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expression of reck and matrix metalloproteinase-2 in ameloblastoma.ameloblastoma is a frequent odontogenic benign tumor characterized by local invasiveness, high risk of recurrence and occasional metastasis and malignant transformation. matrix metalloproteinase-2 (mmp-2) promotes tumor invasion and progression by destroying the extracellular matrix (ecm) and basement membrane. for this proteolytic activity, the endogenous inhibitor is reversion-inducing cysteine rich protein with kazal motifs (reck). the aim of this study was to characterize the relationship be ...200919995435
the structural basis for mrna recognition and cleavage by the ribosome-dependent endonuclease rele.translational control is widely used to adjust gene expression levels. during the stringent response in bacteria, mrna is degraded on the ribosome by the ribosome-dependent endonuclease, rele. the molecular basis for recognition of the ribosome and mrna by rele and the mechanism of cleavage are unknown. here, we present crystal structures of e. coli rele in isolation (2.5 a) and bound to programmed thermus thermophilus 70s ribosomes before (3.3 a) and after (3.6 a) cleavage. rele occupies the a ...200920005802
dissecting the role of critical residues and substrate preference of a fatty acyl-coa synthetase (fadd13) of mycobacterium tuberculosis.newly emerging multi-drug resistant strains of mycobacterium tuberculosis (m.tb) severely limit the treatment options for tuberculosis (tb); hence, new antitubercular drugs are urgently needed. the myma operon is essential for the virulence and intracellular survival of m.tb and thus represents an attractive target for the development of new antitubercular drugs. this study is focused on the structure-function relationship of fatty acyl-coa synthetase (fadd13, rv3089) belonging to the myma opero ...200920027301
crystal and solution structures of a prokaryotic m16b peptidase: an open and shut case.the m16 family of zinc peptidases comprises a pair of homologous domains that form two halves of a "clam-shell" surrounding the active site. the m16a and m16c subfamilies form one class ("peptidasomes"): they degrade 30-70 residue peptides, and adopt both open and closed conformations. the eukaryotic m16b subfamily forms a second class ("processing proteases"): they adopt a single partly-open conformation that enables them to cleave signal sequences from larger proteins. here, we report the solu ...200919913481
the chlamydial functional homolog of ksga confers kasugamycin sensitivity to chlamydia trachomatis and impacts bacterial fitness.rrna adenine dimethyltransferases, represented by the escherichia coli ksga protein, are highly conserved phylogenetically and are generally not essential for growth. they are responsible for the post-transcriptional transfer of two methyl groups to two universally conserved adenosines located near the 3'end of the small subunit rrna and participate in ribosome maturation. all sequenced genomes of chlamydia reveal a ksga homolog in each species, including c. trachomatis. yet absence of a s-adeno ...200920043826
a novel dimerization motif in the c-terminal domain of the thermus thermophilus dead box helicase hera confers substantial flexibility.dead box helicases are involved in nearly all aspects of rna metabolism. they share a common helicase core, and may comprise additional domains that contribute to rna binding. the thermus thermophilus helicase hera is the first dimeric dead box helicase. crystal structures of hera fragments reveal a bipartite c-terminal domain with a novel dimerization motif and an rna-binding module. we provide a first glimpse on the additional rna-binding module outside the hera helicase core. the dimerization ...200919050012
the conserved lysine69 residue plays a catalytic role in mycobacterium tuberculosis shikimate dehydrogenase.the shikimate pathway is an attractive target for the development of antitubercular agents because it is essential in mycobacterium tuberculosis, the causative agent of tuberculosis, but absent in humans. m. tuberculosis aroe-encoded shikimate dehydrogenase catalyzes the forth reaction in the shikimate pathway. structural and functional studies indicate that lysine69 may be involved in catalysis and/or substrate binding in m. tuberculosis shikimate dehydrogenase. investigation of the kinetic pro ...200919917104
h135a controls the redox activity of the sco copper center. kinetic and spectroscopic studies of the his135ala variant of bacillus subtilis sco.sco-like proteins contain copper bound by two cysteines and a histidine residue. although their function is still incompletely understood, there is a clear involvement with the assembly of cytochrome oxidases that contain the cu(a) center in subunit 2, possibly mediating the transfer of copper into the cu(a) binuclear site. we are investigating the reaction chemistry of bsco, the homologue from bacillus subtilis. our studies have revealed that bsco behaves more like a redox protein than a metall ...200919921776
structure of an n-terminally truncated nudix hydrolase dr2204 from deinococcus radiodurans.nudix pyrophosphatases are a well represented protein family in the deinococcus radiodurans genome. these hydrolases, which are known to be enzymatically active towards nucleoside diphosphate derivatives, play a role in cleansing the cell pool of potentially deleterious damage products. here, the structure of dr2204, the only adp-ribose pyrophosphatase in the d. radiodurans genome that is known to be active towards flavin adenosine dinucleotide (fad), is presented at 2.0 angstrom resolution.200919923723
expression, purification and crystallization of an archaeal-type phosphoenolpyruvate carboxylase.an archaeal-type phosphoenolpyruvate carboxylase (pepca) from clostridium perfringens has been expressed in escherichia coli in a soluble form with an amino-terminal his tag. the recombinant protein is enzymatically active and two crystal forms have been obtained. complete diffraction data extending to 3.13 angstrom resolution have been measured from a crystal soaked in kau(cn)(2), using radiation at a wavelength just above the au l(iii) edge. the asymmetric unit contains two tetramers of pepca.200919923749
communication between r481 and cu(b) in cytochrome bo(3) ubiquinol oxidase from escherichia coli.the r481 residue of cytochrome bo(3) ubiquinol oxidase from e. coli is highly conserved in the heme-copper oxidase superfamily. it has been postulated to serve as part of a proton loading site that regulates proton translocation across the protein matrix of the enzyme. along these lines, proton pumping efficiency has been demonstrated to be abolished in many r481 mutants. however, r481q in bo(3) from e. coli has been shown to be fully functional, implying that the positive charge of the arginine ...200919928831
coupling atp utilization to protein remodeling by clpb, a hexameric aaa+ protein.clpb and hsp104 are members of the aaa+ (atpases associated with various cellular activities) family of proteins and are molecular machines involved in thermotolerance. they are hexameric proteins containing 12 atp binding sites with two sites per protomer. clpb and hsp104 possess some innate protein remodeling activities; however, they require the collaboration of the dnak/hsp70 chaperone system to disaggregate and reactivate insoluble aggregated proteins. we investigated the mechanism by which ...200919940245
cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.aspartokinase (ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ask network or from alternative pathways. ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. two subhomology divisions, ask(alpha) and ask(beta), have been recognize ...200919946135
a signal relay between ribosomal protein s12 and elongation factor ef-tu during decoding of mrna.codon recognition by aminoacyl-trna on the ribosome triggers a process leading to gtp hydrolysis by elongation factor tu (ef-tu) and release of aminoacyl-trna into the a site of the ribosome. the nature of this signal is largely unknown. here, we present genetic evidence that a specific set of direct interactions between ribosomal protein s12 and aminoacyl-trna, together with contacts between s12 and 16s rrna, provide a pathway for the signaling of codon recognition to ef-tu. three novel amino a ...200919095621
mitochondrial dna damage in iron overload.chronic iron overload has slow and insidious effects on heart, liver, and other organs. because iron-driven oxidation of most biologic materials (such as lipids and proteins) is readily repaired, this slow progression of organ damage implies some kind of biological "memory." we hypothesized that cumulative iron-catalyzed oxidant damage to mtdna might occur in iron overload, perhaps explaining the often lethal cardiac dysfunction. real time pcr was used to examine the "intactness" of mttdna in cu ...200919095657
redox characterization of the fes protein mitoneet and impact of thiazolidinedione drug binding.mitoneet is a small mitochondrial protein that has been identified recently as a target for the thiazolidinedione (tzd) class of diabetes drugs. mitoneet also binds a unique three-cys- and one-his-ligated [corrected] [2fe-2s] cluster. here we use protein film voltammetry (pfv) as a means to probe the redox properties of mitoneet and demonstrate the direct impact of tzd drug binding upon the redox chemistry of the fes cluster. when tzds bind, the midpoint potential at ph 7 is lowered by more than ...200919791753
mg(2+)-dependent gating of bacterial mgte channel underlies mg(2+) homeostasis.the mgte family of mg(2+) transporters is ubiquitously distributed in all phylogenetic domains. recent crystal structures of the full-length mgte and of its cytosolic domain in the presence and absence of mg(2+) suggested a mg(2+)-homeostasis mechanism, in which the mgte cytosolic domain acts as a 'mg(2+) sensor' to regulate the gating of the ion-conducting pore in response to the intracellular mg(2+) concentration. however, complementary functional analyses to confirm the proposed model have be ...200919798051
crystal structure of ynje from escherichia coli, a sulfurtransferase with three rhodanese domains.rhodaneses/sulfurtransferases are ubiquitous enzymes that catalyze the transfer of sulfane sulfur from a donor molecule to a thiophilic acceptor via an active site cysteine that is modified to a persulfide during the reaction. here, we present the first crystal structure of a triple-domain rhodanese-like protein, namely ynje from escherichia coli, in two states where its active site cysteine is either unmodified or present as a persulfide. compared to well-characterized tandem domain rhodaneses, ...200919798741
multiple biochemical and morphological factors underlie the production of methylketones in tomato trichomes.genetic analysis of interspecific populations derived from crosses between the wild tomato species solanum habrochaites f. sp. glabratum, which synthesizes and accumulates insecticidal methylketones (mk), mostly 2-undecanone and 2-tridecanone, in glandular trichomes, and cultivated tomato (solanum lycopersicum), which does not, demonstrated that several genetic loci contribute to mk metabolism in the wild species. a strong correlation was found between the shape of the glandular trichomes and th ...200919801397
two-dimensional pulsed electron spin resonance characterization of 15n-labeled archaeal rieske-type ferredoxin.two-dimensional electron spin-echo envelope modulation (eseem) analysis of the uniformly (15)n-labeled archaeal rieske-type [2fe-2s] ferredoxin (arf) from sulfolobus solfataricus p1 has been conducted in comparison with the previously characterized high-potential protein homologs. major differences among these proteins were found in the hyperfine sublevel correlation (hyscore) lineshapes and intensities of the signals in the (++) quadrant, which are contributed from weakly coupled (non-coordinat ...200919804777
the cytochrome ba3 oxygen reductase from thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping.the heme-copper oxygen reductases are redox-driven proton pumps that generate a proton motive force in both prokaryotes and mitochondria. these enzymes have been divided into 3 evolutionarily related groups: the a-, b- and c-families. most experimental work on proton-pumping mechanisms has been performed with members of the a-family. these enzymes require 2 proton input pathways (d- and k-channels) to transfer protons used for oxygen reduction chemistry and for proton pumping, with the d-channel ...200919805275
structure of a trna-dependent kinase essential for selenocysteine decoding.compared to bacteria, archaea and eukaryotes employ an additional enzyme for the biosynthesis of selenocysteine (sec), the 21(st) natural amino acid (aa). an essential rna-dependent kinase, o-phosphoseryl-trna(sec) kinase (pstk), converts seryl-trna(sec) to o-phosphoseryl-trna(sec), the immediate precursor of selenocysteinyl-trna(sec). the sequence of methanocaldococcus jannaschii pstk (mjpstk) suggests an n-terminal kinase domain (177 aa) followed by a presumed trna binding region (75 aa). the ...200919805283
features of subunit nuom (nd4) in escherichia coli ndh-1: topology and implication of conserved glu144 for coupling site 1.the bacterial h(+)-pumping nadh-quinone oxidoreductase (ndh-1) is an l-shaped membrane-bound enzymatic complex. escherichia coli ndh-1 is composed of 13 subunits (nuoa-n). nuom (nd4) subunit is one of the hydrophobic subunits that constitute the membrane arm of ndh-1 and was predicted to bear 14 helices. we attempted to clarify the membrane topology of nuom by the introduction of histidine tags into different positions by chromosomal site-directed mutagenesis. from the data, we propose a topolog ...200919815558
structural insights into rna processing by the human risc-loading complex.targeted gene silencing by rna interference (rnai) requires loading of a short guide rna (small interfering rna (sirna) or microrna (mirna)) onto an argonaute protein to form the functional center of an rna-induced silencing complex (risc). in humans, argonaute2 (ago2) assembles with the guide rna-generating enzyme dicer and the rna-binding protein trbp to form a risc-loading complex (rlc), which is necessary for efficient transfer of nascent sirnas and mirnas from dicer to ago2. here, using sin ...200919820710
multistart simulated annealing refinement of the crystal structure of the 70s ribosome.a macromolecular x-ray crystal structure is usually represented as a single static model with a single set of temperature factors representing a simple approximation of motion and disorder of the structure. multiconformer representations of small proteins have been shown to better describe anisotropic motion and disorder and improve the quality of their electron density maps. here, we apply multistart simulated annealing crystallographic refinement to a 70s ribosome-rf1 translation termination c ...200919822758
