| bifunctional nmn adenylyltransferase/adp-ribose pyrophosphatase: structure and function in bacterial nad metabolism. | bacterial nadm-nudix is a bifunctional enzyme containing a nicotinamide mononucleotide (nmn) adenylyltransferase and an adp-ribose (adpr) pyrophosphatase domain. while most members of this enzyme family, such as that from a model cyanobacterium synechocystis sp., are involved primarily in nicotinamide adenine dinucleotide (nad) salvage/recycling pathways, its close homolog in a category-a biodefense pathogen, francisella tularensis, likely plays a central role in a recently discovered novel path ... | 2008 | 18275811 |
| drosophila muscleblind is involved in troponin t alternative splicing and apoptosis. | muscleblind-like proteins (mbnl) have been involved in a developmental switch in the use of defined cassette exons. such transition fails in the ctg repeat expansion disease myotonic dystrophy due, in part, to sequestration of mbnl proteins by cug repeat rna. four protein isoforms (mbla-d) are coded by the unique drosophila muscleblind gene. | 2008 | 18286170 |
| fine structure of the promoter-sigma region 1.2 interaction. | we recently proposed that a nontemplate strand base in the discriminator region of bacterial promoters, the region between the -10 element and the transcription start site, makes sequence-specific contacts to region 1.2 of the sigma subunit of escherichia coli rna polymerase (rnap). because rrna promoters contain sequences within the discriminator region that are suboptimal for interaction with sigma1.2, these promoters have the kinetic properties required for regulation by the rnap-binding fact ... | 2008 | 18287032 |
| role of 16s ribosomal rna methylations in translation initiation in escherichia coli. | translation initiation from the ribosomal p-site is the specialty of the initiator trnas (trna(fmet)). presence of the three consecutive g-c base pairs (g29-c41, g30-c40 and g31-c39) in their anticodon stems, a highly conserved feature of the initiator trnas across the three kingdoms of life, has been implicated in their preferential binding to the p-site. how this feature is exploited by ribosomes has remained unclear. using a genetic screen, we have isolated an escherichia coli strain, carryin ... | 2008 | 18288206 |
| conversion of beta-carotene into astaxanthin: two separate enzymes or a bifunctional hydroxylase-ketolase protein? | abstract: astaxanthin is a xanthophyll of great interest in animal nutrition and human health. the market prospect in the nutraceutics industries for this health-protective molecule is very promising. astaxanthin is synthesized by several bacteria, algae and plants from beta-carotene by the sequential action of two enzymes: a beta-carotene, 3,3'-hydroxylase that introduces an hydroxyl group at the 3 (and 3') positions of each of the two beta-ionone rings of beta-carotene, and a beta-carotene ket ... | 2008 | 18289382 |
| yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine. | prodrug gene therapy (pgt) is a treatment strategy in which tumor cells are transfected with a 'suicide' gene that encodes a metabolic enzyme capable of converting a nontoxic prodrug into a potent cytotoxin. one of the most promising pgt enzymes is cytosine deaminase (cd), a microbial salvage enzyme that converts cytosine to uracil. cd also converts 5-fluorocytosine (5fc) to 5-fluorouracil, an inhibitor of dna synthesis and rna function. over 150 studies of cd-mediated pgt applications have been ... | 2008 | 18291415 |
| methanothermobacter thermautotrophicus trna gln confines the amidotransferase gatcab to asparaginyl-trna asn formation. | many prokaryotes form the amide aminoacyl-trnas glutaminyl-trna and asparaginyl-trna by trna-dependent amidation of the mischarged trna species, glutamyl-trna(gln) or aspartyl-trna(asn). archaea employ two such amidotransferases, gatcab and gatde, while bacteria possess only one, gatcab. the methanothermobacter thermautotrophicus gatde is slightly more efficient using asn as an amide donor than gln (k(cat)/k(m) of 5.4 s(-1)/mm and 1.2 s(-1)/mm, respectively). unlike the bacterial gatcab enzymes ... | 2008 | 18291416 |
| genomic and proteomic analysis of phieco32, a novel escherichia coli bacteriophage. | a novel bacteriophage infecting escherichia coli was isolated during a large-scale screen for bacteriophages that may be used for therapy of mastitis in cattle. the 77,554-bp genome of the bacteriophage, named phieco32, was sequenced and annotated, and its virions were characterized by electron microscopy and proteomics. two phieco32-encoded proteins that interact with host rna polymerase were identified. one of them is an ecf family sigma factor that may be responsible for transcription of some ... | 2008 | 18294652 |
| murine leukemia virus reverse transcriptase: structural comparison with hiv-1 reverse transcriptase. | recent x-ray crystal structure determinations of moloney murine leukemia virus reverse transcriptase (momlv rt) have allowed for more accurate structure/function comparisons to hiv-1 rt than were formerly possible. previous biochemical studies of momlv rt in conjunction with knowledge of sequence homologies to hiv-1 rt and overall fold similarities to rts in general, provided a foundation upon which to build. in addition, numerous crystal structures of the momlv rt fingers/palm subdomain had als ... | 2008 | 18294720 |
| structural insights into an equilibrium folding intermediate of an archaeal ankyrin repeat protein. | repeat proteins are widespread in nature, with many of them functioning as binding molecules in protein-protein recognition. their simple structural architecture is used in biotechnology for generating proteins with high affinities to target proteins. recent folding studies of ankyrin repeat (ar) proteins revealed a new mechanism of protein folding. the formation of an intermediate state is rate limiting in the folding reaction, suggesting a scaffold function of this transient state for intrinsi ... | 2008 | 18305166 |
| evolution of acceptor stem trna recognition by class ii prolyl-trna synthetase. | aminoacyl-trna synthetases (aars) are an essential family of enzymes that catalyze the attachment of amino acids to specific trnas during translation. previously, we showed that base-specific recognition of the trna(pro) acceptor stem is critical for recognition by escherichia coli prolyl-trna synthetase (prors), but not for human prors. to further delineate species-specific differences in acceptor stem recognition, atomic group mutagenesis was used to probe the role of sugar-phosphate backbone ... | 2008 | 18310681 |
| real-time electron transfer in respiratory complex i. | electron transfer in complex i from escherichia coli was investigated by an ultrafast freeze-quench approach. the reaction of complex i with nadh was stopped in the time domain from 90 mus to 8 ms and analyzed by electron paramagnetic resonance (epr) spectroscopy at low temperatures. the data show that after binding of the first molecule of nadh, two electrons move via the fmn cofactor to the iron-sulfur (fe/s) centers n1a and n2 with an apparent time constant of approximately 90 mus, implying t ... | 2008 | 18316732 |
| structure of mouse adp-ribosylhydrolase 3 (marh3). | adp-ribosylation is a reversible and covalent post-translational modification in which the attachment of adp-ribose is catalyzed by adp-ribosyltransferases and the removal of adp-ribose is catalyzed by adp-ribosylhydrolases. adp-ribosylhydrolase 3 from mouse, consisting of 347 amino-acid residues, has been cloned, purified and crystallized. the three-dimensional structure has been resolved at a resolution of 1.8 a. the structure constitutes a compact all-alpha-helical protein with two mg(2+) ion ... | 2008 | 18323597 |
