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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
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
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
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
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
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
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
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
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
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
difference in the distribution pattern of substrate enzymes in the metabolic network of escherichia coli, according to chaperonin requirement.abstract:201121702926
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
gln-trnagln synthesis in a dynamic transamidosome from helicobacter pylori, where glurs2 hydrolyzes excess glu-trnagln.in many bacteria and archaea, an ancestral pathway is used where asparagine and glutamine are formed from their acidic precursors while covalently linked to trna(asn) and trna(gln), respectively. stable complexes formed by the enzymes of these indirect trna aminoacylation pathways are found in several thermophilic organisms, and are called transamidosomes. we describe here a transamidosome forming gln-trna(gln) in helicobacter pylori, an ε-proteobacterium pathogenic for humans; this transamidoso ...201121813455
high resolution structure of the ba3 cytochrome c oxidase from thermus thermophilus in a lipidic environment.the fundamental chemistry underpinning aerobic life on earth involves reduction of dioxygen to water with concomitant proton translocation. this process is catalyzed by members of the heme-copper oxidase (hco) superfamily. despite the availability of crystal structures for all types of hco, the mode of action for this enzyme is not understood at the atomic level, namely how vectorial h(+) and e(-) transport are coupled. toward addressing this problem, we report wild type and a120f mutant structu ...201121814577
noncanonical amino acids in the interrogation of cellular protein synthesis.proteins in living cells can be made receptive to bioorthogonal chemistries through metabolic labeling with appropriately designed noncanonical amino acids (ncaas). in the simplest approach to metabolic labeling, an amino acid analog replaces one of the natural amino acids specified by the protein's gene (or genes) of interest. through manipulation of experimental conditions, the extent of the replacement can be adjusted. this approach, often termed residue-specific incorporation, allows the nca ...201121815659
polyphosphate--an ancient energy source and active metabolic regulator.there are a several molecules on earth that effectively store energy within their covalent bonds, and one of these energy-rich molecules is polyphosphate. in microbial cells, polyphosphate granules are synthesised for both energy and phosphate storage and are degraded to produce nucleotide triphosphate or phosphate. energy released from these energetic carriers is used by the cell for production of all vital molecules such as amino acids, nucleobases, sugars and lipids. polyphosphate chains dire ...201121816086
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 ...201121821893
expression, purification and preliminary crystallographic analysis of o-acetylhomoserine sulfhydrylase from mycobacterium tuberculosis.the gene product of the open reading frame rv3340 from mycobacterium tuberculosis is annotated as encoding a probable o-acetylhomoserine (oah) sulfhydrylase (metc), an enzyme that catalyzes the last step in the biosynthesis of methionine, which is an essential amino acid in bacteria and plants. following overexpression in escherichia coli, the m. tuberculosis metc enzyme was purified and crystallized using the hanging-drop vapor-diffusion method. native diffraction data were collected from cryst ...201121821905
expression, purification, crystallization and preliminary crystallographic analysis of cg1458: a novel oxaloacetate decarboxylase from corynebacterium glutamicum.oxaloacetate decarboxylase catalyses the decarboxylation of oxaloacetate to pyruvate and co(2). recently, the corynebacterium glutamicum gene product cg1458 was determined to be a soluble oxaloacetate decarboxylase. to elucidate the mechanism of oxaloacetate decarboxylation by cg1458, recombinant cg1458 was purified and crystallized. the best crystal was grown from 0.2ôçàm mgcl(2), 0.1ôçàm bis-tris ph 6.0, 25%(w/v) polyethylene glycol 3350 using the hanging-drop method. the crystals belonged to ...201121821907
a single methyltransferase yefa (rlmcd) catalyses both m5u747 and m5u1939 modifications in bacillus subtilis 23s rrna.methyltransferases that use s-adenosylmethionine (adomet) as a cofactor to catalyse 5-methyl uridine (m(5)u) formation in trnas and rrnas are widespread in bacteria and eukaryota, and are also found in certain archaea. these enzymes belong to the cog2265 cluster, and the gram-negative bacterium escherichia coli possesses three paralogues. these comprise the methyltransferases trma that targets u54 in trnas, rlmc that modifies u747 in 23s rrna and rlmd that is specific for u1939 in 23s rrna. the ...201121824914