crystal structure of the atpase domain of the human aaa+ protein paraplegin/spg7.paraplegin is an m-aaa protease of the mitochondrial inner membrane that is linked to hereditary spastic paraplegias. the gene encodes an ftsh-homology protease domain in tandem with an aaa+ homology atpase domain. the protein is believed to form a hexamer that uses atpase-driven conformational changes in its aaa-domain to deliver substrate peptides to its protease domain. we present the crystal structure of the aaa-domain of human paraplegin bound to adp at 2.2 a. this enables assignment of the ...200919841671
yeast aep3p is an accessory factor in initiation of mitochondrial translation.initiation of protein synthesis in mitochondria and chloroplasts normally uses a formylated initiator methionyl-trna (fmet-trna(f)(met)). however, mitochondrial protein synthesis in saccharomyces cerevisiae can initiate with nonformylated met-trna(f)(met), as demonstrated in yeast mutants in which the nuclear gene encoding mitochondrial methionyl-trna formyltransferase (fmt1) has been deleted. the role of formylation of the initiator trna is not known, but in vitro formylation increases binding ...200919843529
the structure of staphylococcus aureus phosphopantetheine adenylyltransferase in complex with 3'-phosphoadenosine 5'-phosphosulfate reveals a new ligand-binding mode.bacterial phosphopantetheine adenylyltransferase (ppat) catalyzes the penultimate step in the coenzyme a (coa) biosynthetic pathway. it catalyzes the reversible transfer of an adenylyl group from atp to 4'-phosphopantetheine (ppant) to form dephospho-coa (dpcoa) and pyrophosphate. previous structural studies have revealed how several ligands are recognized by bacterial ppats. atp, adp, ppant and dpcoa bind to the same binding site in a highly similar manner, while coa binds to a partially overla ...200919851003
crystallization and preliminary x-ray analysis of mannosyl-3-phosphoglycerate synthase from thermus thermophilus hb27.mannosylglycerate (mg) is a compatible solute that is widespread in marine organisms that are adapted to hot environments, with its intracellular pool generally increasing in response to osmotic stress. these observations suggest that mg plays a relevant role in osmoadaptation and thermoadaptation. the pathways for the synthesis of mg have been characterized in a number of thermophilic and hyperthermophilic organisms. mannosyl-3-phosphoglycerate synthase (mpgs) is a key enzyme in the biosynthesi ...200919851010
allosteric control of catalysis by the f loop of rna polymerase.bacterial rna polymerases (rnaps) undergo coordinated conformational changes during catalysis. in particular, concerted folding of the trigger loop and rearrangements of the bridge helix at the rnap active center have been implicated in nucleotide addition and rnap translocation. at moderate temperatures, the rate of catalysis by rnap from thermophilic thermus aquaticus is dramatically reduced compared with its closest mesophilic relative, deinococcus radiodurans. here, we show that a part of th ...200919855007
the structure of the ribosome with elongation factor g trapped in the posttranslocational state.elongation factor g (ef-g) is a guanosine triphosphatase (gtpase) that plays a crucial role in the translocation of transfer rnas (trnas) and messenger rna (mrna) during translation by the ribosome. we report a crystal structure refined to 3.6 angstrom resolution of the ribosome trapped with ef-g in the posttranslocational state using the antibiotic fusidic acid. fusidic acid traps ef-g in a conformation intermediate between the guanosine triphosphate and guanosine diphosphate forms. the interac ...200919833919
the crystal structure of the ribosome bound to ef-tu and aminoacyl-trna.the ribosome selects a correct transfer rna (trna) for each amino acid added to the polypeptide chain, as directed by messenger rna. aminoacyl-trna is delivered to the ribosome by elongation factor tu (ef-tu), which hydrolyzes guanosine triphosphate (gtp) and releases trna in response to codon recognition. the signaling pathway that leads to gtp hydrolysis upon codon recognition is critical to accurate decoding. here we present the crystal structure of the ribosome complexed with ef-tu and amino ...200919833920
v for victory--a v1-atpase structure revealed. 200919834508
the role of upf0157 in the folding of m. tuberculosis dephosphocoenzyme a kinase and the regulation of the latter by ctp.targeting the biosynthetic pathway of coenzyme a (coa) for drug development will compromise multiple cellular functions of the tubercular pathogen simultaneously. structural divergence in the organization of the penultimate and final enzymes of coa biosynthesis in the host and pathogen and the differences in their regulation mark out the final enzyme, dephosphocoenzyme a kinase (coae) as a potential drug target.200919876400
isolation and characterization of tirandamycins from a marine-derived streptomyces sp.the novel dienoyl tetramic acids tirandamycin c (1) and tirandamycin d (2) with activity against vancomycin-resistant enterococcus faecalis were isolated from the marine environmental isolate streptomyces sp. 307-9, which also produces the previously identified compounds tirandamycins a (3) and b (4). spectroscopic analysis of 1 and 2 indicated structural similarity to 3 and 4, with differences only in the pattern of pendant oxygenation on the bicyclic ketal system. the isolation of these putati ...200919883065
atp-induced conformational changes in hsp70: molecular dynamics and experimental validation of an in silico predicted conformation.the 70 kda heat shock proteins (hsp70s) play important roles in preventing the misfolding of proteins and repairing damage under stress by coupling atp binding and hydrolysis to protein substrate release and binding, respectively. atp binding is believed to induce closing of the hsp70 nucleotide binding domain (nbd) around the nucleotide. we report here a combined computational-experimental study of this open-closed transition. all-atom molecular dynamics simulations were performed for isolated ...200919883127
functional specialization of transcription elongation factors.elongation factors nusg and rfah evolved from a common ancestor and utilize the same binding site on rna polymerase (rnap) to modulate transcription. however, although nusg associates with rnap transcribing most escherichia coli genes, rfah regulates just a few operons containing ops, a dna sequence that mediates rfah recruitment. here, we describe the mechanism by which this specificity is maintained. we observe that rfah action is indeed restricted to those several operons that are devoid of n ...200919096362
functional specialization of transcription elongation factors.elongation factors nusg and rfah evolved from a common ancestor and utilize the same binding site on rna polymerase (rnap) to modulate transcription. however, although nusg associates with rnap transcribing most escherichia coli genes, rfah regulates just a few operons containing ops, a dna sequence that mediates rfah recruitment. here, we describe the mechanism by which this specificity is maintained. we observe that rfah action is indeed restricted to those several operons that are devoid of n ...200919096362
a novel insertion mutation in streptomyces coelicolor ribosomal s12 protein results in paromomycin resistance and antibiotic overproduction.we identified a novel paromomycin resistance-associated mutation in rpsl, caused by the insertion of a glycine residue at position 92, in streptomyces coelicolor ribosomal protein s12. this insertion mutation (gi92) resulted in a 20-fold increase in the paromomycin resistance level. in combination with another s12 mutation, k88e, the gi92 mutation markedly enhanced the production of the blue-colored polyketide antibiotic actinorhodin and the red-colored antibiotic undecylprodigiosin. the gene re ...200919104019
