphatic glucosinolate biosynthesis in plants and evolved from leucine biosynthesis. in arabidopsis thaliana, three 3-isopropylmalate dehydrogenases (atipmdhs) play key roles in methionine chain-elongation for the synthesis of aliphatic glucosinolates (e.g. atipmdh1) and leucine (e.g. atipmdh2 and atipmdh3). here we elucidate the molecular basis underlying the metabolic specialization of these enzymes. the 2.25 å resolution crystal structu ...201121697089
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 ...201121695207
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 ...201121693558
kinetic design of the respiratory oxidases.energy conservation in all kingdoms of life involves electron transfer, through a number of membrane-bound proteins, associated with proton transfer across the membrane. in aerobic organisms, the last component of this electron-transfer chain is a respiratory heme-copper oxidase that catalyzes reduction of o(2) to h(2)o, linking this process to transmembrane proton pumping. so far, the molecular mechanism of proton pumping is not known for any system that is driven by electron transfer. here, we ...201121690359
requirements for the catalytic cycle of the n-ethylmaleimide-sensitive factor (nsf).the n-ethylmaleimide-sensitive factor (nsf) was one of the initial members of the atpases associated with various cellular activities plus (aaa(+)) family. in this review, we discuss what is known about the mechanism of nsf action and how that relates to the mechanisms of other aaa(+) proteins. like other family members, nsf binds to a protein complex (i.e., snap-snare complex) and utilizes atp hydrolysis to affect the conformations of that complex. snap-snare complex disassembly is essential fo ...201121689688
requirements for the catalytic cycle of the n-ethylmaleimide-sensitive factor (nsf).the n-ethylmaleimide-sensitive factor (nsf) was one of the initial members of the atpases associated with various cellular activities plus (aaa(+)) family. in this review, we discuss what is known about the mechanism of nsf action and how that relates to the mechanisms of other aaa(+) proteins. like other family members, nsf binds to a protein complex (i.e., snap-snare complex) and utilizes atp hydrolysis to affect the conformations of that complex. snap-snare complex disassembly is essential fo ...201121689688
towards al-induced manganese-containing superoxide dismutase inactivation and conformational changes: an integrating study with docking simulations.superoxide dismutase (sod, ec 1.15.1.1) plays an important antioxidant defense role in skins exposed to oxygen. we studied the inhibitory effects of al(3+) on the activity and conformation of manganese-containing sod (mn-sod). mn-sod was significantly inactivated by al(3+) in a dose-dependent manner. the kinetic studies showed that al(3+) inactivated mn-sod follows the first-order reaction. al(3+) increased the degree of secondary structure of mn-sod and also disrupted the tertiary structure of ...201121687640
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 ...201121685364
alterations in the {beta} flap and {beta}' dock domains of the rna polymerase abolish nusa-mediated feedback regulation of the mety-nusa-infb operon.the rimm protein in escherichia coli is important for the in vivo maturation of 30s ribosomal subunits and a +örimm mutant grows poorly due to assembly and translational defects. these deficiencies are suppressed partially by mutations that increase the synthesis of another assembly protein, rbfa, encoded by the mety-nusa-infb operon. among these suppressors are mutations in nusa that impair the nusa-mediated negative-feedback regulation at internal intrinsic transcriptional terminators of the m ...201121685293
stabilization of c4a-hydroperoxyflavin in a two-component flavin-dependent monooxygenase is achieved through interactions at flavin n5 and c4a atoms.p-hydroxyphenylacetate (hpa) 3-hydroxylase is a two-component flavin-dependent monooxygenase. based on the crystal structure of the oxygenase component (c(2)), his-396 is 4.5 å from the flavin c4a locus, whereas ser-171 is 2.9 å from the flavin n5 locus. we investigated the roles of these two residues in the stability of the c4a-hydroperoxy-fmn intermediate. the results indicated that the rate constant for c4a-hydroperoxy-fmn formation decreased ~30-fold in h396n, 100-fold in h396a, and 300-fold ...201121680741
