Publications

cell-specific differences in the requirements for translation quality control.	protein synthesis has an overall error rate of approximately 10(-4) for each mrna codon translated. the fidelity of translation is mainly determined by two events: synthesis of cognate amino acid:trna pairs by aminoacyl-trna synthetases (aarss) and accurate selection of aminoacyl-trnas (aa-trnas) by the ribosome. to ensure faithful aa-trna synthesis, many aarss employ a proofreading ("editing") activity, such as phenylalanyl-trna synthetases (phers) that hydrolyze mischarged tyr-trna(phe). eukar ...	2010	20160120
reductive coupling of nitrogen monoxide (*no) facilitated by heme/copper complexes.	the interactions of nitrogen monoxide (no; nitric oxide) with transition metal centers continue to be of great interest, in part due to their importance in biochemical processes. here, we describe no((g)) reductive coupling chemistry of possible relevance to that process (i.e., nitric oxide reductase (nor) biochemistry), which occurs at the heme/cu active site of cytochrome c oxidases (ccos). in this report, heme/cu/*no((g)) activity is studied using 1:1 ratios of heme and copper complex compo ...	2010	20030370
protein vivisection reveals elusive intermediates in folding.	although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. here, we outline a powerful strategy to populate partially unfolded intermediates: a buried aliphatic residue is substituted with a charged residue (e.g., leu-->glu(-)) to destabilize and unfold a specific region of the protein. we applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the beta5-strand is unfolded. the intermediate ref ...	2010	20144618
thermodynamic characterization of naturally occurring rna tetraloops.	although tetraloops are one of the most frequently occurring secondary structure motifs in rna, less than one-third of the 30 most frequently occurring rna tetraloops have been thermodynamically characterized. therefore, 24 stem-loop sequences containing common tetraloops were optically melted, and the thermodynamic parameters deltah degrees , deltas degrees , deltag degrees (37,) and t(m) for each stem-loop were determined. these new experimental values, on average, are 0.7 kcal/mol different f ...	2010	20047989
genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles.	enzymes belonging to acyl:coa synthetase (acs) superfamily activate wide variety of substrates and play major role in increasing the structural and functional diversity of various secondary metabolites in microbes and plants. however, due to the large sequence divergence within the superfamily, it is difficult to predict their substrate preference by annotation transfer from the closest homolog. therefore, a large number of acs sequences present in public databases lack any functional annotation ...	2010	20105319
heterologous laccase production and its role in industrial applications.	laccases are blue multicopper oxidases, catalyzing the oxidation of an array of aromatic substrates concomitantly with the reduction of molecular oxygen to water. these enzymes are implicated in a variety of biological activities. most of the laccases studied thus far are of fungal origin. the large range of substrates oxidized by laccases has raised interest in using them within different industrial fields, such as pulp delignification, textile dye bleaching, and bioremediation. laccases secret ...	2010	21327057
the balance between pre- and post-transfer editing in trna synthetases.	the fidelity of trna aminoacylation is dependent in part on amino acid editing mechanisms. a hydrolytic activity that clears mischarged trnas typically resides in an active site on the trna synthetase that is distinct from its synthetic aminoacylation active site. a second pre-transfer editing pathway that hydrolyzes the trna synthetase aminoacyl adenylate intermediate can also be activated. pre- and post-transfer editing activities can co-exist within a single trna synthetase resulting in a red ...	2010	19941860
trnas: cellular barcodes for amino acids.	the role of trna in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mrna codon. over the same period, it has also become increasingly clear that the ribosome is not the only destination to which trnas deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoac ...	2010	19903480
structural insights into rna interference.	virtually all animals and plants utilize small rna molecules to control protein expression during different developmental stages and in response to viral infection. structural and mechanistic studies have begun to illuminate three fundamental aspects of these pathways: small rna biogenesis, formation of rna-induced silencing complexes (riscs), and targeting of complementary mrnas. here we review exciting recent progress in understanding how regulatory rnas are produced and how they trigger speci ...	2010	20053548