| purification, crystallization and preliminary x-ray diffraction analysis of aspartate semialdehyde dehydrogenase (rv3708c) from mycobacterium tuberculosis. | aspartate semialdehyde dehydrogenase from mycobacterium tuberculosis (asd, asadh, rv3708c), which is the second enzyme in the lysine/homoserine-biosynthetic pathways, has been expressed heterologously in escherichia coli. the enzyme was purified using affinity and gel-filtration chromatographic techniques and crystallized in two different crystal forms. preliminary diffraction data analysis suggested the presence of up to four monomers in the asymmetric unit of the orthorhombic crystal form a an ... | 2008 | 18323599 |
| expression, purification, crystallization and preliminary x-ray characterization of two crystal forms of stationary-phase survival e protein from campylobacter jejuni. | survival e (sure) protein from campylobacter jejuni, a gram-negative mesophile, has been overexpressed in escherichia coli as a soluble protein, successfully purified and crystallized in two distinct crystal forms. the first form belongs to space group p2(1)2(1)2(1), with a tetramer in the asymmetric unit and unit-cell parameters a = 80.5, b = 119.0, c = 135.3 a. the second form belongs to space group c2, with unit-cell parameters a = 121.4, b = 47.1, c = 97.8 a, and contains a dimer in the asym ... | 2008 | 18323612 |
| quality control of bacterial mrna decoding and decay. | studies in eukaryotes and prokaryotes have revealed that gene expression is not only controlled through altering the rate of transcription but also through varying rates of translation and mrna decay. indeed, the expression level of a protein is strongly affected by the steady state level of its mrna. rna decay can, along with transcription, play an important role in regulating gene expression by fine-tuning the steady state level of a given transcript and affecting its subsequent decoding durin ... | 2008 | 18342642 |
| altering the coenzyme preference of xylose reductase to favor utilization of nadh enhances ethanol yield from xylose in a metabolically engineered strain of saccharomyces cerevisiae. | abstract: | 2008 | 18346277 |
| the bacterial and mitochondrial ribosomal a-site molecular switches possess different conformational substates. | the a site of the small ribosomal subunit participates in the fidelity of decoding by switching between two states, a resting 'off' state and an active decoding 'on' state. eight crystal structures of rna duplexes containing two minimal decoding a sites of the homo sapiens mitochondrial wild-type, the a1555g mutant or bacteria have been solved. the resting 'off' state of the mitochondrial wild-type a site is surprisingly different from that of the bacterial a site. the mitochondrial a1555g mutan ... | 2008 | 18346970 |
| structural insight into the mechanism of substrate specificity and catalytic activity of an hd-domain phosphohydrolase: the 5'-deoxyribonucleotidase yfbr from escherichia coli. | hd-domain phosphohydrolases have nucleotidase and phosphodiesterase activities and play important roles in the metabolism of nucleotides and in signaling. we present three 2.1-a-resolution crystal structures (one in the free state and two complexed with natural substrates) of an hd-domain phosphohydrolase, the escherichia coli 5'-nucleotidase yfbr. the free-state structure of yfbr contains a large cavity accommodating the metal-coordinating hd motif (h33, h68, d69, and d137) and other conserved ... | 2008 | 18353368 |
| genome comparison and proteomic characterization of thermus thermophilus bacteriophages p23-45 and p74-26: siphoviruses with triplex-forming sequences and the longest known tails. | the genomes of two closely related lytic thermus thermophilus siphoviruses with exceptionally long (approximately 800 nm) tails, bacteriophages p23-45 and p74-26, were sequenced completely. the p23-45 genome consists of 84,201 bp with 117 putative open reading frames (orfs), and the p74-26 genome has 83,319 bp and 116 putative orfs. the two genomes are 92% identical with 113 orfs shared. only 25% of phage gene product functions can be predicted from similarities to proteins and protein domains w ... | 2008 | 18355836 |
| roles of pgaabcd genes in synthesis, modification, and export of the escherichia coli biofilm adhesin poly-beta-1,6-n-acetyl-d-glucosamine. | the linear homopolymer poly-beta-1,6-n-acetyl-d-glucosamine (beta-1,6-glcnac; pga) serves as an adhesin for the maintenance of biofilm structural stability in diverse eubacteria. its function in escherichia coli k-12 requires the gene products of the pgaabcd operon, all of which are necessary for biofilm formation. pgac is an apparent glycosyltransferase that is required for pga synthesis. using a monoclonal antibody directed against e. coli pga, we now demonstrate that pgad is also needed for p ... | 2008 | 18359807 |
| evolution of the arginase fold and functional diversity. | novel structural superfamilies can be identified among the large number of protein structures deposited in the protein data bank based on conservation of fold in addition to conservation of amino acid sequence. since sequence diverges more rapidly than fold in protein evolution, proteins with little or no significant sequence identity are occasionally observed to adopt similar folds, thereby reflecting unanticipated evolutionary relationships. here, we review the unique alpha/beta fold first obs ... | 2008 | 18360740 |
| the structure of lepa, the ribosomal back translocase. | lepa is a highly conserved elongation factor that promotes the back translocation of trnas on the ribosome during the elongation cycle. we have determined the crystal structure of lepa from escherichia coli at 2.8-a resolution. the high degree of sequence identity between lepa and ef-g is reflected in the structural similarity between the individual homologous domains of lepa and ef-g. however, the orientation of domains iii and v in lepa differs from their orientations in ef-g. lepa also contai ... | 2008 | 18362332 |
| functional segregation of a predicted "hinge" site within the beta-strand linkers of escherichia coli leucyl-trna synthetase. | some aminoacyl-trna synthetases (aarss) employ an editing mechanism to ensure the fidelity of protein synthesis. leucyl-trna synthetase (leurs), isoleucyl-trna synthetase (ilers), and valyl-trna synthetase (valrs) share a common insertion, called the cp1 domain, which is responsible for clearing misformed products. this discrete domain is connected to the main body of the enzyme via two beta-strand tethers. the cp1 hydrolytic editing active site is located approximately 30 a from the aminoacylat ... | 2008 | 18363380 |
| crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism. | the crystal structures of two ternary complexes of human spermine synthase (ec 2.5.1.22), one with 5'-methylthioadenosine and spermidine and the other with 5'-methylthioadenosine and spermine, have been solved. they show that the enzyme is a dimer of two identical subunits. each monomer has three domains: a c-terminal domain, which contains the active site and is similar in structure to spermidine synthase; a central domain made up of four beta-strands; and an n-terminal domain with remarkable s ... | 2008 | 18367445 |
| creation of a bi-directional protein transduction system for suppression of hiv-1 expression by p27sj. | p27sj is a novel protein from a callus culture of st. john's wort that modulates transcription of the hiv-1 promoter in several mammalian cells [darbinian-sarkissian, n., darbinyan, a., otte, j., radhakrishnan, s., sawaya, b.e., arzumanyan, a., chipitsyna, g., popov, y., rappaport, j., amini, s., khalili, k., 2006. p27(sj), a novel protein from st. john's wort, that suppresses expression of hiv-1 genome. gene ther. 13, 288-295]. here, we armed p27sj with signals from ig-kappa light chain that al ... | 2008 | 18378326 |