carotenoid ╬▓-ring hydroxylase and ketolase from marine bacteria-promiscuous enzymes for synthesizing functional xanthophylls.marine bacteria belonging to genera paracoccus and brevundimonas of the ╬▒-proteobacteria class can produce côéäôéç-type dicyclic carotenoids containing two ╬▓-end groups (╬▓ rings) that are modified with keto and hydroxyl groups. these bacteria produce astaxanthin, adonixanthin, and their derivatives, which are ketolated by carotenoid ╬▓-ring 4(4')-ketolase (4(4')-oxygenase; crtw) and hydroxylated by carotenoid ╬▓-ring 3(3')-hydroxylase (crtz). in addition, the genus brevundimonas possesses a g ...201121673887
a pilot study of bacterial genes with disrupted orfs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment.bacterial genome annotations contain a number of coding sequences (cdss) that, in spite of reading frame disruptions, encode a single continuous polypeptide. such disruptions have different origins: sequencing errors, frameshift, or stop codon mutations, as well as instances of utilization of nontriplet decoding. we have extracted over 1,000 cdss with annotated disruptions and found that about 75% of them can be clustered into 64 groups based on sequence similarity. analysis of the clusters reve ...201121673094
markus: a server to navigate sequence-structure-function space.we describe markus, a web server for analysis and comparison of the structural and functional properties of proteins. in contrast to a 'structure in/function out' approach to protein function annotation, the server is designed to be highly interactive and to allow flexibility in the examination of possible functions, suggested either automatically by various similarity measures or specified by a user directly. this is combined with tools that allow a user to assess independently whether or not a ...201121672961
structural and kinetic mapping of side-chain exposure onto the protein energy landscape.identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. native-state hydrogen exchange (nshx) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating t ...201121670244
the rpb2 flap loop of human rna polymerase ii is dispensable for transcription initiation and elongation.the flap domain of multisubunit rna polymerases (rnaps), also called the wall, forms one side of the rna exit channel. in bacterial rnap, the mobile part of the flap is called the flap tip and makes essential contacts with initiation and elongation factors. cocrystal structures suggest that the orthologous part of eukaryotic rnapii, called the flap loop, contacts transcription factor iib (tfiib), but the function of the flap loop has not been assessed. we constructed and tested a deletion of the ...201121670157
small noncoding rnas in the germline.small noncoding rnas have emerged as potent regulators of gene expression, especially in the germline. we review the biogenesis and regulatory function of three major small noncoding rna pathways in the germline: the small interfering rna (sirna) pathway that leads to the degradation of target mrnas, the microrna (mirna) pathway that mostly represses the translation of target mrnas, and the newly discovered piwi-interacting rna (pirna) pathway that appears to have diverse functions in epigenetic ...201121669983
high tolerance to mutations in a chlamydia trachomatis peptide deformylase loop.to determine if and how a loop region in the peptide deformylase (pdf) of chlamydia trachomatis regulates enzyme function.201121666811
a sulfite respiration pathway from thermus thermophilus and the key role of newly identified cytochrome côéàôéàôéç.sulfite, produced for instance during amino acid metabolism, is a very reactive and toxic compound. various detoxification mechanisms exist, but sulfite oxidoreductases (sors) are one of the major actors in sulfite remediation in bacteria and animals. here we describe the existence of an operon in the extreme thermophilic bacterium thermus thermophilus hb8 encoding both a sor and a diheme c-type cytochrome. the in vitro analysis clearly showed that the newly identified cytochrome côéàôéàôéç acts ...201121665981
uracil-dna glycosylase of thermoplasma acidophilumdirects long-patch base excision repair, which is promoted by deoxynucleoside triphosphates and atp/adp, into short-patch repair.hydrolytic deamination of cytosine to uracil in dna is increased in organisms adapted to high temperatures. hitherto, the uracil base excision repair (ber) pathway has only been described in two archaeons, the crenarchaeon pyrobaculum aerophilumand the euryarchaeon archaeoglobus fulgidus, which are hyperthermophiles and use single-nucleotide replacement. in the former the apurinic/apyrimidinic (ap) site intermediate is removed by the sequential action of a 5'-acting ap endonuclease and a 5'-deox ...201121665970