a novel insertion mutation in streptomyces coelicolor ribosomal s12 protein results in paromomycin resistance and antibiotic overproduction.we identified a novel paromomycin resistance-associated mutation in rpsl, caused by the insertion of a glycine residue at position 92, in streptomyces coelicolor ribosomal protein s12. this insertion mutation (gi92) resulted in a 20-fold increase in the paromomycin resistance level. in combination with another s12 mutation, k88e, the gi92 mutation markedly enhanced the production of the blue-colored polyketide antibiotic actinorhodin and the red-colored antibiotic undecylprodigiosin. the gene re ...200919104019
epr evidence of cyanide binding to the mn(mg) center of cytochrome c oxidase: support for cu(a)-mg involvement in proton pumping.we examined the anion binding behavior of the mg(mn) site in cytochrome c oxidase to test a possible role of this center in proton pumping. rhodobacter sphaeroides grown in a mn(ii)-rich medium replaces the intrinsic mg(ii) ion with an epr-detectable mn(ii) ion without change in activity. due to its close proximity and a shared ligand, oxidized cu(a) is spin-coupled to the mn(ii) ion, affecting the epr spectrum. an examination of both bovine and r.s. oxidase crystal structures reveals a hydrogen ...200919108635
characterization of two novel alpha-glucosidases from bifidobacterium breve ucc2003.two alpha-glucosidase-encoding genes (agl1 and agl2) from bifidobacterium breve ucc2003 were identified and characterized. based on their similarity to characterized carbohydrate hydrolases, the agl1 and agl2 enzymes are both assigned to a subgroup of the glycosyl hydrolase family 13, the alpha-1,6-glucosidases (ec 3.2.1.10). recombinant agl1 and agl2 into which a his(12) sequence was incorporated (agl1(his) and agl2(his), respectively) exhibited hydrolytic activity towards panose, isomaltose, i ...200919114534
characterization of two novel alpha-glucosidases from bifidobacterium breve ucc2003.two alpha-glucosidase-encoding genes (agl1 and agl2) from bifidobacterium breve ucc2003 were identified and characterized. based on their similarity to characterized carbohydrate hydrolases, the agl1 and agl2 enzymes are both assigned to a subgroup of the glycosyl hydrolase family 13, the alpha-1,6-glucosidases (ec 3.2.1.10). recombinant agl1 and agl2 into which a his(12) sequence was incorporated (agl1(his) and agl2(his), respectively) exhibited hydrolytic activity towards panose, isomaltose, i ...200919114534
the crystal structure of galacto-n-biose/lacto-n-biose i phosphorylase: a large deformation of a tim barrel scaffold.galacto-n-biose/lacto-n-biose i phosphorylase (glnbp) from bifidobacterium longum, a key enzyme for intestinal growth, phosphorolyses galacto-n-biose and lacto-n-biose i with anomeric inversion. glnbp homologues are often found in human pathogenic and commensal bacteria, and their substrate specificities potentially define the nutritional acquisition ability of these microbes in their habitat. we report the crystal structures of glnbp in five different ligand-binding forms. this is the first thr ...200919124470
architectural underpinnings of the genetic code for glutamine.structure-based mutational analysis was used to probe the architecture of the glutamine binding pocket in escherichia coli glutaminyl-trna synthetase (glnrs). crystallographic studies of several different glnrs complexes in a lattice that supports catalytic activity have shown that the glutamine amide group makes only ambiguous hydrogen-bonding interactions with a tyrosine hydroxyl and bound water molecule, rather than the highly specific hydrogen-bonding and electrostatic interactions made by t ...200919128026
dihydroorotase from the hyperthermophile aquifex aeolicus is activated by stoichiometric association with aspartate transcarbamoylase and forms a one-pot reactor for pyrimidine biosynthesis.in prokaryotes, the first three enzymes in pyrimidine biosynthesis, carbamoyl phosphate synthetase (cps), aspartate transcarbamoylase (atc), and dihydroorotase (dho), are commonly expressed separately and either function independently (escherichia coli) or associate into multifunctional complexes (aquifex aeolicus). in mammals the enzymes are expressed as a single polypeptide chain (cad) in the order cps-dho-atc and associate into a hexamer. this study presents the three-dimensional structure of ...200919128030
ribosome hijacking: a role for small protein b during trans-translation.tight recognition of codon-anticodon pairings by the ribosome ensures the accuracy and fidelity of protein synthesis. in eubacteria, translational surveillance and ribosome rescue are performed by the 'tmrna-smpb' system (transfer messenger rna-small protein b). remarkably, entry and accommodation of aminoacylated-tmrna into stalled ribosomes occur without a codon-anticodon interaction but in the presence of smpb. here, we show that within a stalled ribosome, smpb interacts with the three univer ...200919132006
combined microspectrophotometric and crystallographic examination of chemically reduced and x-ray radiation-reduced forms of cytochrome ba3 oxidase from thermus thermophilus: structure of the reduced form of the enzyme.three paths for obtaining crystals of reduced (ii-e4q/i-k258r) cytochrome ba(3) are described, and the structures of these are reported at approximately 2.8-3.0 a resolution. microspectrophotometry of single crystals of thermus ba(3) oxidase at 100 k was used to show that crystals of the oxidized enzyme are reduced in an intense x-ray (beam line 7-1 at the stanford synchrotron radiation laboratory), being nearly complete in 1 min. the previously reported structures of ba(3) (protein data bank en ...200919140675
a conserved active site tyrosine residue of proline dehydrogenase helps enforce the preference for proline over hydroxyproline as the substrate.proline dehydrogenase (prodh) catalyzes the oxidation of l-proline to delta-1-pyrroline-5-carboxylate. prodhs exhibit a pronounced preference for proline over hydroxyproline (trans-4-hydroxy-l-proline) as the substrate, but the basis for specificity is unknown. the goal of this study, therefore, is to gain insight into the structural determinants of substrate specificity of this class of enzyme, with a focus on understanding how prodhs discriminate between the two closely related molecules, prol ...200919140736
coarse-grained modeling of large rna molecules with knowledge-based potentials and structural filters.understanding the function of complex rna molecules depends critically on understanding their structure. however, creating three-dimensional (3d) structural models of rna remains a significant challenge. we present a protocol (the nucleic acid simulation tool [nast]) for rna modeling that uses an rna-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate plausible 3d structures. we demonstrate nast's capabilities by using only secondary structure and tertiar ...200919144906
genetic and structural analysis of base substitutions in the central pseudoknot of thermus thermophilus 16s ribosomal rna.characterization of base substitutions in rrnas has provided important insights into the mechanism of protein synthesis. knowledge of the structural effects of such alterations is limited, and could be greatly expanded with the development of a genetic system based on an organism amenable to both genetics and structural biology. here, we describe the genetic analysis of base substitutions in 16s ribosomal rna of the extreme thermophile thermus thermophilus, and an analysis of the conformational ...200919144908