fundamentals of three-dimensional reconstruction from projections.	three-dimensional (3d) reconstruction of an object mass density from the set of its 2d line projections lies at a core of both single-particle reconstruction technique and electron tomography. both techniques utilize electron microscope to collect a set of projections of either multiple objects representing in principle the same macromolecular complex in an isolated form, or a subcellular structure isolated in situ. therefore, the goal of macromolecular electron microscopy is to invert the proje ...	2010	20888956
trinuclear metal clusters in catalysis by terpenoid synthases.	terpenoid synthases are ubiquitous enzymes that catalyze the formation of structurally and stereochemically diverse isoprenoid natural products. many isoprenoid coupling enzymes and terpenoid cyclases from bacteria, fungi, protists, plants, and animals share the class i terpenoid synthase fold. despite generally low amino acid sequence identity among these examples, class i terpenoid synthases contain conserved metal binding motifs that coordinate to a trinuclear metal cluster. this cluster not ...	2010	21562622
an rna molecular switch: intrinsic flexibility of 23s rrna helices 40 and 68 5'-uaa/5'-gan internal loops studied by molecular dynamics methods.	functional rna molecules such as ribosomal rnas frequently contain highly conserved internal loops with a 5'-uaa/5'-gan (uaa/gan) consensus sequence. the uaa/gan internal loops adopt distinctive structure inconsistent with secondary structure predictions. the structure has a narrow major groove and forms a trans hoogsteen/sugar edge (ths) a/g base pair followed by an unpaired stacked adenine, a trans watson-crick/hoogsteen (twh) u/a base pair and finally by a bulged nucleotide (n). the structure ...	2010	21132104
genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements.	the mobility of restriction-modification (rm) gene complexes and their association with genome rearrangements is a subject of active investigation. here we conducted systematic genome comparisons and genome context analysis on fully sequenced prokaryotic genomes to detect rm-linked genome rearrangements. rm genes were frequently found to be linked to mobility-related genes such as integrase and transposase homologs. they were flanked by direct and inverted repeats at a significantly high frequen ...	2010	20071371
filling the gap, evolutionarily conserved omp85 in plastids of chromalveolates.	chromalveolates are a diverse group of protists that include many ecologically and medically relevant organisms such as diatoms and apicomplexan parasites. they possess plastids generally surrounded by four membranes, which evolved by engulfment of a red alga. today, most plastid proteins must be imported, but many aspects of protein import into complex plastids are still cryptic. in particular, how proteins cross the third outermost membrane has remained unexplained. we identified a protein in ...	2010	20042599
filling the gap, evolutionarily conserved omp85 in plastids of chromalveolates.	chromalveolates are a diverse group of protists that include many ecologically and medically relevant organisms such as diatoms and apicomplexan parasites. they possess plastids generally surrounded by four membranes, which evolved by engulfment of a red alga. today, most plastid proteins must be imported, but many aspects of protein import into complex plastids are still cryptic. in particular, how proteins cross the third outermost membrane has remained unexplained. we identified a protein in ...	2010	20042599
structure and function of enzymes in heme biosynthesis.	tetrapyrroles like hemes, chlorophylls, and cobalamin are complex macrocycles which play essential roles in almost all living organisms. heme serves as prosthetic group of many proteins involved in fundamental biological processes like respiration, photosynthesis, and the metabolism and transport of oxygen. further, enzymes such as catalases, peroxidases, or cytochromes p450 rely on heme as essential cofactors. heme is synthesized in most organisms via a highly conserved biosynthetic route. in h ...	2010	20506125
crispr interference: rna-directed adaptive immunity in bacteria and archaea.	sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. the importance of such pathways is highlighted by the extensive study of rna interference (rnai) and related processes in eukaryotes. in many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (crisprs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. crisp ...	2010	20125085
the crispr system: small rna-guided defense in bacteria and archaea.	all cellular systems evolve ways to combat predators and genomic parasites. in bacteria and archaea, numerous resistance mechanisms have developed against phage. our understanding of this defensive repertoire has recently been expanded to include the crispr system of clustered, regularly interspaced short palindromic repeats. in this remarkable pathway, short sequence tags from invading genetic elements are actively incorporated into the host's crispr locus to be transcribed and processed into a ...	2010	20129051