crystal structure of the mid-piwi lobe of a eukaryotic argonaute protein.argonaute proteins (agos) are essential effectors in rna-mediated gene silencing pathways. they are characterized by a bilobal architecture, in which one lobe contains the n-terminal and paz domains and the other contains the mid and piwi domains. here, we present the first crystal structure of the mid-piwi lobe from a eukaryotic ago, the neurospora crassa qde-2 protein. compared to prokaryotic agos, the domain orientation is conserved, indicating a conserved mode of nucleic acid binding. the pi ...201121646546
microbial ecology of the dark ocean above, at, and below the seafloor.the majority of life on earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. ...201121646433
a new family of deamination repair enzymes in the uracil dna glycosylase superfamily.dna glycoyslases play a major role in the repair of deaminated dna damage. previous investigations identified five families within the uracil dna glycosylase (udg) superfamily. all enzymes within the superfamily studied thus far exhibit uracil dna glycosylase activity. here we identify a new class of dna glycosylases in the udg superfamily that lacks udg activity. instead, these enzymes act as hypoxanthine dna glycosylases in vitro and in vivo. molecular modeling and structure-guided mutational ...201121642431
allosteric communication between the nucleotide binding domains of caseinolytic peptidase b(clpb).clpb is a hexameric chaperone that solubilizes and reactivates protein aggregates in cooperation with the hsp70/dnak chaperone system. each of the identical protein monomer contains two nucleotide binding domains (nbd), whose atpase activity must be coupled to exert on the substrate the mechanical work required for its reactivation. however, how communication between these sites occurs is at present poorly understood. we have studied herein the affinity of each of the nbds for nucleotides in wt ...201121642426
expression, crystallization and preliminary x-ray analysis of a ferric binding protein from thermus thermophilus hb8.a ferric binding protein from thermus thermophilus hb8 (ttfbpa) was expressed, purified and crystallized using the hanging-drop vapour-diffusion method. four different crystal forms were obtained and characterized by x-ray diffraction. two crystal forms with ttfbpa in the apo state belonged to the orthorhombic space group p2(1)2(1)2(1) (unit-cell parameters a = 42.1, b = 139.3, c = 326.5 å and a = 42.1, b = 139.3, c = 218.9 å). the third form with ttfbpa also in the apo state belonged to the mon ...201121636922
crystallization and preliminary x-ray crystallographic analysis of dihydrouridine synthase from thermus thermophilus and its complex with trna.dihydrouridine synthase (dus) is responsible for catalyzing dihydrouridine formation in rna by the reduction of uridine. to elucidate its rna-recognition mechanism, dus from thermus thermophilus (tthdus) and its complex with trna were crystallized. diffraction data sets were collected from crystals of native and selenomethionine-substituted tthdus to resolutions of 1.70 and 2.30 å, respectively. these crystals belonged to space group p1. preliminary x-ray crystallographic analysis showed that tw ...201121636912
crystallization and preliminary x-ray analysis of argininosuccinate lyase from streptococcus mutans.argininosuccinate lyase (asl) is an important enzyme in arginine synthesis and the urea cycle, which are highly conserved from bacteria to eukaryotes. the gene encoding streptococcus mutans asl (smasl) was amplified and cloned into expression vector pet28a. the recombinant smasl protein was expressed in a soluble form in escherichia coli strain bl21 (de3) and purified to homogeneity by two-step column chromatography. crystals suitable for x-ray analysis were obtained and x-ray diffraction data w ...201121636911
differences in dinucleotide frequencies of thermophilic genes encoding water soluble and membrane proteins.the occurrence frequencies of the dinucleotides of genes of three thermophilic and three mesophilic species from both archaea and eubacteria were investigated in this study. the genes encoding water soluble proteins were rich in the dinucleotides of purine dimers, whereas the genes encoding membrane proteins were rich in pyrimidine dimers. the dinucleotides of purine dimers are the counterparts of pyrimidine dimers in a double-stranded dna. the purine/pyrimidine dimers were favored in the thermo ...201121634034