unveiling the structural basis for translational ambiguity tolerance in a human fungal pathogen.in a restricted group of opportunistic fungal pathogens the universal leucine cug codon is translated both as serine (97%) and leucine (3%), challenging the concept that translational ambiguity has a negative impact in living organisms. to elucidate the molecular mechanisms underlying the in vivo tolerance to a nonconserved genetic code alteration, we have undertaken an extensive structural analysis of proteins containing cug-encoded residues and solved the crystal structures of the two natural ...201121825144
a computational study of elongation factor g (efg) duplicated genes: diverged nature underlying the innovation on the same structural template.elongation factor g (efg) is a core translational protein that catalyzes the elongation and recycling phases of translation. a more complex picture of efg's evolution and function than previously accepted is emerging from analyzes of heterogeneous efg family members. whereas the gene duplication is postulated to be a prominent factor creating functional novelty, the striking divergence between efg paralogs can be interpreted in terms of innovation in gene function.201121829651
structural classification and properties of ketoacyl synthases.ketoacyl synthases (kss) catalyze condensing reactions combining acyl-coa or acyl-acyl carrier protein (acp) with malonyl-coa to form 3-ketoacyl-coa, or with malonyl-acp to form 3-ketoacyl-acp. in each case the resulting acyl chain is two carbon atoms longer than before, and co(2) and either coa or acp are formed. kss also join other activated molecules in the polyketide synthesis cycle. our classification of kss by their primary and tertiary structures instead of by their substrates and the rea ...201121830247
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 ...201121831041
rnase h-dependent pcr (rhpcr): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers.abstract: background: the polymerase chain reaction (pcr) is commonly used to detect the presence of nucleic acid sequences both in research and diagnostic settings. while high specificity is often achieved, biological requirements sometimes require that primers are placed in suboptimal locations which lead to problems with the formation of primer dimers and/or misamplification of homologous sequences. results: pyrococcus abyssi (p.a.) rnase h2 was used to enable pcr to be performed using blocke ...201121831278
engineering the respiratory complex i to an energy-converting nadph:ubiquinone oxidoreductase.the respiratory complex i couples the electron transfer from nadh to ubiquinone with a translocation of protons across the membrane. its nucleotide binding site is made up of a unique rossmann fold to accommodate the binding of the substrate nadh and of the primary electron acceptor flavin mononucleotide. binding of nadh includes interactions of the hydroxyl groups of the adenosine ribose with a conserved glutamic acid residue. structural analysis revealed that due to steric hinderance and elect ...201121832062
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 ...201121833314
mechanisms and evolution of oxidative sulfur metabolism in green sulfur bacteria.green sulfur bacteria (gsb) constitute a closely related group of photoautotrophic and thiotrophic bacteria with limited phenotypic variation. they typically oxidize sulfide and thiosulfate to sulfate with sulfur globules as an intermediate. based on genome sequence information from 15 strains, the distribution and phylogeny of enzymes involved in their oxidative sulfur metabolism was investigated. at least one homolog of sulfide:quinone oxidoreductase (sqr) is present in all strains. in all sul ...201121833341
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 ...201121835926
cbpa acts as a modulator of hspr repressor dna binding activity in helicobacter pylori.the ability of pathogens to cope with disparate environmental stresses is a crucial feature for bacterial survival and for the establishment of a successful infection and colonization of the host; in this respect, chaperones and heat-shock proteins (hsps) play a fundamental role in host-pathogen interactions. in helicobacter pylori, the expression of the major hsps is tightly regulated through dedicated transcriptional repressors (named hspr and hrca), as well as via a groesl-dependent post-tran ...201121840971
mechanistic analysis of trehalose synthase from mycobacterium smegmatis.trehalose synthase (tres) catalyzes the reversible interconversion of maltose and trehalose and has been recently shown to function primarily in the mobilisation of trehalose as a glycogen precursor. consequently the mechanism of this intriguing isomerase is of both academic and potential pharmacological interest. tres catalyzes the hydrolytic cleavage of +¦-aryl glucosides, as well as +¦-glucosyl fluoride, thereby allowing facile continuous assays. reaction of tres with 5-fluoroglycosyl fluorid ...201121840994