| creation of a bi-directional protein transduction system for suppression of hiv-1 expression by p27sj. | p27sj is a novel protein from a callus culture of st. john's wort that modulates transcription of the hiv-1 promoter in several mammalian cells [darbinian-sarkissian, n., darbinyan, a., otte, j., radhakrishnan, s., sawaya, b.e., arzumanyan, a., chipitsyna, g., popov, y., rappaport, j., amini, s., khalili, k., 2006. p27(sj), a novel protein from st. john's wort, that suppresses expression of hiv-1 genome. gene ther. 13, 288-295]. here, we armed p27sj with signals from ig-kappa light chain that al ... | 2008 | 18378326 |
| the conserved wobble uridine trna thiolase ctu1-ctu2 is required to maintain genome integrity. | modified nucleosides close to the anticodon are important for the proper decoding of mrna by the ribosome. particularly, the uridine at the first anticodon position (u34) of glutamate, lysine, and glutamine trnas is universally thiolated (s(2)u34), which is proposed to be crucial for both restriction of wobble in the corresponding split codon box and efficient codon-anticodon interaction. here we show that the highly conserved complex ctu1-ctu2 (cytosolic thiouridylase) is responsible for the 2- ... | 2008 | 18391219 |
| function, structure and regulation of the vacuolar (h+)-atpases. | the vacuolar atpases (or v-atpases) are atp-driven proton pumps that function to both acidify intracellular compartments and to transport protons across the plasma membrane. intracellular v-atpases function in such normal cellular processes as receptor-mediated endocytosis, intracellular membrane traffic, prohormone processing, protein degradation and neurotransmitter uptake, as well as in disease processes, including infection by influenza and other viruses and killing of cells by anthrax and d ... | 2008 | 18406336 |
| protective action of ppgpp in microcin j25-sensitive strains. | as escherichia coli strains enter the stationary phase of growth they become more resistant to the peptide antibiotic microcin j25. it is known that starvation for nutrients such as amino acids or glucose leads to increases in guanosine 3',5'-bispyrophosphate (ppgpp) levels and that the intracellular concentration of this nucleotide increases as cells enter the stationary phase of growth. therefore, we examined the effects of artificially manipulating the ppgpp levels on sensitivity to microcin ... | 2008 | 18408024 |
| hydrodynamic characterization of the sufbc and sufcd complexes and their interaction with fluorescent adenosine nucleotides. | bacteria, as well as the plastid organelles of algae and higher plants, utilize proteins of the suf operon. these are involved in fe-s cluster assembly, particularly under conditions of iron limitation or oxidative stress. genetic experiments in some organisms found that the atpase sufc is essential, though its role in fe-s biogenesis remains unclear. to ascertain how interactions with other individual suf proteins affect the activity of sufc we coexpressed it with either sufb or sufd from therm ... | 2008 | 18413861 |
| structure of the integrin alphaiib transmembrane segment. | integrin cell-adhesion receptors transduce signals bidirectionally across the plasma membrane via the single-pass transmembrane segments of each alpha and beta subunit. while the beta3 transmembrane segment consists of a linear 29-residue alpha-helix, the structure of the alphaiib transmembrane segment reveals a linear 24-residue alpha-helix (ile-966 -lys-989) followed by a backbone reversal that packs phe-992-phe-993 against the transmembrane helix. the length of the alphaiib transmembrane heli ... | 2008 | 18417472 |
| analysis of dbc1 and its homologs suggests a potential mechanism for regulation of sirtuin domain deacetylases by nad metabolites. | deleted in breast cancer-1 (dbc1) and its paralog carp-1 are large multi-domain proteins, with a nuclear or perinuclear localization, and a role in promoting apoptosis upon processing by caspases. recent studies on human dbc1 show that it is a specific inhibitor of the sirtuin-type deacetylase, sirt1, which deacetylates histones and p53. using sensitive sequence profile searches and hmm-hmm comparisons we show that the central conserved globular domain present in the dbc1 and it homologs from di ... | 2008 | 18418069 |
| the yqfn protein of bacillus subtilis is the trna: m1a22 methyltransferase (trmk). | n(1)-methylation of adenosine to m(1)a occurs in several different positions in trnas from various organisms. a methyl group at position n(1) prevents watson-crick-type base pairing by adenosine and is therefore important for regulation of structure and stability of trna molecules. thus far, only one family of genes encoding enzymes responsible for m(1)a methylation at position 58 has been identified, while other m(1)a methyltransferases (mtases) remain elusive. here, we show that bacillus subti ... | 2008 | 18420655 |
| characterization of aquifex aeolicus 4-diphosphocytidyl-2c-methyl-d-erythritol kinase - ligand recognition in a template for antimicrobial drug discovery. | 4-diphosphocytidyl-2c-methyl-d-erythritol kinase (ispe) catalyses the atp-dependent conversion of 4-diphosphocytidyl-2c-methyl-d-erythritol (cdpme) to 4-diphosphocytidyl-2c-methyl-d-erythritol 2-phosphate with the release of adp. this reaction occurs in the non-mevalonate pathway of isoprenoid precursor biosynthesis and because it is essential in important microbial pathogens and absent from mammals it represents a potential target for anti-infective drugs. we set out to characterize the biochem ... | 2008 | 18422643 |
| structural basis for the inactivation of thermus thermophilus proline dehydrogenase by n-propargylglycine. | the flavoenzyme proline dehydrogenase catalyzes the first step of proline catabolism, the oxidation of proline to pyrroline-5-carboxylate. here we report the first crystal structure of an irreversibly inactivated proline dehydrogenase. the 1.9 a resolution structure of thermus thermophilus proline dehydrogenase inactivated by the mechanism-based inhibitor n-propargylglycine shows that n5 of the flavin cofactor is covalently connected to the -amino group of lys99 via a three-carbon linkage, consi ... | 2008 | 18426222 |
| evidence for the intense exchange of mazg in marine cyanophages by horizontal gene transfer. | s-pm2 is a phage capable of infecting strains of unicellular cyanobacteria belonging to the genus synechococcus. s-pm2, like other myoviruses infecting marine cyanobacteria, encodes a number of bacterial-like genes. amongst these genes is one encoding a mazg homologue that is hypothesized to be involved in the adaption of the infected host for production of progeny phage. | 2008 | 18431505 |
| assembly of viral metagenomes from yellowstone hot springs. | thermophilic viruses were reported decades ago; however, knowledge of their diversity, biology, and ecological impact is limited. previous research on thermophilic viruses focused on cultivated strains. this study examined metagenomic profiles of viruses directly isolated from two mildly alkaline hot springs, bear paw (74 degrees c) and octopus (93 degrees c). using a new method for constructing libraries from picograms of dna, nearly 30 mb of viral dna sequence was determined. in contrast to pr ... | 2008 | 18441115 |