the yeast rapid trna decay pathway primarily monitors the structural integrity of the acceptor and t-stems of mature trna.trnas, like other rnas, are subject to quality control steps during and after biosynthesis. we previously described a rapid trna degradation (rtd) pathway in which the 5'-3' exonucleases rat1 and xrn1 degrade mature trna(val(aac)) in yeast mutants lacking m(7)g and m(5)c, and mature trna(ser(cga)) in mutants lacking um and ac(4)c. to understand how the rtd pathway selects substrate trnas among different trnas lacking the same modifications, we used a genetic screen to examine trna(ser(cga)) vari ...201121632824
crystal structure of the heme d1 biosynthesis enzyme nire in complex with its substrate reveals new insights into the catalytic mechanism of s-adenosyl-l-methionine dependent uroporphyrinogen iii methyltransferases.during the biosynthesis of heme d(1), the essential cofactor of cytochrome cd(1) nitrite reductase, the nire protein catalyzes the methylation of uroporphyrinogen iii to precorrin-2 using s-adenosyl-l-methionine (sam) as the methyl group donor. the crystal structure of pseudomonas aeruginosa nire in complex with its substrate uroporphyrinogen iii and the reaction by-product s-adenosyl-l-homocysteine (sah) was solved to 2.0 angstrom resolution. this represents the first enzyme-substrate complex s ...201121632530
the influence of the local sequence environment on rna loop structures.rna folding is assumed to be a hierarchical process. the secondary structure of an rna molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. subsequently, the rna molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). to what extent the backbone conformation of rna loops also r ...201121628431
an extensive network of information flow through the b1b/c intersubunit bridge of the yeast ribosome.yeast ribosomal proteins l11 and s18 form a dynamic intersubunit interaction called the b1b/c bridge. recent high resolution images of the ribosome have enabled targeting of specific residues in this bridge to address how distantly separated regions within the large and small subunits of the ribosome communicate with each other. mutations were generated in the l11 side of the b1b/c bridge with a particular focus on disrupting the opposing charge motifs that have previously been proposed to be in ...201121625514
allosteric nucleotide-binding site in the mitochondrial nadh:ubiquinone oxidoreductase (respiratory complex i).the rotenone-insensitive nadh:hexaammineruthenium iii (har) oxidoreductase reactions catalyzed by bovine heart and yarrowia lipolytica submitochondrial particles or purified bovine complex i are stimulated by atp and other purine nucleotides. the soluble fraction of mammalian complex i (fp) and prokaryotic complex i homolog ndh-1 in paracoccus denitrificans plasma membrane lack stimulation of their activities by atp. the stimulation appears as a decrease in apparent k(m) values for nadh and har. ...201121624365
isoprenoid precursor biosynthesis offers potential targets for drug discovery against diseases caused by apicomplexan parasites.two, simple, c5 compounds, dimethylally diphosphate and isopentenyl diphosphate, are the universal precursors of isoprenoids, a large family of natural products involved in numerous important biological processes. two distinct biosynthetic pathways have evolved to supply these precursors. humans use the mevalonate route whilst many species of bacteria including important pathogens, plant chloroplasts and apicomplexan parasites exploit the non-mevalonate pathway. the absence from humans, combined ...201121619509
converting structural information into an allosteric-energy-based picture for elongation factor tu activation by the ribosome.the crucial process of aminoacyl-trna delivery to the ribosome is energized by the gtpase reaction of the elongation factor tu (ef-tu). advances in the elucidation of the structure of the ef-tu/ribosome complex provide the rare opportunity of gaining a detailed understanding of the activation process of this system. here, we use quantitative simulation approaches and reproduce the energetics of the gtpase reaction of ef-tu with and without the ribosome and with several key mutants. our study pro ...201121617092