the elusive middle domain of hsp104 and clpb: location and function.hsp104 in yeast and clpb in bacteria are homologous, hexameric aaa+ proteins and hsp100 chaperones, which function in the stress response as ring-translocases that drive protein disaggregation and reactivation. both hsp104 and clpb contain a distinctive coiled-coil middle domain (md) inserted in the first aaa+ domain, which distinguishes them from other aaa+ proteins and hsp100 family members. here, we focus on recent developments concerning the location and function of the md in these hexameric ...201121843558
the elusive middle domain of hsp104 and clpb: location and function.hsp104 in yeast and clpb in bacteria are homologous, hexameric aaa+ proteins and hsp100 chaperones, which function in the stress response as ring-translocases that drive protein disaggregation and reactivation. both hsp104 and clpb contain a distinctive coiled-coil middle domain (md) inserted in the first aaa+ domain, which distinguishes them from other aaa+ proteins and hsp100 family members. here, we focus on recent developments concerning the location and function of the md in these hexameric ...201121843558
substrate trna recognition mechanism of a multi-site-specific trna methyltransferase, aquifex aeolicus trm1, based on the x-ray crystal structure.archaeal and eukaryotic trna (n(2)-, n(2)-guanine) dimethyltransferase (trm1) produces n(2)-, n(2)-dimethylguanine at position 26 in trna. in contrast, trm1 from aquifex aeolicus, a hyper-thermophilic eubacterium, modifies g27 as well as g26. here, a gel-mobility shift assay revealed that the t-arm in trna is the binding site of a. aeolicus trm1. to address the multi-site specificity, we performed an x-ray crystal structure study. the overall structure of a. aeolicus trm1 is similar to that of a ...201121844194
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 ...201121844375
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 ...201121845105
insights into folate/fad-dependent trna methyltransferase mechanism: role of two highly conserved cysteines in catalysis.the flavoprotein trmfo methylates specifically the c5 carbon of the highly conserved uridine 54 in trnas. contrary to most methyltransferases, the 1-carbon unit transferred by trmfo derives from 5,10-methylenetetrahydrofolate and not from s-adenosyl-l-methionine. the enzyme also employs the fad hydroquinone as a reducing agent of the c5 methylene u54-trna intermediate in vitro. by analogy with the catalytic mechanism of thymidylate synthase thya, a conserved cysteine located near the fad isoallo ...201121846722
Structural analysis of the Ras-like G protein MglA and its cognate GAP MglB and implications for bacterial polarity.The bacterium Myxococcus xanthus uses a G protein cycle to dynamically regulate the leading/lagging pole polarity axis. The G protein MglA is regulated by its GTPase-activating protein (GAP) MglB, thus resembling Ras family proteins. Here, we show structurally and biochemically that MglA undergoes a dramatic, GDP-GTP-dependent conformational change involving a screw-type forward movement of the central ß2-strand, never observed in any other G protein. This movement and complex formation with Mgl ...201121847100
tolerance to changes in membrane lipid composition as a selected trait of membrane proteins.membrane lipid composition can vary dramatically across the three domains of life and even within single organisms. here we review evidence that the lipid-exposed surfaces of membrane proteins have generally evolved to maintain correct structure and function in the face of major changes in lipid composition. such tolerance has allowed evolution to extensively remodel membrane lipid compositions during the emergence of new species without having to extensively remodel the associated membrane prot ...201121848311
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 ...201121849506
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 ...201121856301
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- ...201121858139
Properties and crystal structure of methylenetetrahydrofolate reductase from Thermus thermophilus HB8.Methylenetetrahydrofolate reductase (MTHFR) is one of the enzymes involved in homocysteine metabolism. Despite considerable genetic and clinical attention, the reaction mechanism and regulation of this enzyme are not fully understood because of difficult production and poor stability. While recombinant enzymes from thermophilic organisms are often stable and easy to prepare, properties of thermostable MTHFRs have not yet been reported.201121858212
new target for inhibition of bacterial rna polymerase: 'switch region'.a new drug target - the 'switch region' - has been identified within bacterial rna polymerase (rnap), the enzyme that mediates bacterial rna synthesis. the new target serves as the binding site for compounds that inhibit bacterial rna synthesis and kill bacteria. since the new target is present in most bacterial species, compounds that bind to the new target are active against a broad spectrum of bacterial species. since the new target is different from targets of other antibacterial agents, com ...201121862392