| role of bacillus subtilis rnase j1 endonuclease and 5'-exonuclease activities in trp leader rna turnover. | the 140-nucleotide trp leader rna, which is formed by transcription termination under conditions of high intracellular tryptophan, was used to study rna turnover in bacillus subtilis. we showed in vivo that the amount of endonuclease cleavage at approximately nucleotide 100 is decreased under conditions where rnase j1 concentration is reduced. in addition, under these conditions the level of 3'-terminal rna fragments, which contain the strong transcription terminator structure, increases dramati ... | 2008 | 18445592 |
| perturbation of the trna tertiary core differentially affects specific steps of the elongation cycle. | the trna tertiary core region is important for both trna stability and activity in the translation elongation cycle. here we report the effects of mutating each of two highly conserved base pairs in the tertiary core of phe-trna(phe), 18-55 and 19-56, on rate and equilibrium constants for specific steps of this cycle, beginning with formation of aminoacyl-trna.ef-tu.gtp ternary complexs and culminating with translocation of a-site-bound peptidyl-trna into the p-site. we find that codon-dependent ... | 2008 | 18448426 |
| structure of 3-oxoacyl-(acyl-carrier protein) synthase ii from thermus thermophilus hb8. | the beta-ketoacyl-(acyl carrier protein) synthases (beta-keto-acp synthases; kas) catalyse the addition of two-carbon units to the growing acyl chain during the elongation phase of fatty-acid synthesis. as key regulators of bacterial fatty-acid synthesis, they are promising targets for the development of new antibacterial agents. the crystal structure of 3-oxoacyl-acp synthase ii from thermus thermophilus hb8 (ttkas ii) has been solved by molecular replacement and refined at 2.0 a resolution. th ... | 2008 | 18453702 |
| mutations outside the anisomycin-binding site can make ribosomes drug-resistant. | eleven mutations that make haloarcula marismortui resistant to anisomycin, an antibiotic that competes with the amino acid side chains of aminoacyl trnas for binding to the a-site cleft of the large ribosomal unit, have been identified in 23s rrna. the correlation observed between the sensitivity of h. marismortui to anisomycin and the affinity of its large ribosomal subunits for the drug indicates that its response to anisomycin is determined primarily by the binding of the drug to its large ri ... | 2008 | 18455733 |
| functional analysis of the essential gtp-binding-protein-coding gene cgta of vibrio cholerae. | the cgta gene, coding for the conserved g protein cgta, is essential in bacteria. in contrast to a previous report, here we show by using genetic analysis that cgta is essential in vibrio cholerae even in a delta rela background. depletion of cgta affected the growth of v. cholerae and rendered the cells highly sensitive to the replication inhibitor hydroxyurea. overexpression of v. cholerae cgta caused distinct elongation of escherichia coli cells. deletion analysis indicated that the c-termina ... | 2008 | 18456812 |
| omp85(tt) from thermus thermophilus hb27: an ancestral type of the omp85 protein family. | proteins belonging to the omp85 family are involved in the assembly of beta-barrel outer membrane proteins or in the translocation of proteins across the outer membrane in bacteria, mitochondria, and chloroplasts. the cell envelope of the thermophilic bacterium thermus thermophilus hb27 is multilayered, including an outer membrane that is not well characterized. neither the precise lipid composition nor much about integral membrane proteins is known. the genome of hb27 encodes one omp85-like pro ... | 2008 | 18456816 |
| purification and characterization of a novel recombinant highly enantioselective short-chain nad(h)-dependent alcohol dehydrogenase from thermus thermophilus. | the gene encoding a novel alcohol dehydrogenase (adh) that belongs to the short-chain dehydrogenase/reductase (sdr) superfamily was identified in the extremely thermophilic, halotolerant gram-negative eubacterium thermus thermophilus hb27. the t. thermophilus adh gene (adh(tt)) was heterologously overexpressed in escherichia coli, and the protein (adh(tt)) was purified to homogeneity and characterized. adh(tt) is a tetrameric enzyme consisting of identical 26,961-da subunits composed of 256 amin ... | 2008 | 18456852 |
| mutation analysis of carbamoyl phosphate synthetase: does the structurally conserved glutamine amidotransferase triad act as a functional dyad? | evolutionarily conserved triad glutamine amidotransferase (gat) domains catalyze the cleavage of glutamine to yield ammonia and sequester the ammonia in a tunnel until delivery to a variety of acceptor substrates in synthetase domains of variable structure. whereas a conserved hydrolytic triad (cys/his/glu) is observed in the solved gat structures, the specificity pocket for glutamine is not apparent, presumably because its formation is dependent on the conformational change that couples accepto ... | 2008 | 18458150 |
| synthesis of beta-(s-methyl)thioaspartic acid and derivatives. | beta-(s-methyl)thioaspartic acid occurs as a posttranslational modification at position 88 in escherichia coli ribosomal protein s12, a position that is a mutational hotspot resulting in both antibiotic-resistant and antibiotic-sensitive phenotypes. critical to research designed to determine the biological function of beta-(s-methyl)thioaspartic acid will be the availability of synthetic beta-(s-methyl)thioaspartic acid as well as derivatives designed for peptide incorporation. we report here th ... | 2008 | 18468905 |
| streptococcus pyogenes psm19035 requires dynamic assembly of atp-bound para and parb on pars dna during plasmid segregation. | the accurate partitioning of firmicute plasmid psm19035 at cell division depends on atp binding and hydrolysis by homodimeric atpase delta(2) (para) and binding of omega(2) (parb) to its cognate pars dna. the 1.83 a resolution crystal structure of delta(2) in a complex with non-hydrolyzable atpgammas reveals a unique para dimer assembly that permits nucleotide exchange without requiring dissociation into monomers. in vitro, delta(2) had minimal atpase activity in the absence of omega(2) and pars ... | 2008 | 18477635 |
| a rationally engineered misacylating aminoacyl-trna synthetase. | information transfer from nucleic acid to protein is mediated by aminoacyl-trna synthetases, which catalyze the specific pairings of amino acids with transfer rnas. despite copious sequence and structural information on the 22 trna synthetase families, little is known of the enzyme signatures that specify amino acid selectivities. here, we show that transplanting a conserved arginine residue from glutamyl-trna synthetase (glurs) to glutaminyl-trna synthetase (glnrs) improves the k(m) of glnrs fo ... | 2008 | 18477696 |
| prediction of membrane-protein topology from first principles. | the current best membrane-protein topology-prediction methods are typically based on sequence statistics and contain hundreds of parameters that are optimized on known topologies of membrane proteins. however, because the insertion of transmembrane helices into the membrane is the outcome of molecular interactions among protein, lipids and water, it should be possible to predict topology by methods based directly on physical data, as proposed >20 years ago by kyte and doolittle. here, we present ... | 2008 | 18477697 |
| a novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. | clustered regularly interspaced short palindromic repeats (crisprs) together with the associated cas proteins protect microbial cells from invasion by foreign genetic elements using presently unknown molecular mechanisms. all crispr systems contain proteins of the cas2 family, suggesting that these uncharacterized proteins play a central role in this process. here we show that the cas2 proteins represent a novel family of endoribonucleases. six purified cas2 proteins from diverse organisms cleav ... | 2008 | 18482976 |