prediction and analysis of the modular structure of cytochrome p450 monooxygenases.	cytochrome p450 monooxygenases (cyps) form a vast and diverse family of highly variable sequences. they catalyze a wide variety of oxidative reactions and are therefore of great relevance in drug development and biotechnological applications. despite their differences in sequence and substrate specificity, the structures of cyps are highly similar. although being in research focus for years, factors mediating selectivity and activity remain vague.	2010	20950472
mustang-mr structural sieving server: applications in protein structural analysis and crystallography.	a central tenet of structural biology is that related proteins of common function share structural similarity. this has key practical consequences for the derivation and analysis of protein structures, and is exploited by the process of "molecular sieving" whereby a common core is progressively distilled from a comparison of two or more protein structures. this paper reports a novel web server for "sieving" of protein structures, based on the multiple structural alignment program mustang.	2010	20386610
bioprocessing data for the production of marine enzymes.	this review is a synopsis of different bioprocess engineering approaches adopted for the production of marine enzymes. three major modes of operation: batch, fed-batch and continuous have been used for production of enzymes (such as protease, chitinase, agarase, peroxidase) mainly from marine bacteria and fungi on a laboratory bioreactor and pilot plant scales. submerged, immobilized and solid-state processes in batch mode were widely employed. the fed-batch process was also applied in several b ...	2010	20479981
structures of membrane proteins.	in reviewing the structures of membrane proteins determined up to the end of 2009, we present in words and pictures the most informative examples from each family. we group the structures together according to their function and architecture to provide an overview of the major principles and variations on the most common themes. the first structures, determined 20 years ago, were those of naturally abundant proteins with limited conformational variability, and each membrane protein structure det ...	2010	20667175
the nucleotide addition cycle of rna polymerase is controlled by two molecular hinges in the bridge helix domain.	cellular rna polymerases (rnaps) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. previous work showed that kinking of a hinge region near the c-terminus of the bridge helix (bh-h(c)) plays a critical role in controlling the catalytic rate.	2010	21034443
the architecture of rna polymerase fidelity.	the basis for transcriptional fidelity by rna polymerase is not understood, but the 'trigger loop', a conserved structural element that is rearranged in the presence of correct substrate nucleotides, is thought to be critical. a study just published in bmc biology sheds new light on the ways in which the trigger loop may promote selection of correct nucleotide triphosphate substrates. see research article http://www.biomedcentral.com/1741-7007/8/54.	2010	20598112
modulation of rna polymerase activity through the trigger loop folding.	folding of the trigger loop of rna polymerase promotes nucleotide addition through creating a closed, catalytically competent conformation of the active center. here, we discuss the impact of adjacent rna polymerase elements, including the f loop and the jaw domain, as well as external regulatory factors on the trigger loop folding and catalysis.	2010	21326898
stepwise mechanism for transcription fidelity.	transcription is the first step of gene expression and is characterized by a high fidelity of rna synthesis. during transcription, the rna polymerase active centre discriminates against not just non-complementary ribo ntp substrates but also against complementary 2'- and 3'-deoxy ntps. a flexible domain of the rna polymerase active centre, the trigger loop, was shown to play an important role in this process, but the mechanisms of this participation remained elusive.	2010	20459653
non-canonical dna transcription enzymes and the conservation of two-barrel rna polymerases.	dna transcription depends on multimeric rna polymerases that are exceptionally conserved in all cellular organisms, with an active site region of >500 amino acids mainly harboured by their rpb1 and rpb2 subunits. together with the distantly related eukaryotic rna-dependent polymerases involved in gene silencing, they form a monophyletic family of ribonucleotide polymerases with a similarly organized active site region based on two double-psi barrels. recent viral and phage genome sequencing have ...	2010	20360047