crystal structure of alkyl hydroperoxidase d like protein pa0269 from pseudomonas aeruginosa: homology of the ahpd-like structural family.abstract: background: alkyl hydroperoxidase activity provides an important antioxidant defense for bacterial cells. the catalytic mechanism requires two peroxidases, ahpc and ahpd, where ahpd plays the role of an essential adaptor protein. results: the crystal structure of a putative ahpd from pseudomonas aeruginosa has been determined at 1.9 a. the protein has an all-helical fold with a chain topology similar to a known ahpd from mycobacterium tuberculosis despite a low overall sequence identit ...201121615954
cross-linking, ligation, and sequencing of hybrids reveals rna-rna interactions in yeast.many protein-protein and protein-nucleic acid interactions have been experimentally characterized, whereas rna-rna interactions have generally only been predicted computationally. here, we describe a high-throughput method to identify intramolecular and intermolecular rna-rna interactions experimentally by cross-linking, ligation, and sequencing of hybrids (clash). as validation, we identified 39 known target sites for box c/d modification-guide small nucleolar rnas (snornas) on the yeast pre-rr ...201121610164
the role of the precursor structure in the biogenesis of microrna.the human genome contains more than 1,000 microrna (mirna) genes, which are transcribed mainly by rna polymerase ii. the canonical pathway of mirna biogenesis includes the nuclear processing of primary transcripts (pri-mirnas) by the ribonuclease drosha and further cytoplasmic processing of pre-mirnas by the ribonuclease dicer. this review discusses the issue of mirna end heterogeneity generated primarily by drosha and dicer cleavage and focuses on the structural aspects of the dicer step of mir ...201121607569
insights into the composition and assembly of the membrane arm of plant complex i through analysis of subcomplexes in arabidopsis mutant lines.nadh-ubiquinone oxidoreductase (complex i, ec 1.6.5.3) is the largest complex of the mitochondrial respiratory chain. in eukaryotes, it is composed of more than 40 subunits that are encoded by both the nuclear and mitochondrial genomes. plant complex i differs from the enzyme described in other eukaryotes, most notably due to the large number of plant-specific subunits in the membrane arm of the complex. the elucidation of the assembly pathway of complex i has been a long-standing research aim i ...201121606486
hcv ires domain iib affects the configuration of coding rna in the 40s subunit's decoding groove.hepatitis c virus (hcv) uses a structured internal ribosome entry site (ires) rna to recruit the translation machinery to the viral rna and begin protein synthesis without the ribosomal scanning process required for canonical translation initiation. different ires structural domains are used in this process, which begins with direct binding of the 40s ribosomal subunit to the ires rna and involves specific manipulation of the translational machinery. we have found that upon initial 40s subunit b ...201121606179
expression, purification, and characterisation of dehydroquinate synthase from pyrococcus furiosus.dehydroquinate synthase (dhqs) catalyses the second step of the shikimate pathway to aromatic compounds. dhqs from the archaeal hyperthermophile pyrococcus furiosus was insoluble when expressed in escherichia coli but was partially solubilised when kcl was included in the cell lysis buffer. a purification procedure was developed, involving lysis by sonication at 30°c followed by a heat treatment at 70°c and anion exchange chromatography. purified recombinant p. furiosus dhqs is a dimer with a su ...201121603259
the evolution of respiratory chain complex i from a smaller last common ancestor consisting of 11 protein subunits.the nadh:quinone oxidoreductase (complex i) has evolved from a combination of smaller functional building blocks. chloroplasts and cyanobacteria contain a complex i-like enzyme having only 11 subunits. this enzyme lacks the n-module which harbors the nadh binding site and the flavin and iron-sulfur cluster prosthetic groups. a complex i-homologous enzyme found in some archaea contains an f(420) dehydrogenase subunit denoted as fpof rather than the n-module. in the present study, all currently av ...201121597881
structure of the pilm-piln inner membrane type iv pilus biogenesis complex from thermus thermophilus.type iv pili are surface-exposed filaments which extend from a variety of bacterial pathogens and play a major role in pathogenesis, motility and dna uptake. here we present the crystal structure of a complex between a cytoplasmic component of the type iv pilus biogenesis system from thermus thermophilus, pilm, in complex with a peptide derived from the cytoplasmic portion of the inner membrane protein piln. pilm also binds atp, and its structure is most similar to the actin-like protein ftsa. p ...201121596754