| a basic/hydrophobic cleft of the t4 activator mota interacts with the c-terminus of e.coli sigma70 to activate middle gene transcription. | transcriptional activation often employs a direct interaction between an activator and rna polymerase. for activation of its middle genes, bacteriophage t4 appropriates escherichia coli rna polymerase through the action of two phage-encoded proteins, mota and asia. alone, asia inhibits transcription from a large class of host promoters by structurally remodelling region 4 of sigma(70), the primary specificity subunit of e. coli rna polymerase. mota interacts both with sigma(70) region 4 and with ... | 2008 | 18485078 |
| were there any "misassignments" among iron-sulfur clusters n4, n5 and n6b in nadh-quinone oxidoreductase (complex i)? | nadh-quinone oxidoreductase (complex i) in bovine heart mitochondria has a molecular weight of approximately 1 million da composed of 45 distinct subunits. it is the largest energy transducing complex so far known. bacterial complex i is simpler and smaller, but the essential redox components and the basic mechanisms of electron and proton translocation are the same. over the past three decades, ohnishi et al. have pursued extensive epr studies near liquid helium temperatures and characterized m ... | 2008 | 18486592 |
| genes and enzymes of azetidine-2-carboxylate metabolism: detoxification and assimilation of an antibiotic. | l-(-)-azetidine-2-carboxylate (ac) is a toxic, natural product analog of l-proline. this study revealed the genes and biochemical strategy employed by pseudomonas sp. strain a2c to detoxify and assimilate ac as its sole nitrogen source. the gene region from pseudomonas sp. strain a2c required for detoxification was cloned into escherichia coli and sequenced. the 7.0-kb region contained eight identifiable genes. four encoded putative transporters or permeases for gamma-amino acids or drugs. anoth ... | 2008 | 18487339 |
| atp hydrolysis and synthesis of a rotary motor v-atpase from thermus thermophilus. | vacuolar-type h(+)-atpase (v-atpase) catalyzes atp synthesis and hydrolysis coupled with proton translocation across membranes via a rotary motor mechanism. here we report biochemical and biophysical catalytic properties of v-atpase from thermus thermophilus. atp hydrolysis of v-atpase was severely inhibited by entrapment of mg-adp in the catalytic site. in contrast, the enzyme was very active for atp synthesis (approximately 70 s(-1)) with the k(m) values for adp and phosphate being 4.7 +/- 0.5 ... | 2008 | 18492667 |
| the iron-sulphur protein ind1 is required for effective complex i assembly. | nadh:ubiquinone oxidoreductase (complex i) of the mitochondrial inner membrane is a multi-subunit protein complex containing eight iron-sulphur (fe-s) clusters. little is known about the assembly of complex i and its fe-s clusters. here, we report the identification of a mitochondrial protein with a nucleotide-binding domain, named ind1, that is required specifically for the effective assembly of complex i. deletion of the ind1 open reading frame in the yeast yarrowia lipolytica carrying an inte ... | 2008 | 18497740 |
| structure of escherichia coli tyrosine kinase etk reveals a novel activation mechanism. | while protein tyrosine (tyr) kinases (ptks) have been extensively characterized in eukaryotes, far less is known about their emerging counterparts in prokaryotes. the inner-membrane wzc/etk protein belongs to the bacterial ptk family, which has an important function in regulating the polymerization and transport of virulence-determining capsular polysaccharide (cps). the kinase uses a unique two-step activation process involving intra-phosphorylation of a tyr residue, although the molecular mech ... | 2008 | 18497741 |
| identification of the mitochondrial nd3 subunit as a structural component involved in the active/deactive enzyme transition of respiratory complex i. | mitochondrial complex i (nadh:ubiquinone oxidoreductase) undergoes reversible deactivation upon incubation at 30-37 degrees c. the active/deactive transition could play an important role in the regulation of complex i activity. it has been suggested recently that complex i may become modified by s-nitrosation under pathological conditions during hypoxia or when the nitric oxide:oxygen ratio increases. apparently, a specific cysteine becomes accessible to chemical modification only in the deactiv ... | 2008 | 18502755 |
| chemo-enzymatic synthesis of c-9 acetylated sialosides. | a chemo-enzymatic synthesis of [(5-acetamido-9-o-acetyl-3,5-dideoxy-d-glycero-alpha-d-galacto-2-nonulopyranosylonic acid)-(2-->3)-o-(beta-d-galactopyranosyl)-(1-->3)-o-(2-acetamido-2-deoxy-alpha-d-galactopyranosyl)]-l-serine acetate (1) has been accomplished by a regioselective chemical acetylation of neu5ac (2) to give 9-o-acetylated sialic acid 3, which was enzymatically converted into cmp-neu5,9ac(2) (4) employing a recombinant cmp-sialic acid synthetase from neisseria meningitis [ec 2.7.7.43 ... | 2008 | 18508039 |
| functional guanine-arginine interaction between trnapro and prolyl-trna synthetase that couples binding and catalysis. | aminoacyl-trna synthetases catalyze the attachment of specific amino acids to their cognate trnas. specific aminoacylation is dictated by a set of recognition elements that mark trna molecules as substrates for particular synthetases. escherichia coli prolyl-trna synthetase (prors) has previously been shown to recognize specific bases of trna(pro) in both the anticodon domain, which mediate initial complex formation, and in the acceptor stem, which is proximal to the site of catalysis. in this w ... | 2008 | 18513497 |
| structures and functional implications of an amp-binding cystathionine beta-synthase domain protein from a hyperthermophilic archaeon. | cystathionine beta-synthase domains are found in a myriad of proteins from organisms across the tree of life and have been hypothesized to function as regulatory modules that sense the energy charge of cells. here we characterize the structure and stability of pae2072, a dimeric tandem cystathionine beta-synthase domain protein from the hyperthermophilic crenarchaeon pyrobaculum aerophilum. crystal structures of the protein in unliganded and amp-bound forms, determined at resolutions of 2.10 and ... | 2008 | 18513746 |
| design of a fluorescence polarization assay platform for the study of human hsp70. | the 70kda heat shock proteins (hsp70) are molecular chaperones that assist in folding of newly synthesized polypeptides, refolding or denaturation of misfolded proteins, and translocation of proteins across biological membranes. in addition, hsp70 play regulatory roles in signal transduction, cell cycle, and apoptosis. here, we present a novel assay platform based on fluorescence polarization that is suitable for investigating the yet elusive molecular mechanics of human hsp70 allosteric regulat ... | 2008 | 18515098 |
| structure-guided mutational analysis of the ob, hhh, and brct domains of escherichia coli dna ligase. | nad(+)-dependent dna ligases (ligas) are ubiquitous in bacteria and essential for growth. liga enzymes have a modular structure in which a central catalytic core composed of nucleotidyltransferase and oligonucleotide-binding (ob) domains is linked via a tetracysteine zinc finger to distal helix-hairpin-helix (hhh) and brct (brca1-like c-terminal) domains. the ob and hhh domains contribute prominently to the protein clamp formed by liga around nicked duplex dna. here we conducted a structure-func ... | 2008 | 18515356 |