electronic structure of the ground and excited states of the cu(a) site by nmr spectroscopy.the electronic properties of thermus thermophilus cu(a) in the oxidized form were studied by (1)h and (13)c nmr spectroscopy. all of the (1)h and (13)c resonances from cysteine and imidazole ligands were observed and assigned in a sequence-specific fashion. the detection of net electron spin density on a peptide moiety is attributed to the presence of a h-bond to a coordinating sulfur atom. this hydrogen bond is conserved in all natural cu(a) variants and plays an important role for maintaining ...200919146411
proteomic analysis of protein tyrosine nitration after ischemia reperfusion injury: mitochondria as the major target.endothelial nitric oxide synthase-derived no and its derivative, peroxynitrite (onoo(-)), suppresses oxygen consumption by nitration of mitochondrial proteins after reperfusion. however, very few nitrated proteins are identified to date. in this paper, ischemia/reperfusion (i/r) injury was induced in mouse heart by ligation and release of the left anterior descending coronary artery. western blotting showed that tyrosine nitration was higher in i/r hearts. nitrated proteins were identified by ca ...200919150419
proteomic analysis of protein tyrosine nitration after ischemia reperfusion injury: mitochondria as the major target.endothelial nitric oxide synthase-derived no and its derivative, peroxynitrite (onoo(-)), suppresses oxygen consumption by nitration of mitochondrial proteins after reperfusion. however, very few nitrated proteins are identified to date. in this paper, ischemia/reperfusion (i/r) injury was induced in mouse heart by ligation and release of the left anterior descending coronary artery. western blotting showed that tyrosine nitration was higher in i/r hearts. nitrated proteins were identified by ca ...200919150419
mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at trna wobble positions.the wobble modification in trnas, 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)u), is required for the proper decoding of nnr codons in eukaryotes. the 2-thio group confers conformational rigidity of mcm(5)s(2)u by largely fixing the c3'-endo ribose puckering, ensuring stable and accurate codon-anticodon pairing. we have identified five genes in saccharomyces cerevisiae, yil008w (urm1), yhr111w (uba4), yor251c (tum1), ynl119w (ncs2) and ygl211w (ncs6), that are required for 2-thiolation of m ...200919151091
cloning, expression, crystallization and preliminary x-ray crystallographic analysis of glutamyl-trna synthetase (xoo1504) from xanthomonas oryzae pv. oryzae.the gltx gene from xanthomonas oryzae pv. oryzae (xoo1504) encodes glutamyl-trna synthetase (glurs), one of the most important enzymes involved in bacterial blight (bb), which causes huge production losses of rice worldwide. glurs is a class i-type aminoacyl-trna synthetase (aars) that is primarily responsible for the glutamylation of trna(glu). it plays an essential role in protein synthesis, as well as the regulation of cells, in all organisms. as it represents an important target for the deve ...200919153456
cloning, expression, crystallization and preliminary x-ray crystallographic analysis of glutamyl-trna synthetase (xoo1504) from xanthomonas oryzae pv. oryzae.the gltx gene from xanthomonas oryzae pv. oryzae (xoo1504) encodes glutamyl-trna synthetase (glurs), one of the most important enzymes involved in bacterial blight (bb), which causes huge production losses of rice worldwide. glurs is a class i-type aminoacyl-trna synthetase (aars) that is primarily responsible for the glutamylation of trna(glu). it plays an essential role in protein synthesis, as well as the regulation of cells, in all organisms. as it represents an important target for the deve ...200919153456
x-ray diffraction analysis of a human trna(gly) acceptor-stem microhelix isoacceptor at 1.18 a resolution.interest has been focused on comparative x-ray structure analyses of different trna(gly) acceptor-stem helices. trna(gly)/glycyl-trna synthetase belongs to the so-called class ii system, in which the trna identity elements consist of simple and unique determinants that are located in the trna acceptor stem and the discriminator base. comparative structure investigations of trna(gly) microhelices provide insight into the role of trna identity elements. predominant differences in the structures of ...200919153458
x-ray diffraction analysis of a human trna(gly) acceptor-stem microhelix isoacceptor at 1.18 a resolution.interest has been focused on comparative x-ray structure analyses of different trna(gly) acceptor-stem helices. trna(gly)/glycyl-trna synthetase belongs to the so-called class ii system, in which the trna identity elements consist of simple and unique determinants that are located in the trna acceptor stem and the discriminator base. comparative structure investigations of trna(gly) microhelices provide insight into the role of trna identity elements. predominant differences in the structures of ...200919153458
characterization of a heat-stable enzyme possessing gtp-dependent rna ligase activity from a hyperthermophilic archaeon, pyrococcus furiosus.using an expression protein library of a hyperthermophilic archaeon, pyrococcus furiosus, we identified a gene (pf0027) that encodes a protein with heat-stable cyclic nucleotide phosphodiesterase (cpdase) activity. the pf0027 gene encoded a 21-kda protein and an amino acid sequence that showed approximately 27% identity to that of the 2'-5' trna ligase protein, ligt (20 kda), from escherichia coli. we found that the purified pf0027 protein possessed gtp-dependent rna ligase activity and that syn ...200919155324
new role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.using fmn and a reducing agent such as nad(p)h, type 2 isopentenyl-diphosphate isomerase catalyzes isomerization between isopentenyl diphosphate and dimethylallyl diphosphate, both of which are elemental units for the biosynthesis of highly diverse isoprenoid compounds. although the flavin cofactor is expected to be integrally involved in catalysis, its exact role remains controversial. here we report the crystal structures of the substrate-free and complex forms of type 2 isopentenyl-diphosphat ...200919158086
a novel bicistronic vector for overexpressing mycobacterium tuberculosis proteins in escherichia coli.a putative dna glycosylase encoded by the rv3297 gene (mtunei2) has been identified in mycobacterium tuberculosis. our efforts to express this gene in escherichia coli either by supplementing trnas for rare codons or optimizing the gene with preferred codons for e. coli resulted in little or no expression. on the other hand, high-level expression was observed using a bicistronic expression vector in which the target gene was translationally coupled to an upstream leader sequence. further compari ...200919162193
a novel bicistronic vector for overexpressing mycobacterium tuberculosis proteins in escherichia coli.a putative dna glycosylase encoded by the rv3297 gene (mtunei2) has been identified in mycobacterium tuberculosis. our efforts to express this gene in escherichia coli either by supplementing trnas for rare codons or optimizing the gene with preferred codons for e. coli resulted in little or no expression. on the other hand, high-level expression was observed using a bicistronic expression vector in which the target gene was translationally coupled to an upstream leader sequence. further compari ...200919162193