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 ...201121862575
enzymatic synthesis of long double-stranded dna labeled with haloderivatives of nucleobases in a precisely pre-determined sequence.restriction endonucleases are widely applied in recombinant dna technology. among them, enzymes of class iis, which cleave dna beyond recognition sites, are especially useful. we use bsai enzyme for the pinpoint introduction of halogen nucleobases into dna. this has been done for the purpose of anticancer radio- and phototherapy that is our long-term objective.201121864341
termination of protein synthesis in mammalian mitochondria.all mechanisms of protein synthesis can be considered in four stages: initiation, elongation, termination, and ribosome recycling. remarkable progress has been made in understanding how these processes are mediated in the cytosol of many species; however, details of organellar protein synthesis remain sketchy. this is an important omission, as defects in human mitochondrial translation are known to cause disease and may contribute to the aging process itself. in this minireview, we focus on the ...201121873426
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 ...201121876144
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 ...201121878618
the universally conserved prokaryotic gtpases.members of the large superclass of p-loop gtpases share a core domain with a conserved three-dimensional structure. in eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. as targets of mutation and toxins, gtpases are involved in the pathogenesis of cancer and infectious diseases. in prokaryotes also, it is hard to overestimate the importance of gtpases in cell physiology. nu ...201121885683
tracing the trail of protons through complex i of the mitochondrial respiratory chain.mitochondria are the structures that produce the bulk part of the cellular energy currency atp, which drives numerous energy requiring processes in the cell. this process involves a series of large enzyme complexes--the respiratory chain--that couples the transfer of electrons to the creation of a concentration gradient of protons across the inner mitochondrial membrane, which drives atp synthesis. complex i (or nadh-quinone oxidoreductase) is the largest and by far the most complicated of the r ...201121886481
Crystal structures of an archaeal class II DNA photolyase and its complex with UV-damaged duplex DNA.Class II photolyases ubiquitously occur in plants, animals, prokaryotes and some viruses. Like the distantly related microbial class I photolyases, these enzymes repair UV-induced cyclobutane pyrimidine dimer (CPD) lesions within duplex DNA using blue/near-UV light. Methanosarcina mazei Mm0852 is a class II photolyase of the archaeal order of Methanosarcinales, and is closely related to plant and metazoan counterparts. Mm0852 catalyses light-driven DNA repair and photoreduction, but in contrast ...201121892138
ribonuclease j: how to lead a double life. 201121893280
Is the sequence-specific binding of aminoacyl-tRNAs by EF-Tu universal among bacteria?Three base pairs in the T-stem are primarily responsible for the sequence-specific interaction of tRNA with Escherichia coli and Thermus thermophilus EF-Tu. While the amino acids on the surface of EF-Tu that contact aminoacyl-tRNA (aa-tRNA) are highly conserved among bacteria, the T-stem sequences of individual tRNA are variable, making it unclear whether or not this protein-nucleic acid interaction is also sequence specific in other bacteria. We propose and validate a thermodynamic model that p ...201121893586
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 ...201121898642
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.201121899737
structural basis for leucine-induced allosteric activation of glutamate dehydrogenase.glutamate dehydrogenase (gdh) catalyzes reversible conversion between glutamate and 2-oxoglutarate using nad(p)(h) as a coenzyme. although mammalian gdh is regulated by gtp through the antenna domain, little is known about the mechanism of allosteric activation by leucine. an extremely thermophilic bacterium, thermus thermophilus, possesses gdh with a unique subunit configuration composed of two different subunits, gdha (regulatory subunit) and gdhb (catalytic subunit). t. thermophilus gdh is un ...201121900230
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.201121903180
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 ...201121903932
structures of phosphopantetheine adenylyltransferase from burkholderia pseudomallei.phosphopantetheine adenylyltransferase (ppat) catalyzes the fourth of five steps in the coenzyme a biosynthetic pathway, reversibly transferring an adenylyl group from atp onto 4'-phosphopantetheine to yield dephospho-coenzyme a and pyrophosphate. burkholderia pseudomallei is a soil- and water-borne pathogenic bacterium and the etiologic agent of melioidosis, a potentially fatal systemic disease present in southeast asia. two crystal structures are presented of the ppat from b. pseudomallei with ...201121904046
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 ...201121904048
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