| presence of a family of plasmids (29 to 65 kilobases) with a 26-kilobase common region in different strains of the sulfur-oxidizing bacterium acidithiobacillus caldus. | three large cryptic plasmids from different isolates of acidithiobacillus caldus were rescued by using an in vitro transposition system that delivers a kanamycin-selectable marker and an escherichia coli plasmid origin of replication. the largest of the plasmids, the 65-kb plasmid ptcm1, was isolated from a south african a. caldus strain, mng. this plasmid was sequenced and compared to that of ptcf1 (39 kb, from strain "f," south africa) and pc-sh12 (29 kb, from strain c-sh12, australia). with t ... | 2008 | 18515486 |
| evolutionary persistence of the molybdopyranopterin-containing sulfite oxidase protein fold. | summary: the importance of molybdoenzymes is exemplified both by the debilitating and fatal human diseases caused by their deficiency and by their persistence throughout evolution. here, we show that the protein fold of the molybdopyranopterin-containing domain of sulfite oxidase (the suox fold) can be found in all three domains of life. analyses of sequence data and protein structure comparisons (secondary structure matching) show that the suox fold is found in enzymes that have quite distinct ... | 2008 | 18535145 |
| regulation of pyrimidine biosynthetic gene expression in bacteria: repression without repressors. | summary: dna-binding repressor proteins that govern transcription initiation in response to end products generally regulate bacterial biosynthetic genes, but this is rarely true for the pyrimidine biosynthetic (pyr) genes. instead, bacterial pyr gene regulation generally involves mechanisms that rely only on regulatory sequences embedded in the leader region of the operon, which cause premature transcription termination or translation inhibition in response to nucleotide signals. studies with es ... | 2008 | 18535147 |
| molecular mechanism of energy conservation in polysulfide respiration. | bacterial polysulfide reductase (psrabc) is an integral membrane protein complex responsible for quinone-coupled reduction of polysulfide, a process important in extreme environments such as deep-sea vents and hot springs. we determined the structure of polysulfide reductase from thermus thermophilus at 2.4-a resolution, revealing how the psra subunit recognizes and reduces its unique polyanionic substrate. the integral membrane subunit psrc was characterized using the natural substrate menaquin ... | 2008 | 18536726 |
| the rna polymerase ii trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. | structural, biochemical, and genetic studies have led to proposals that a mobile element of multisubunit rna polymerases, the trigger loop (tl), plays a critical role in catalysis and can be targeted by antibiotic inhibitors. here we present evidence that the saccharomyces cerevisiae rna polymerase ii (pol ii) tl participates in substrate selection. amino acid substitutions within the pol ii tl preferentially alter substrate usage and enzyme fidelity, as does inhibition of transcription by alpha ... | 2008 | 18538653 |
| the effect of mutated mitochondrial ribosomal proteins s16 and s22 on the assembly of the small and large ribosomal subunits in human mitochondria. | mutations in mitochondrial small subunit ribosomal proteins mrps16 or mrps22 cause severe, fatal respiratory chain dysfunction due to impaired translation of mitochondrial mrnas. the loss of either mrps16 or mrps22 was accompanied by the loss of most of another small subunit protein mrps11. however, mrps2 was reduced only about 2-fold in patient fibroblasts. this observation suggests that the small ribosomal subunit is only partially able to assemble in these patients. two large subunit ribosoma ... | 2008 | 18539099 |
| characterization of single and double inactivation strains reveals new physiological roles for group 2 sigma factors in the cyanobacterium synechocystis sp. pcc 6803. | cyanobacteria are eubacteria that perform oxygenic photosynthesis like plants. the initiation of transcription, mediated by the rna polymerase holoenzyme, is the main determinant of gene regulation in eubacteria. the sigma factor of the rna polymerase holoenzyme is responsible for the recognition of a promoter sequence. in the cyanobacterium synechocystis sp. pcc 6803, the primary sigma factor, siga, is essential for cell viability. the sigb, sigc, sigd, and sige factors show significant sequenc ... | 2008 | 18539776 |
| crystallization screening test for the whole-cell project on thermus thermophilus hb8. | it was essential for the structural genomics of thermus thermophilus hb8 to efficiently crystallize a number of proteins. to this end, three conventional robots, an hts-80 (sitting-drop vapour diffusion), a crystal finder (hanging-drop vapour diffusion) and a tera (modified microbatch) robot, were subjected to a crystallization condition screening test involving 18 proteins from t. thermophilus hb8. in addition, a topaz (microfluidic free-interface diffusion) designed specifically for initial sc ... | 2008 | 18540056 |
| expression, crystallization and preliminary x-ray analysis of an outer membrane protein from thermus thermophilus hb27. | the cell envelope of the thermophilic bacterium thermus thermophilus is multilayered and includes an outer membrane with integral outer membrane proteins that are not well characterized. the hypothetical protein ttc0834 from t. thermophilus hb27 was identified as a 22 kda outer membrane protein containing eight predicted beta-strands. ttc0834 was expressed with an n-terminal his tag in t. thermophilus hb8 and detected in the s-layer/outer membrane envelope fraction. his-ttc0834 was purified and ... | 2008 | 18540069 |
| expression, purification, crystallization and preliminary x-ray analysis of rv3117, a probable thiosulfate sulfurtransferase (cysa3) from mycobacterium tuberculosis. | the gene product of open reading frame rv3117 from mycobacterium tuberculosis (mtb) strain h37rv is annotated as encoding a probable rhodanese-like thiosulfate sulfurtransferase (mtbcysa3). mtbcysa3 was expressed and purified and then crystallized using the sitting-drop vapour-diffusion method. x-ray diffraction data were collected and processed to a maximum resolution of 2.5 a. the crystals belong to the monoclinic space group p2(1), with unit-cell parameters a = 38.86, b = 91.43, c = 83.57 a, ... | 2008 | 18540071 |
| the torsin-family aaa+ protein ooc-5 contains a critical disulfide adjacent to sensor-ii that couples redox state to nucleotide binding. | a subgroup of the aaa+ proteins that reside in the endoplasmic reticulum and the nuclear envelope including human torsina, a protein mutated in hereditary dystonia, is called the torsin family of aaa+ proteins. a multiple-sequence alignment of this family with hsp100 proteins of known structure reveals a conserved cysteine in the c-terminus of torsin proteins within the sensor-ii motif. a structural model predicts this cysteine to be a part of an intramolecular disulfide bond, suggesting that it ... | 2008 | 18550799 |
| the homotetrameric phosphoseryl-trna synthetase from methanosarcina mazei exhibits half-of-the-sites activity. | synthesis of cysteinyl-trna(cys) in methanogenic archaea proceeds by a two-step pathway in which trna(cys) is first aminoacylated with phosphoserine by phosphoseryl-trna synthetase (seprs). characterization of seprs from the mesophile methanosarcina mazei by gel filtration and nondenaturing mass spectrometry shows that the native enzyme exists as an alpha4 tetramer when expressed at high levels in escherichia coli. however, active site titrations monitored by atp/pp(i) burst kinetics, together w ... | 2008 | 18559342 |