ribonucleotide reduction - horizontal transfer of a required function spans all three domains.	ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of dna. the reaction is catalysed by ribonucleotide reductases (rnrs), an ancient enzyme family comprised of three classes. each class has distinct operational constraints, and are broadly distributed across organisms from all three domains, though few class i rnrs have been identified in archaeal genomes, and classes ii and iii likewise appear rare across eukaryotes. in this study, we ...	2010	21143941
metabolic engineering for improved microbial pentose fermentation.	global concern over the depletion of fossil fuel reserves, and the detrimental impact that combustion of these materials has on the environment, is focusing attention on initiatives to create sustainable approaches for the production and use of biofuels from various biomass substrates. the development of a low-cost, safe and eco-friendly process for the utilization of renewable resources to generate value-added products with biotechnological potential as well as robust microorganisms capable of ...	2010	21468211
functional role of ribosomal signatures.	although structure and sequence signatures in ribosomal rna and proteins are defining characteristics of the three domains of life and instrumental in constructing the modern phylogeny, little is known about their functional roles in the ribosome. in this work, the largest coevolving rna/protein signatures in the bacterial 30s ribosome are investigated both experimentally and computationally through all-atom molecular-dynamics simulations. the complex includes the n-terminal fragment of the ribo ...	2010	21156135
intrinsic resistance to aminoglycosides in enterococcus faecium is conferred by the 16s rrna m5c1404-specific methyltransferase efmm.	aminoglycosides are ribosome-targeting antibiotics and a major drug group of choice in the treatment of serious enterococcal infections. here we show that aminoglycoside resistance in enterococcus faecium strain cip 54-32 is conferred by the chromosomal gene efmm, encoding the e. faecium methyltransferase, as well as by the previously characterized aac(6')-ii that encodes a 6'-n-aminoglycoside acetyltransferase. inactivation of efmm in e. faecium increases susceptibility to the aminoglycosides k ...	2010	21159796
biochemistry. catalyzing no to n2o in the nitrogen cycle.		2010	21164002
methylthioadenosine/s-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism.	the importance of methylthioadenosine/s-adenosylhomocysteine (mta/sah) nucleosidase in bacteria has started to be appreciated only in the past decade. a comprehensive analysis of its various roles here demonstrates that it is an integral component of the activated methyl cycle, which recycles adenine and methionine through s-adenosylmethionine (sam)-mediated methylation reactions, and also produces the universal quorum-sensing signal, autoinducer-2 (ai-2). sam is also essential for synthesis of ...	2010	21166890
methylthioadenosine/s-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism.	the importance of methylthioadenosine/s-adenosylhomocysteine (mta/sah) nucleosidase in bacteria has started to be appreciated only in the past decade. a comprehensive analysis of its various roles here demonstrates that it is an integral component of the activated methyl cycle, which recycles adenine and methionine through s-adenosylmethionine (sam)-mediated methylation reactions, and also produces the universal quorum-sensing signal, autoinducer-2 (ai-2). sam is also essential for synthesis of ...	2010	21166890
a mechanism for single-stranded dna-binding protein (ssb) displacement from single-stranded dna upon ssb-reco interaction.	displacement of single-stranded dna (ssdna)-binding protein (ssb) from ssdna is necessary for filament formation of reca on ssdna to initiate homologous recombination. the interaction between reco and ssb is considered to be important for ssb displacement; however, the interaction has not been characterized at the atomic level. in this study, to clarify the mechanism underlying ssb displacement from ssdna upon reco binding, we examined the interaction between thermus thermophilus reco and cognat ...	2010	21169364
metagenomic analyses: past and future trends.	metagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. metagenomics comprising construction and screening of metagenomic dna libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. so far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. recently, metage ...	2010	21169428
metagenomic analyses: past and future trends.	metagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. metagenomics comprising construction and screening of metagenomic dna libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. so far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. recently, metage ...	2010	21169428