a peroxide bridge between fe and cu ions in the o2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump.the fully oxidized form of cytochrome c oxidase, immediately after complete oxidation of the fully reduced form, pumps protons upon each of the initial 2 single-electron reduction steps, whereas protons are not pumped during single-electron reduction of the fully oxidized "as-isolated" form (the fully oxidized form without any reduction/oxidation treatment) [bloch d, et al. (2004) the catalytic cycle of cytochrome c oxidase is not the sum of its two halves. proc natl acad sci usa 101:529-533]. f ...200919164527
identification of amino acids in the n-terminal domain of atypical methanogenic-type seryl-trna synthetase critical for trna recognition.seryl-trna synthetase (serrs) from methanogenic archaeon methanosarcina barkeri, contains an idiosyncratic n-terminal domain, composed of an antiparallel beta-sheet capped by a helical bundle, connected to the catalytic core by a short linker peptide. it is very different from the coiled-coil trna binding domain in bacterial-type serrs. because the crystal structure of the methanogenic-type serrsxtrna complex has not been obtained, a docking model was produced, which indicated that highly conser ...200919734148
biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from pyrococcus furiosus.apurinic/apyrimidinic (ap) sites are the most frequently found mutagenic lesions in dna, and they arise mainly from spontaneous base loss or modified base removal by damage-specific dna glycosylases. ap sites are cleaved by ap endonucleases, and the resultant gaps in the dna are repaired by dna polymerase/dna ligase reactions. we identified the gene product that is responsible for the ap endonuclease activity in the hyperthermophilic euryarchaeon, pyrococcus furiosus. furthermore, we detected th ...200919734344
srmb, a dead-box helicase involved in escherichia coli ribosome assembly, is specifically targeted to 23s rrna in vivo.dead-box proteins play specific roles in remodeling rna or ribonucleoprotein complexes. yet, in vitro, they generally behave as nonspecific rna-dependent atpases, raising the question of what determines their specificity in vivo. srmb, one of the five escherichia coli dead-box proteins, participates in the assembly of the large ribosomal subunit. moreover, when overexpressed, it compensates for a mutation in l24, the ribosomal protein (r-protein) thought to initiate assembly. here, using the tan ...200919734346
the interaction of bacillus subtilis sigmaa with rna polymerase.rna polymerase (rnap) is an essential and highly conserved enzyme in all organisms. the process of transcription initiation is fundamentally different between prokaryotes and eukaryotes. in prokaryotes, initiation is regulated by sigma factors, making the essential interaction between sigma factors and rnap an attractive target for antimicrobial agents. our objective was to achieve the first step in the process of developing novel antimicrobial agents, namely to prove experimentally that the int ...200919735077
continuous-wave and pulsed epr characterization of the [2fe-2s](cys)3(his)1 cluster in rat mitoneet.cw epr spectra of reduced [2fe-2s](cys)(3)(his)(1) clusters of mammalian mitoneet soluble domain appear to produce features resulting from the interaction of the electron spins of the two adjacent clusters, which can be explained by employing the local spin model. this model favors the reduction of the outermost iron with his87 and cys83 ligands, which is supported by orientation-selected hyperfine sublevel correlation (hyscore) characterization of the uniformly (15)n-labeled mitoneet showing on ...200919736979
characterization of rimo, a new member of the methylthiotransferase subclass of the radical sam superfamily.rimo, encoded by the ylig gene in escherichia coli, has been recently identified in vivo as the enzyme responsible for the attachment of a methylthio group on the beta-carbon of asp88 of the small ribosomal protein s12 [anton, b. p., saleh, l., benner, j. s., raleigh, e. a., kasif, s., and roberts, r. j. (2008) proc. natl. acad. sci. u.s.a. 105, 1826-1831]. to date, it is the only enzyme known to catalyze methylthiolation of a protein substrate; the four other naturally occurring methylthio modi ...200919736993
promiscuous substrate recognition in folding and assembly activities of the trigger factor chaperone.trigger factor (tf) is a molecular chaperone that binds to bacterial ribosomes where it contacts emerging nascent chains, but tf is also abundant free in the cytosol where its activity is less well characterized. in vitro studies show that tf promotes protein refolding. we find here that ribosome-free tf stably associates with and rescues from misfolding a large repertoire of full-length proteins. we identify over 170 members of this cytosolic escherichia coli tf substrate proteome, including ri ...200919737520
p38sj, a novel dingg protein protects neuronal cells from alcohol induced injury and death.ethanol induces neuronal cell injury and death by dysregulating several signaling events that are controlled, in part, by activation of mapk/erk1/2 and/or inactivation of its corresponding phosphatase, pp1. recently, we have purified a novel protein of 38 kda in size, p38sj, from a callus culture of hypericum perforatum, which belongs to an emerging dingg family of proteins with phosphate binding activity. here, we show that treatment of neuronal cells with p38sj protects cells against injury in ...200919739100
structural insights into the mechanism of the allosteric transitions of mycobacterium tuberculosis camp receptor protein.the camp receptor protein (crp) from mycobacterium tuberculosis is a camp-responsive global transcriptional regulator, responsible for the regulation of a multitude of diverse proteins. we have determined the crystal structures of the crp.camp and crp.n(6)-camp derivative-bound forms of the enzyme to 2.2- and 2.3 a-resolution, respectively, to investigate camp-mediated conformational and structural changes. the allosteric switch from the open, inactive conformation to the closed, active conforma ...200919740754
dual role of dna in regulating atp hydrolysis by the sopa partition protein.in bacteria, mitotic stability of plasmids and many chromosomes depends on replicon-specific systems, which comprise a centromere, a centromere-binding protein and an atpase. dynamic self-assembly of the atpase appears to enable active partition of replicon copies into cell-halves, but for walker-box partition atpases the molecular mechanism is unknown. atpase activity appears to be essential for this process. dna and centromere-binding proteins are known to stimulate the atpase activity but mol ...200919740757
in vitro metal uptake by recombinant human manganese superoxide dismutase.metal uptake by the antioxidant defense metalloenzyme manganese superoxide dismutase (mnsod) is an essential step in the functional maturation of the protein that is just beginning to be investigated in detail. we have extended earlier in vitro studies on metal binding by the dimeric escherichia coli apo-mnsod to investigate the mechanism of metal uptake by tetrameric human and thermus thermophilus apo-mnsods. like the e. coli apo-mnsod, these proteins also bind metal ions in vitro in a thermall ...200919755112