| physical and functional interactions between uracil-dna glycosylase and proliferating cell nuclear antigen from the euryarchaeon pyrococcus furiosus. | uracil-dna glycosylase (udg) is an important repair enzyme in all organisms to remove uracil bases from dna. recent biochemical studies have revealed that human nuclear udg (ung2) forms a multiprotein complex in replication foci and initiates the base excision repair pathway by interacting with proliferating cell nuclear antigen (pcna). here, we show the physical and functional interactions between udg and pcna from the hyperthermophilic euryarchaeon, pyrococcus furiosus. the physical interactio ... | 2008 | 18562313 |
| long-range, high-throughput haplotype determination via haplotype-fusion pcr and ligation haplotyping. | ligation haplotyping is a robust, novel method for experimental determination of haplotypes over long distances, which can be applied to assaying both sequence and structural variation. the simplicity and efficacy of the method for genotyping large chromosomal rearrangements and haplotyping snps over long distances make it a valuable and powerful addition to the methodological repertoire, which will be beneficial to studies of population genetics and evolution, disease association and inheritanc ... | 2008 | 18562465 |
| structural basis for hygromycin b inhibition of protein biosynthesis. | aminoglycosides are one of the most widely used and clinically important classes of antibiotics that target the ribosome. hygromycin b is an atypical aminoglycoside antibiotic with unique structural and functional properties. here we describe the structure of the intact escherichia coli 70s ribosome in complex with hygromycin b. the antibiotic binds to the mrna decoding center in the small (30s) ribosomal subunit of the 70s ribosome and induces a localized conformational change, in contrast to i ... | 2008 | 18567815 |
| basal dna repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria. | ionizing-radiation-resistant bacteria (irrb) show a surprising capacity for adaptation to ionizing radiation and desiccation. positive darwinian selection is expected to play an important role in this trait, but no data are currently available regarding the role of positive adaptive selection in resistance to ionizing-radiation and tolerance of desiccation. we analyzed the four known genome sequences of irrb (deinococcus geothermalis, deinococcus radiodurans, kineococcus radiotolerans, and rubro ... | 2008 | 18570673 |
| structural modules of rna polymerase required for transcription from promoters containing downstream basal promoter element ggga. | we recently described a novel basal bacterial promoter element that is located downstream of the -10 consensus promoter element and is recognized by region 1.2 of the sigma subunit of rna polymerase (rnap). in the case of thermus aquaticus rnap, this element has a consensus sequence ggga and allows transcription initiation in the absence of the -35 element. in contrast, the escherichia coli rnap is unable to initiate transcription from ggga-containing promoters that lack the -35 element. in the ... | 2008 | 18574242 |
| footprinting analysis demonstrates extensive similarity between eukaryotic rnase p and rnase mrp holoenzymes. | eukaryotic ribonuclease (rnase) p and rnase mrp are evolutionary related rna-based enzymes involved in metabolism of various rna molecules, including trna and rrna. in contrast to the closely related eubacterial rnase p, which is comprised of an rna component and a single small protein, these enzymes contain multiple protein components. here we report the results of footprinting studies performed on purified saccharomyces cerevisiae rnase mrp and rnase p holoenzymes. the results identify regions ... | 2008 | 18579867 |
| the linear chromosome of the plant-pathogenic mycoplasma 'candidatus phytoplasma mali'. | phytoplasmas are insect-transmitted, uncultivable bacterial plant pathogens that cause diseases in hundreds of economically important plants. they represent a monophyletic group within the class mollicutes (trivial name mycoplasmas) and are characterized by a small genome with a low gc content, and the lack of a firm cell wall. all mycoplasmas, including strains of 'candidatus (ca.) phytoplasma asteris' and 'ca. p. australiense', examined so far have circular chromosomes, as is the case for almo ... | 2008 | 18582369 |
| location and flexibility of the unique c-terminal tail of aquifex aeolicus co-chaperonin protein 10 as derived by cryo-electron microscopy and biophysical techniques. | co-chaperonin protein 10 (cpn10, groes in escherichia coli) is a ring-shaped heptameric protein that facilitates substrate folding when in complex with cpn60 (groel in e. coli). the cpn10 from the hyperthermophilic, ancient bacterium aquifex aeolicus (aacpn10) has a 25-residue c-terminal extension in each monomer not found in any other cpn10 protein. earlier in vitro work has shown that this tail is not needed for heptamer assembly or protein function. without the tail, however, the heptamers (a ... | 2008 | 18588898 |
| the role of upstream sequences in selecting the reading frame on tmrna. | tmrna acts first as a trna and then as an mrna to rescue stalled ribosomes in eubacteria. two unanswered questions about tmrna function remain: how does tmrna, lacking an anticodon, bypass the decoding machinery and enter the ribosome? secondly, how does the ribosome choose the proper codon to resume translation on tmrna? according to the -1 triplet hypothesis, the answer to both questions lies in the unique properties of the three nucleotides upstream of the first tmrna codon. these nucleotides ... | 2008 | 18590561 |
| complete genome sequence of the extremely acidophilic methanotroph isolate v4, methylacidiphilum infernorum, a representative of the bacterial phylum verrucomicrobia. | the phylum verrucomicrobia is a widespread but poorly characterized bacterial clade. although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. we have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the verrucomicrobia, strain v4, isolated from the hell's gate ... | 2008 | 18593465 |
| nitrogen metabolism in haloarchaea. | the nitrogen cycle (n-cycle), principally supported by prokaryotes, involves different redox reactions mainly focused on assimilatory purposes or respiratory processes for energy conservation. as the n-cycle has important environmental implications, this biogeochemical cycle has become a major research topic during the last few years. however, although n-cycle metabolic pathways have been studied extensively in bacteria or eukarya, relatively little is known in the archaea. halophilic archaea ar ... | 2008 | 18593475 |
| crystal structure of rimi from salmonella typhimurium lt2, the gnat responsible for n(alpha)-acetylation of ribosomal protein s18. | the three ribosomal proteins l7, s5, and s18 are included in the rare subset of prokaryotic proteins that are known to be n(alpha)-acetylated. the gcn5-related n-acetyltransferase (gnat) protein rimi, responsible for the n(alpha)-acetylation of the ribosomal protein s18, was cloned from salmonella typhimurium lt2 (rimi(st)), overexpressed, and purified to homogeneity. steady-state kinetic parameters for rimi(st) were determined for accoa and a peptide substrate consisting of the first six amino ... | 2008 | 18596200 |
| seca, the motor of the secretion machine, binds diverse partners on one interactive surface. | in all living cells, regulated passage across membranes of specific proteins occurs through a universally conserved secretory channel. in bacteria and chloroplasts, the energy for the mechanical work of moving polypeptides through that channel is provided by seca, a regulated atpase. here, we use site-directed spin labeling and electron paramagnetic resonance spectroscopy to identify the interactive surface used by seca for each of the diverse binding partners encountered during the dynamic cycl ... | 2008 | 18602400 |