lateral transfer of the denitrification pathway genes among thermus thermophilus strains.	nitrate respiration is a common and strain-specific property in thermus thermophilus encoded by the nitrate respiration conjugative element (nce) that can be laterally transferred by conjugation. in contrast, nitrite respiration and further denitrification steps are restricted to a few isolates of this species. these later steps of the denitrification pathway are under the regulatory control of an nce-encoded transcription factor, but nothing is known about their coding sequences or its putative ...	2010	21169443
a proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of escherichia coli ribosomal protein s12.	β-methylthiolation is a novel post-translational modification mapping to a universally conserved asp 88 of the bacterial ribosomal protein s12. this s12 specific modification has been identified on orthologs from multiple bacterial species. the origin and functional significance was investigated with both a proteomic strategy to identify candidate s12 interactors and expression microarrays to search for phenotypes that result from targeted gene knockouts of select candidates. utilizing an endoge ...	2010	21169565
a proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of escherichia coli ribosomal protein s12.	β-methylthiolation is a novel post-translational modification mapping to a universally conserved asp 88 of the bacterial ribosomal protein s12. this s12 specific modification has been identified on orthologs from multiple bacterial species. the origin and functional significance was investigated with both a proteomic strategy to identify candidate s12 interactors and expression microarrays to search for phenotypes that result from targeted gene knockouts of select candidates. utilizing an endoge ...	2010	21169565
crystal structure of stable protein cuta1 from psychrotrophic bacterium shewanella sp. sib1.	cuta1 is widely found in bacteria, plants and animals, including humans. the functions of cuta1, however, have not been well clarified. it is known that cuta1s from pyrococcus horikoshii, thermus thermophilus and oryza sativa unfold at temperatures remarkably higher than the growth temperatures of the host organisms. in this work the crystal structure of cuta1 from the psychrotrophic bacterium shewanella sp. sib1 (sib1-cuta1) in a trimeric form was determined at 2.7 å resolution. this is the fir ...	2010	21169681
the structural and biochemical characterization of human rnase h2 complex reveals the molecular basis for substrate recognition and aicardi-goutières syndrome defects.	rnase h2 cleaves rna sequences that are part of rna/dna hybrids or that are incorporated into dna, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces aicardi-goutières syndrome, a severe autoimmune disorder. the 3.1 å crystal structure of human rnase h2 presented here allowed us to map the positions of all 29 mutations found in aicardi-goutières syndrome patients, several of which were not visible in the previously reported mouse rnase h2. ...	2010	21177858
the structural and biochemical characterization of human rnase h2 complex reveals the molecular basis for substrate recognition and aicardi-goutières syndrome defects.	rnase h2 cleaves rna sequences that are part of rna/dna hybrids or that are incorporated into dna, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces aicardi-goutières syndrome, a severe autoimmune disorder. the 3.1 å crystal structure of human rnase h2 presented here allowed us to map the positions of all 29 mutations found in aicardi-goutières syndrome patients, several of which were not visible in the previously reported mouse rnase h2. ...	2010	21177858
valproate uncompetitively inhibits arachidonic acid acylation by rat acyl-coa synthetase 4: relevance to valproate's efficacy against bipolar disorder.	the ability of chronic valproate (vpa) to reduce arachidonic acid (aa) turnover in brain phospholipids of unanesthetized rats has been ascribed to its inhibition of acyl-coa synthetase (acsl)-mediated activation of aa to aa-coa. our aim was to identify a rat acsl isoenzyme that could be inhibited by vpa in vitro.	2010	21184843
valproate uncompetitively inhibits arachidonic acid acylation by rat acyl-coa synthetase 4: relevance to valproate's efficacy against bipolar disorder.	the ability of chronic valproate (vpa) to reduce arachidonic acid (aa) turnover in brain phospholipids of unanesthetized rats has been ascribed to its inhibition of acyl-coa synthetase (acsl)-mediated activation of aa to aa-coa. our aim was to identify a rat acsl isoenzyme that could be inhibited by vpa in vitro.	2010	21184843