recognition of trnagln by helicobacter pylori glurs2--a trnagln-specific glutamyl-trna synthetase.accurate aminoacylation of trnas by the aminoacyl-trna synthetases (aarss) plays a critical role in protein translation. however, some of the aarss are missing in many microorganisms. helicobacter pylori does not have a glutaminyl-trna synthetase (glnrs) but has two divergent glutamyl-trna synthetases: glurs1 and glurs2. like a canonical glurs, glurs1 aminoacylates trna(glu1) and trna(glu2). in contrast, glurs2 only misacylates trna(gln) to form glu-trna(gln). it is not clear how glurs2 achieves ...200919755501
demonstration and characterization of the heterodimerization of znt5 and znt6 in the early secretory pathway.the majority of cdf/znt zinc transporters form homo-oligomers. however, znt5, znt6, and their orthologues form hetero-oligomers in the early secretory pathway where they load zinc onto zinc-requiring enzymes and maintain secretory pathway functions. the details of this hetero-oligomerization remain to be elucidated, and much more is known about homo-oligomerization that occurs in other cdf/znt family proteins. here, we addressed this issue using co-immunoprecipitation experiments, mutagenesis, a ...200919759014
the schizosaccharomyces pombe hsp104 disaggregase is unable to propagate the [psi] prion.the molecular chaperone hsp104 is a crucial factor in the acquisition of thermotolerance in yeast. under stress conditions, the disaggregase activity of hsp104 facilitates the reactivation of misfolded proteins. hsp104 is also involved in the propagation of fungal prions. for instance, the well-characterized [psi(+)] prion of saccharomyces cerevisiae does not propagate in deltahsp104 cells or in cells overexpressing hsp104. in this study, we characterized the functional homolog of hsp104 from sc ...200919759825
zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for gtp cyclohydrolase ib.gtp cyclohydrolase i (gcyh-i) is an essential zn(2+)-dependent enzyme that catalyzes the first step of the de novo folate biosynthetic pathway in bacteria and plants, the 7-deazapurine biosynthetic pathway in bacteria and archaea, and the biopterin pathway in mammals. we recently reported the discovery of a new prokaryotic-specific gcyh-i (gcyh-ib) that displays no sequence identity to the canonical enzyme and is present in approximately 25% of bacteria, the majority of which lack the canonical ...200919767425
structure of d-alanine-d-alanine ligase from thermus thermophilus hb8: cumulative conformational change and enzyme-ligand interactions.d-alanine-d-alanine ligase (ddl) is one of the key enzymes in peptidoglycan biosynthesis and is an important target for drug discovery. the enzyme catalyzes the condensation of two d-ala molecules using atp to produce d-ala-d-ala, which is the terminal peptide of a peptidoglycan monomer. the structures of five forms of the enzyme from thermus thermophilus hb8 (ttddl) were determined: unliganded ttddl (2.3 a resolution), ttddl-adenylyl imidodiphosphate (2.6 a), ttddl-adp (2.2 a), ttddl-adp-d-ala ...200919770507
adenosine triphosphate stimulates aquifex aeolicus mutl endonuclease activity.background: human pms2 (hpms2) homologues act to nick 5' and 3' to misincorporated nucleotides during mismatch repair in organisms that lack muth. mn(++) was previously found to stimulate the endonuclease activity of these homologues. atp was required for the nicking activity of hpms2 and ypms1, but was reported to inhibit bacterial mutl proteins from thermus thermophilus and aquifex aeolicus that displayed homology to hpms2. mutational analysis has identified the dqha(x)(2)e(x)(4)e motif presen ...200919777055
increased expression of the oxidative pentose phosphate pathway and gluconeogenesis in anaerobically growing xylose-utilizing saccharomyces cerevisiae.fermentation of xylose to ethanol has been achieved in s. cerevisiae by genetic engineering. xylose utilization is however slow compared to glucose, and during anaerobic conditions addition of glucose has been necessary for cellular growth. in the current study, the xylose-utilizing strain tmb 3415 was employed to investigate differences between anaerobic utilization of glucose and xylose. this strain carried a xylose reductase (xyl1 k270r) engineered for increased nadh utilization and was capab ...200919778438
inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic v1-atpase.v-type atpases (v-atpases) are categorized as rotary atp synthase/atpase complexes. the v-atpases are distinct from f-atpases in terms of their rotation scheme, architecture and subunit composition. however, there is no detailed structural information on v-atpases despite the abundant biochemical and biophysical research. here, we report a crystallographic study of v1-atpase, from thermus thermophilus, which is a soluble component consisting of a, b, d and f subunits. the structure at 4.5 a reso ...200919779483
ion-induced folding of a kink turn that departs from the conventional sequence.kink turns (k-turns) are important structural motifs that create a sharp axial bend in rna. most conform to a consensus in which a three-nucleotide bulge is followed by consecutive g*a and a*g base pairs, and when these g*a pairs are modified in vitro this generally leads to a failure to adopt the k-turn conformation. kt-23 in the 30s ribosomal subunit of thermus thermophilus is a rare exception in which the bulge-distal a*g pair is replaced by a non-watson-crick a*u pair. in the context of the ...200919783814
recr-mediated modulation of recf dimer specificity for single- and double-stranded dna.recf pathway proteins play an important role in the restart of stalled replication and dna repair in prokaryotes. following dna damage, recf, recr, and reco initiate homologous recombination (hr) by loading of the reca recombinase on single-stranded (ss) dna, protected by ssdna-binding protein. the specific role of recf in this process is not well understood. previous studies have proposed that recf directs the recor complex to boundaries of damaged dna regions by recognizing single-stranded/dou ...200919017635
novel escherichia coli rf1 mutants with decreased translation termination activity and increased sensitivity to the cytotoxic effect of the bacterial toxins kid and rele.novel mutations in prfa, the gene for the polypeptide release factor rf1 of escherichia coli, were isolated using a positive genetic screen based on the pard (kis, kid) toxin-antitoxin system. this original approach allowed the direct selection of mutants with altered translational termination efficiency at uag codons. the isolated prfa mutants displayed a approximately 10-fold decrease in uag termination efficiency with no significant changes in rf1 stability in vivo. all three mutations, g121s ...200919019162
phylogenetic analysis of rubella virus strains from an outbreak in madrid, spain, from 2004 to 2005.an outbreak of rubella affected 460 individuals in 2004 and 2005 in the community of madrid, spain. most of the patients were nonvaccinated latin american immigrants or spanish males. this study presents the first data on rubella virus genotypes in spain. forty selected clinical samples (2 urine, 5 serum, 3 blood, 2 saliva, and 28 pharyngeal exudate samples) from 40 cases were collected. the 739-nucleotide sequence recommended by the world health organization obtained from viral rna in these sam ...200919020066
phylogenetic analysis of rubella virus strains from an outbreak in madrid, spain, from 2004 to 2005.an outbreak of rubella affected 460 individuals in 2004 and 2005 in the community of madrid, spain. most of the patients were nonvaccinated latin american immigrants or spanish males. this study presents the first data on rubella virus genotypes in spain. forty selected clinical samples (2 urine, 5 serum, 3 blood, 2 saliva, and 28 pharyngeal exudate samples) from 40 cases were collected. the 739-nucleotide sequence recommended by the world health organization obtained from viral rna in these sam ...200919020066