| iron-sulfur cluster n5 is coordinated by an hxxxcxxcxxxxxc motif in the nuog subunit of escherichia coli nadh:quinone oxidoreductase (complex i). | nadh:quinone oxidoreductase (complex i) plays a central role in cellular energy metabolism, and its dysfunction is found in numerous human mitochondrial diseases. although the understanding of its structure and function has been limited, the x-ray crystal structure of the hydrophilic part of thermus thermophilus complex i recently became available. it revealed the localization of all redox centers, including 9 iron-sulfur clusters and their coordinating ligands, and confirmed the predictions mos ... | 2008 | 18603533 |
| tbmp42 is a structure-sensitive ribonuclease that likely follows a metal ion catalysis mechanism. | rna editing in african trypanosomes is characterized by a uridylate-specific insertion and/or deletion reaction that generates functional mitochondrial transcripts. the process is catalyzed by a multi-enzyme complex, the editosome, which consists of approximately 20 proteins. while for some of the polypeptides a contribution to the editing reaction can be deduced from their domain structure, the involvement of other proteins remains elusive. tbmp42, is a component of the editosome that is charac ... | 2008 | 18603593 |
| purification, crystallization and preliminary x-ray diffraction analysis of adenosine triphosphate sulfurylase (atps) from the sulfate-reducing bacterium desulfovibrio desulfuricans atcc 27774. | native zinc/cobalt-containing atp sulfurylase (atps; ec 2.7.7.4; mgatp:sulfate adenylyltransferase) from desulfovibrio desulfuricans atcc 27774 was purified to homogeneity and crystallized. the orthorhombic crystals diffracted to beyond 2.5 a resolution and the x-ray data collected should allow the determination of the structure of the zinc-bound form of this atps. although previous biochemical studies of this protein indicated the presence of a homotrimer in solution, a dimer was found in the a ... | 2008 | 18607083 |
| multiple-site trimethylation of ribosomal protein l11 by the prma methyltransferase. | ribosomal protein l11 is a universally conserved component of the large subunit, and plays a significant role during initiation, elongation, and termination of protein synthesis. in escherichia coli, the lysine methyltransferase prma trimethylates the n-terminal alpha-amino group and the epsilon-amino groups of lys3 and lys39. here, we report four prma-l11 complex structures in different orientations with respect to the prma active site. two structures capture the l11 n-terminal alpha-amino grou ... | 2008 | 18611379 |
| complex i within oxidatively stressed bovine heart mitochondria is glutathionylated on cys-531 and cys-704 of the 75-kda subunit: potential role of cys residues in decreasing oxidative damage. | complex i has reactive thiols on its surface that interact with the mitochondrial glutathione pool and are implicated in oxidative damage in many pathologies. however, the cys residues and the thiol modifications involved are not known. here we investigate complex i thiol modification within oxidatively stressed mammalian mitochondria, containing physiological levels of glutathione and glutaredoxin 2. in mitochondria incubated with the thiol oxidant diamide, complex i is only glutathionylated on ... | 2008 | 18611857 |
| ribosome performance is enhanced by a rich cluster of pseudouridines in the a-site finger region of the large subunit. | the large subunit rrna in eukaryotes contains an unusually dense cluster of 8-10 pseudouridine (psi) modifications located in a three-helix structure (h37-h39) implicated in several functions. this region is dominated by a long flexible helix (h38) known as the "a-site finger" (asf). the asf protrudes from the large subunit just above the a-site of trna binding, interacts with 5 s rrna and trna, and through the terminal loop, forms a bridge (b1a) with the small subunit. in yeast, the three-helix ... | 2008 | 18611858 |
| different aa-trnas are selected uniformly on the ribosome. | ten e. coli aminoacyl-trnas (aa-trnas) were assessed for their ability to decode cognate codons on e. coli ribosomes by using three assays that evaluate the key steps in the decoding pathway. despite a wide variety of structural features, each aa-trna exhibited similar kinetic and thermodynamic properties in each assay. this surprising kinetic and thermodynamic uniformity is likely to reflect the importance of ribosome conformational changes in defining the rates and affinities of the decoding p ... | 2008 | 18614050 |
| substrate specificity and structure of human aminoadipate aminotransferase/kynurenine aminotransferase ii. | kat (kynurenine aminotransferase) ii is a primary enzyme in the brain for catalysing the transamination of kynurenine to kyna (kynurenic acid). kyna is the only known endogenous antagonist of the n-methyl-d-aspartate receptor. the enzyme also catalyses the transamination of aminoadipate to alpha-oxoadipate; therefore it was initially named aadat (aminoadipate aminotransferase). as an endotoxin, aminoadipate influences various elements of glutamatergic neurotransmission and kills primary astrocyt ... | 2008 | 18620547 |
| frameshifting rna pseudoknots: structure and mechanism. | programmed ribosomal frameshifting (prf) is one of the multiple translational recoding processes that fundamentally alters triplet decoding of the messenger rna by the elongating ribosome. the ability of the ribosome to change translational reading frames in the -1 direction (-1 prf) is employed by many positive strand rna viruses, including economically important plant viruses and many human pathogens, such as retroviruses, e.g., hiv-1, and coronaviruses, e.g., the causative agent of severe acu ... | 2009 | 18621088 |
| frameshifting rna pseudoknots: structure and mechanism. | programmed ribosomal frameshifting (prf) is one of the multiple translational recoding processes that fundamentally alters triplet decoding of the messenger rna by the elongating ribosome. the ability of the ribosome to change translational reading frames in the -1 direction (-1 prf) is employed by many positive strand rna viruses, including economically important plant viruses and many human pathogens, such as retroviruses, e.g., hiv-1, and coronaviruses, e.g., the causative agent of severe acu ... | 2009 | 18621088 |
| revealing unique properties of the ribosome using a network based analysis. | the ribosome is a complex molecular machine that offers many potential sites for functional interference, therefore representing a major target for antibacterial drugs. the growing number of high-resolution structures of ribosomes from different organisms, in free form and in complex with various ligands, provides unique data for structural and comparative analyses of rna structures. we model the ribosome structure as a network, where nucleotides are represented as nodes and intermolecular inter ... | 2008 | 18625614 |
| conserved discrimination against misacylated trnas by two mesophilic elongation factor tu orthologs. | elongation factor tu (ef-tu) binds and loads elongating aminoacyl-trnas (aa-trnas) onto the ribosome for protein biosynthesis. many bacteria biosynthesize gln-trna (gln) and asn-trna (asn) by an indirect, two-step pathway that relies on the misacylated trnas glu-trna (gln) and asp-trna (asn) as intermediates. previous thermodynamic and experimental analyses have demonstrated that thermus thermophilus ef-tu does not bind asp-trna (asn) and predicted a similar discriminatory response against glu-t ... | 2008 | 18627126 |