structural and functional studies of fatty acyl adenylate ligases from e. coli and l. pneumophila.	fatty acyl-amp ligase (faal) is a new member of a family of adenylate-forming enzymes that were recently discovered in mycobacterium tuberculosis. they are similar in sequence to fatty acyl-coenzyme a (coa) ligases (facls). however, while facls perform a two-step catalytic reaction, amp ligation followed by coa ligation using atp and coa as cofactors, faals produce only the acyl adenylate and are unable to perform the second step. we report x-ray crystal structures of full-length faal from esche ...	2010	21185305
structural and functional studies of fatty acyl adenylate ligases from e. coli and l. pneumophila.	fatty acyl-amp ligase (faal) is a new member of a family of adenylate-forming enzymes that were recently discovered in mycobacterium tuberculosis. they are similar in sequence to fatty acyl-coenzyme a (coa) ligases (facls). however, while facls perform a two-step catalytic reaction, amp ligation followed by coa ligation using atp and coa as cofactors, faals produce only the acyl adenylate and are unable to perform the second step. we report x-ray crystal structures of full-length faal from esche ...	2010	21185305
rna polymerase and transcription elongation factor spt4/5 complex structure.	spt4/5 in archaea and eukaryote and its bacterial homolog nusg is the only elongation factor conserved in all three domains of life and plays many key roles in cotranscriptional regulation and in recruiting other factors to the elongating rna polymerase. here, we present the crystal structure of spt4/5 as well as the structure of rna polymerase-spt4/5 complex using cryoelectron microscopy reconstruction and single particle analysis. the spt4/5 binds in the middle of rna polymerase claw and enclo ...	2010	21187417
rna polymerase and transcription elongation factor spt4/5 complex structure.	spt4/5 in archaea and eukaryote and its bacterial homolog nusg is the only elongation factor conserved in all three domains of life and plays many key roles in cotranscriptional regulation and in recruiting other factors to the elongating rna polymerase. here, we present the crystal structure of spt4/5 as well as the structure of rna polymerase-spt4/5 complex using cryoelectron microscopy reconstruction and single particle analysis. the spt4/5 binds in the middle of rna polymerase claw and enclo ...	2010	21187417
asymmetric atp hydrolysis cycle of the heterodimeric multidrug abc transport complex tmrab from thermus thermophilus.	atp-binding cassette (abc) systems translocate a wide range of solutes across cellular membranes. the thermophilic gram-negative eubacterium thermus thermophilus, a model organism for structural genomics and systems biology, discloses ∼46 abc proteins, which are largely uncharacterized. here, we functionally analyzed the first two and only abc half-transporters of the hyperthermophilic bacterium, tmra and tmrb. the abc system mediates uptake of the drug hoechst 33342 in inside-out oriented vesic ...	2010	21190941
structural basis for pirna 2'-o-methylated 3'-end recognition by piwi paz (piwi/argonaute/zwille) domains.	argonaute and piwi proteins are key players in the rna silencing pathway, with the former interacting with micro-rnas (mirnas) and sirnas, whereas the latter targets piwi-interacting rnas (pirnas) that are 2'-o-methylated (2(')-och(3)) at their 3' ends. germline-specific pirnas and piwi proteins play a critical role in genome defense against transposable elements, thereby protecting the genome against transposon-induced defects in gametogenesis and fertility. humans contain four piwi family prot ...	2010	21193640
structural basis for pirna 2'-o-methylated 3'-end recognition by piwi paz (piwi/argonaute/zwille) domains.	argonaute and piwi proteins are key players in the rna silencing pathway, with the former interacting with micro-rnas (mirnas) and sirnas, whereas the latter targets piwi-interacting rnas (pirnas) that are 2'-o-methylated (2(')-och(3)) at their 3' ends. germline-specific pirnas and piwi proteins play a critical role in genome defense against transposable elements, thereby protecting the genome against transposon-induced defects in gametogenesis and fertility. humans contain four piwi family prot ...	2010	21193640
genetic evidence for a novel interaction between transcriptional activator soxs and region 4 of the σ(70) subunit of rna polymerase at class ii soxs-dependent promoters in escherichia coli.	escherichia coli soxs activates transcription of the genes of the soxrs regulon, which provide the cell's defense against oxidative stress. in response to this stress, soxs is synthesized de novo. because the dna binding site of soxs is highly degenerate, soxs efficiently activates transcription by the mechanism of prerecruitment. in prerecruitment, newly synthesized soxs first forms binary complexes with rna polymerase. these complexes then scan the chromosome for class i and ii soxs-dependent ...	2010	21195716