structure and function of hiv-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition.the rapid replication of hiv-1 and the errors made during viral replication cause the virus to evolve rapidly in patients, making the problems of vaccine development and drug therapy particularly challenging. in the absence of an effective vaccine, drugs are the only useful treatment. anti-hiv drugs work; so far drug therapy has saved more than three million years of life. unfortunately, hiv-1 develops resistance to all of the available drugs. although a number of useful anti-hiv drugs have been ...200919022262
structure and function of hiv-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition.the rapid replication of hiv-1 and the errors made during viral replication cause the virus to evolve rapidly in patients, making the problems of vaccine development and drug therapy particularly challenging. in the absence of an effective vaccine, drugs are the only useful treatment. anti-hiv drugs work; so far drug therapy has saved more than three million years of life. unfortunately, hiv-1 develops resistance to all of the available drugs. although a number of useful anti-hiv drugs have been ...200919022262
glucose- and glucokinase-controlled mal gene expression in escherichia coli.malt is the central transcriptional activator of all mal genes in escherichia coli. its activity is controlled by the inducer maltotriose. it can be inhibited by the interaction with certain proteins, and its expression can be controlled. we report here a novel aspect of mal gene regulation: the effect of cytoplasmic glucose and glucokinase (glk) on the activity and the expression of malt. amylomaltase (malq) is essential for the metabolism of maltose. it forms maltodextrins and glucose from mal ...200919028900
glucose- and glucokinase-controlled mal gene expression in escherichia coli.malt is the central transcriptional activator of all mal genes in escherichia coli. its activity is controlled by the inducer maltotriose. it can be inhibited by the interaction with certain proteins, and its expression can be controlled. we report here a novel aspect of mal gene regulation: the effect of cytoplasmic glucose and glucokinase (glk) on the activity and the expression of malt. amylomaltase (malq) is essential for the metabolism of maltose. it forms maltodextrins and glucose from mal ...200919028900
biochemical and structural properties of mouse kynurenine aminotransferase iii.kynurenine aminotransferase iii (kat iii) has been considered to be involved in the production of mammalian brain kynurenic acid (kyna), which plays an important role in protecting neurons from overstimulation by excitatory neurotransmitters. the enzyme was identified based on its high sequence identity with mammalian kat i, but its activity toward kynurenine and its structural characteristics have not been established. in this study, the biochemical and structural properties of mouse kat iii (m ...200919029248
biochemical and structural properties of mouse kynurenine aminotransferase iii.kynurenine aminotransferase iii (kat iii) has been considered to be involved in the production of mammalian brain kynurenic acid (kyna), which plays an important role in protecting neurons from overstimulation by excitatory neurotransmitters. the enzyme was identified based on its high sequence identity with mammalian kat i, but its activity toward kynurenine and its structural characteristics have not been established. in this study, the biochemical and structural properties of mouse kat iii (m ...200919029248
rrna suppressor of a eukaryotic translation initiation factor 5b/initiation factor 2 mutant reveals a binding site for translational gtpases on the small ribosomal subunit.the translational gtpases promote initiation, elongation, and termination of protein synthesis by interacting with the ribosome. mutations that impair gtp hydrolysis by eukaryotic translation initiation factor 5b/initiation factor 2 (eif5b/if2) impair yeast cell growth due to failure to dissociate from the ribosome following subunit joining. a mutation in helix h5 of the 18s rrna in the 40s ribosomal subunit and intragenic mutations in domain ii of eif5b suppress the toxic effects associated wit ...200919029250
rrna suppressor of a eukaryotic translation initiation factor 5b/initiation factor 2 mutant reveals a binding site for translational gtpases on the small ribosomal subunit.the translational gtpases promote initiation, elongation, and termination of protein synthesis by interacting with the ribosome. mutations that impair gtp hydrolysis by eukaryotic translation initiation factor 5b/initiation factor 2 (eif5b/if2) impair yeast cell growth due to failure to dissociate from the ribosome following subunit joining. a mutation in helix h5 of the 18s rrna in the 40s ribosomal subunit and intragenic mutations in domain ii of eif5b suppress the toxic effects associated wit ...200919029250
function and ribosomal localization of aif6, a translational regulator shared by archaea and eukarya.the translation factor if6 is shared by the archaea and the eukarya, but is not found in bacteria. the properties of eukaryal if6 (eif6) have been extensively studied, but remain somewhat elusive. eif6 behaves as a ribosome-anti-association factor and is involved in mirna-mediated gene silencing; however, it also seems to participate in ribosome synthesis and export. here we have determined the function and ribosomal localization of the archaeal (sulfolobus solfataricus) if6 homologue (aif6). we ...200919036786
function and ribosomal localization of aif6, a translational regulator shared by archaea and eukarya.the translation factor if6 is shared by the archaea and the eukarya, but is not found in bacteria. the properties of eukaryal if6 (eif6) have been extensively studied, but remain somewhat elusive. eif6 behaves as a ribosome-anti-association factor and is involved in mirna-mediated gene silencing; however, it also seems to participate in ribosome synthesis and export. here we have determined the function and ribosomal localization of the archaeal (sulfolobus solfataricus) if6 homologue (aif6). we ...200919036786
minor changes largely restore catalytic activity of archaeal rnase p rna from methanothermobacter thermoautotrophicus.the increased protein proportion of archaeal and eukaryal ribonuclease (rnase) p holoenzymes parallels a vast decrease in the catalytic activity of their rna subunits (p rnas) alone. we show that a few mutations toward the bacterial p rna consensus substantially activate the catalytic (c-) domain of archaeal p rna from methanothermobacter, in the absence and presence of the bacterial rnase p protein. large increases in ribozyme activity required the cooperative effect of at least two structural ...200919036794
minor changes largely restore catalytic activity of archaeal rnase p rna from methanothermobacter thermoautotrophicus.the increased protein proportion of archaeal and eukaryal ribonuclease (rnase) p holoenzymes parallels a vast decrease in the catalytic activity of their rna subunits (p rnas) alone. we show that a few mutations toward the bacterial p rna consensus substantially activate the catalytic (c-) domain of archaeal p rna from methanothermobacter, in the absence and presence of the bacterial rnase p protein. large increases in ribozyme activity required the cooperative effect of at least two structural ...200919036794
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