tmrna on its way through the ribosome: two steps of resume, and what next?trans-translation is a universal quality-control process eubacteria use to degrade incompletely synthesized proteins and rescue ribosome stalled on defective mrnas. this process is facilitated by a ribonucleoprotein complex composed of transfer-messenger rna (tmrna)-a chimera made of a trna-like molecule and a short open reading frame (orf) -and small protein b (smpb). determination of the structure of tmrna and smpb in complex with the ribosome, at the stage when translation has resumed on tmrn ...201121593606
bis{μ-4,4'-dimeth-oxy-2,2'-[propane-1,2-diylbis(nitrilo-methyl-idyne)]diphenolato}bis-({4,4'-dimeth-oxy-2,2'-[propane-1,2-diylbis(nitrilo-methyl-idyne)]diphenol}manganese(iii)) bis-(hexa-fluorido-phosphate).in the title complex, [mn(2)(c(19)h(20)n(2)o(4))(2)(c(19)h(22)n(2)o(4))(2)](pf(6))(2), the mn(iii) ion is coordinated by two o [mn-o = 1.855 (2) and 1.887 (2) å] and two n [mn-n = 1.982 (3) and 1.977 (3) å] atoms from the tetra-dentate schiff base ligand and a coordinated axial ligand [mn-o = 2.129 (2) å]. the centrosymmetric dimer contains two jahn-teller-distorted mn(iii) ions, each in a nearly octa-hedral geometry, connected through two phenolate bridges from two ligands. there are two stereo ...200921583304
unsuspected diversity of arsenite-oxidizing bacteria as revealed by widespread distribution of the aoxb gene in prokaryotes.in this study, new strains were isolated from an environment with elevated arsenic levels, sainte-marie-aux-mines (france), and the diversity of aoxb genes encoding the arsenite oxidase large subunit was investigated. the distribution of bacterial aoxb genes is wider than what was previously thought. aoxb subfamilies characterized by specific signatures were identified. an exhaustive analysis of aoxb sequences from this study and from public databases shows that horizontal gene transfer has like ...201121571879
in medicago truncatula, water deficit modulates the transcript accumulation of components of small rna pathways.small rnas (srnas) are 20-24 nucleotide (nt) rnas and are involved in plant development and response to abiotic stresses. plants have several srna pathways implicated in the transcriptional and post-transcriptional silencing of gene expression. two key enzyme families common to all pathways are the dicer-like (dcl) proteins involved in srnas maturation and the argonautes (agos) involved in the targeting and functional action of srnas. post-transcriptional silencing mediated by agos may occur by ...201121569262
structure and activity of a novel archaeal β-casp protein with n-terminal kh domains.mth1203, a β-casp metallo-β-lactamase family nuclease from the archaeon methanothermobacter thermautotrophicus, was identified as a putative nuclease that might contribute to rna processing. the crystal structure of mth1203 reveals that, in addition to the metallo-β-lactamase nuclease and the β-casp domains, it contains two contiguous kh domains that are unique to mth1203 and its orthologs. rna-binding experiments indicate that mth1203 preferentially binds u-rich sequences with a dissociation co ...201121565697
secretins: dynamic channels for protein transport across membranes.secretins form megadalton bacterial-membrane channels in at least four sophisticated multiprotein systems that are crucial for translocation of proteins and assembled fibers across the outer membrane of many species of bacteria. secretin subunits contain multiple domains, which interact with numerous other proteins, including pilotins, secretion-system partner proteins, and exoproteins. our understanding of the structure of secretins is rapidly progressing, and it is now recognized that features ...201121565514
trinuclear metal clusters in catalysis by terpenoid synthases.terpenoid synthases are ubiquitous enzymes that catalyze the formation of structurally and stereochemically diverse isoprenoid natural products. many isoprenoid coupling enzymes and terpenoid cyclases from bacteria, fungi, protists, plants, and animals share the class i terpenoid synthase fold. despite generally low amino acid sequence identity among these examples, class i terpenoid synthases contain conserved metal binding motifs that coordinate to a trinuclear metal cluster. this cluster not ...201021562622