genetic evidence for a novel interaction between transcriptional activator soxs and region 4 of the σ(70) subunit of rna polymerase at class ii soxs-dependent promoters in escherichia coli.	escherichia coli soxs activates transcription of the genes of the soxrs regulon, which provide the cell's defense against oxidative stress. in response to this stress, soxs is synthesized de novo. because the dna binding site of soxs is highly degenerate, soxs efficiently activates transcription by the mechanism of prerecruitment. in prerecruitment, newly synthesized soxs first forms binary complexes with rna polymerase. these complexes then scan the chromosome for class i and ii soxs-dependent ...	2010	21195716
structure of leishmania major methionyl-trna synthetase in complex with intermediate products methionyladenylate and pyrophosphate.	leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions of people at risk. due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from leishmania major in hopes of creating a platform for the rational design of new therapeutics. crystals of the catalytic core of methionyl-trna synthetase from l. major (lmmetrs) were obtained with the substrates mgatp and methionine presen ...	2010	21144880
structure of leishmania major methionyl-trna synthetase in complex with intermediate products methionyladenylate and pyrophosphate.	leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions of people at risk. due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from leishmania major in hopes of creating a platform for the rational design of new therapeutics. crystals of the catalytic core of methionyl-trna synthetase from l. major (lmmetrs) were obtained with the substrates mgatp and methionine presen ...	2010	21144880
electron cryomicroscopy structure of a membrane-anchored mitochondrial aaa protease.	ftsh-related aaa proteases are conserved membrane-anchored, atp-dependent molecular machines, which mediate the processing and turnover of soluble and membrane-embedded proteins in eubacteria, mitochondria, and chloroplasts. homo- and hetero-oligomeric proteolytic complexes exist, which are composed of homologous subunits harboring an atpase domain of the aaa family and an h41 metallopeptidase domain. mutations in subunits of mitochondrial m-aaa proteases have been associated with different neur ...	2010	21147776
electron cryomicroscopy structure of a membrane-anchored mitochondrial aaa protease.	ftsh-related aaa proteases are conserved membrane-anchored, atp-dependent molecular machines, which mediate the processing and turnover of soluble and membrane-embedded proteins in eubacteria, mitochondria, and chloroplasts. homo- and hetero-oligomeric proteolytic complexes exist, which are composed of homologous subunits harboring an atpase domain of the aaa family and an h41 metallopeptidase domain. mutations in subunits of mitochondrial m-aaa proteases have been associated with different neur ...	2010	21147776
phenotypic characterization of transgenic mice overexpressing neuregulin-1.	neuregulin-1 (nrg1) is one of the susceptibility genes for schizophrenia and implicated in the neurotrophic regulation of gabaergic and dopaminergic neurons, myelination, and nmda receptor function. postmortem studies often indicate a pathologic association of increased nrg1 expression or signaling with this illness. however, the psychobehavioral implication of nrg1 signaling has mainly been investigated using hypomorphic mutant mice for individual nrg1 splice variants.	2010	21151609
molecular dynamics of ribosomal elongation factors g and tu.	translation on the ribosome is controlled by external factors. during polypeptide lengthening, elongation factors ef-tu and ef-g consecutively interact with the bacterial ribosome. ef-tu binds and delivers an aminoacyl-trna to the ribosomal a site and ef-g helps translocate the trnas between their binding sites after the peptide bond is formed. these processes occur at the expense of gtp. ef-tu:trna and ef-g are of similar shape, share a common binding site, and undergo large conformational chan ...	2010	21152913
molecular dynamics of ribosomal elongation factors g and tu.	translation on the ribosome is controlled by external factors. during polypeptide lengthening, elongation factors ef-tu and ef-g consecutively interact with the bacterial ribosome. ef-tu binds and delivers an aminoacyl-trna to the ribosomal a site and ef-g helps translocate the trnas between their binding sites after the peptide bond is formed. these processes occur at the expense of gtp. ef-tu:trna and ef-g are of similar shape, share a common binding site, and undergo large conformational chan ...	2010	21152913
breps: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation.	models for the simulation of metabolic networks require the accurate prediction of enzyme function. based on a genomic sequence, enzymatic functions of gene products are today mainly predicted by sequence database searching and operon analysis. other methods can support these techniques: we have developed an automatic method "breps" that creates highly specific sequence patterns for the functional annotation of enzymes.	2010	21122127