structure and function of a membrane component secdf that enhances protein export.protein translocation across the bacterial membrane, mediated by the secretory translocon secyeg and the seca atpase, is enhanced by proton motive force and membrane-integrated secdf, which associates with secyeg. the role of secdf has remained unclear, although it is proposed to function in later stages of translocation as well as in membrane protein biogenesis. here, we determined the crystal structure of thermus thermophilus secdf at 3.3 å resolution, revealing a pseudo-symmetrical, 12-helix ...201121562494
a bioinformatics classifier and database for heme-copper oxygen reductases.heme-copper oxygen reductases (hcos) are the last enzymatic complexes of most aerobic respiratory chains, reducing dioxygen to water and translocating up to four protons across the inner mitochondrial membrane (eukaryotes) or cytoplasmatic membrane (prokaryotes). the number of completely sequenced genomes is expanding exponentially, and concomitantly, the number and taxonomic distribution of hco sequences. these enzymes were initially classified into three different types being this classificati ...201121559461
crystal structures of burkholderia cenocepacia dihydropteroate synthase in the apo-form and complexed with the product 7,8-dihydropteroate.abstract:201121554707
inactivation of the dna repair genes muts, mutl or the anti-recombination gene muts2 leads to activation of vitamin b(1) biosynthesis genes.oxidative stress generates harmful reactive oxygen species (ros) that attack biomolecules including dna. in living cells, there are several mechanisms for detoxifying ros and repairing oxidatively-damaged dna. in this study, transcriptomic analyses clarified that disruption of dna repair genes muts and mutl, or the anti-recombination gene muts2, in thermus thermophilus hb8, induces the biosynthesis pathway for vitamin b(1), which can serve as an ros scavenger. in addition, disruption of muts, mu ...201121552516
the 2'-oh group of the peptidyl-trna stabilizes an active conformation of the ribosomal ptc.the ribosome accelerates the rate of peptidyl transfer by >10(6)-fold relative to the background rate. a widely accepted model for this rate enhancement invokes entropic effects whereby the ribosome and the 2'-oh of the peptidyl-trna substrate precisely position the reactive moieties through an extensive network of hydrogen bonds that allows proton movement through them. some studies, however, have called this model into question because they find the 2'-oh of the peptidyl-trna to be dispensable ...201121552203
mitochondrial targeting of human nadh dehydrogenase (ubiquinone) flavoprotein 2 (ndufv2) and its association with early-onset hypertrophic cardiomyopathy and encephalopathy.abstract: background: nadh dehydrogenase (ubiquinone) flavoprotein 2 (ndufv2), containing one iron sulfur cluster ([2fe-2s] binuclear cluster n1a), is one of the core nuclear-encoded subunits existing in human mitochondrial complex i. defects in this subunit have been associated with parkinson's disease, alzheimer's disease, bipolar disorder, and schizophrenia. the aim of this study is to examine the mitochondrial targeting of ndufv2 and dissect the pathogenetic mechanism of one human deletion m ...201121548921
isolation of xylose isomerases by sequence- and function-based screening from a soil metagenome library.abstract: background: xylose isomerase (xi) catalyses the isomerization of xylose to xylulose in bacteria and some fungi. currently, only a limited number of xi genes have been functionally expressed in saccharomyces cerevisiae, the microorganism of choice for lignocellulosic ethanol production. the objective of the present study was to search for novel xi genes in the vastly diverse microbial habitat present in soil. as the exploitation of microbial diversity is impaired by the ability to culti ...201121545702
crystallization and preliminary x-ray diffraction analysis of transaldolase from thermoplasma acidophilum.the metabolic enzyme transaldolase from thermoplasma acidophilum was recombinantly expressed in escherichia coli and could be crystallized in two polymorphic forms. crystals were grown by the hanging-drop vapour-diffusion method using peg 6000 as precipitant. native data sets for crystal forms 1 and 2 were collected in-house to resolutions of 3.0 and 2.7 å, respectively. crystal form 1 belonged to the orthorhombic space group c222(1) with five monomers per asymmetric unit and crystal form 2 belo ...201121543867
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