head swivel on the ribosome facilitates translocation by means of intra-subunit trna hybrid sites.	the elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer rnas to the aminoacyl-trna-binding site (a site) of the ribosome, followed by peptide-bond formation and translocation of the trnas through the ribosome to reopen the a site. the translocation reaction is catalysed by elongation factor g (ef-g) in a gtp-dependent manner. despite the availability of structures of various ef-g-ribosome complexes, the precise mechanism by which trnas move through the ribosome stil ...	2010	21124459
construction and analyses of tetrameric forms of yeast nad(+)-specific isocitrate dehydrogenase.	yeast nad(+)-specific isocitrate dehydrogenase (idh) is an octameric enzyme composed of four heterodimers of regulatory idh1 and catalytic idh2 subunits. the crystal structure suggested that the interactions between tetramers in the octamer are restricted to defined regions in idh1 subunits from each tetramer. using truncation and mutagenesis, we constructed three tetrameric forms of idh. truncation of five residues from the amino terminus of idh1 did not alter the octameric form of the enzyme, ...	2010	21133413
construction and analyses of tetrameric forms of yeast nad(+)-specific isocitrate dehydrogenase.	yeast nad(+)-specific isocitrate dehydrogenase (idh) is an octameric enzyme composed of four heterodimers of regulatory idh1 and catalytic idh2 subunits. the crystal structure suggested that the interactions between tetramers in the octamer are restricted to defined regions in idh1 subunits from each tetramer. using truncation and mutagenesis, we constructed three tetrameric forms of idh. truncation of five residues from the amino terminus of idh1 did not alter the octameric form of the enzyme, ...	2010	21133413
mutations in the intersubunit bridge regions of 16s rrna affect decoding and subunit-subunit interactions on the 70s ribosome.	the small and large subunits of the ribosome are held together by a series of bridges, involving rna-rna, rna-protein and protein-protein interactions. some 12 bridges have been described for the escherichia coli 70s ribosome. in this work, we have targeted for mutagenesis, some of the 16s rrna residues involved in the formation of intersubunit bridges b3, b5, b6, b7b and b8. in addition to effects on subunit association, the mutant ribosomes also affect the fidelity of translation; bridges b5, ...	2010	21138965
mutations in the intersubunit bridge regions of 16s rrna affect decoding and subunit-subunit interactions on the 70s ribosome.	the small and large subunits of the ribosome are held together by a series of bridges, involving rna-rna, rna-protein and protein-protein interactions. some 12 bridges have been described for the escherichia coli 70s ribosome. in this work, we have targeted for mutagenesis, some of the 16s rrna residues involved in the formation of intersubunit bridges b3, b5, b6, b7b and b8. in addition to effects on subunit association, the mutant ribosomes also affect the fidelity of translation; bridges b5, ...	2010	21138965
structure of a crispr-associated protein cas2 from desulfovibrio vulgaris.	crisprs (clustered regularly interspaced short palindromic repeats) provide bacteria and archaea with rna-guided acquired immunity to invasive dnas. crispr-associated (cas) proteins carry out the immune effector functions. cas2 is a universal component of the crispr system. here, a 1.35 å resolution crystal structure of cas2 from the bacterium desulfovibrio vulgaris (dvucas2) is reported. dvucas2 is a homodimer, with each protomer consisting of an n-terminal βαββαβ ferredoxin fold (amino acids 1 ...	2010	21139194
cloning, purification, crystallization and preliminary x-ray crystallographic analysis of the n-terminal domain of dead-box rna helicase from staphylococcus aureus strain mu50.	dead-box helicases are enzymes with an atp-dependent rna-unwinding function that are involved in a variety of cellular processes including rna splicing, ribosome biogenesis and rna degradation. in this study, the n-terminal domain of dead-box rna helicase from staphylococcus aureus strain mu50 was overexpressed in escherichia coli, purified and crystallized. diffraction data were collected to 2.60 å resolution using a synchrotron-radiation source. the crystal belonged to space group p1, with uni ...	2010	21139222
effects of site-directed mutagenesis of mgla on motility and swarming of myxococcus xanthus.	the mgla gene from the bacterium myxococcus xanthus encodes a 22kda protein related to the ras superfamily of monomeric gtpases. mgla is required for the normal function of a-motility (adventurous), s-motility (social), fruiting body morphogenesis, and sporulation. mgla and its homologs differ from all eukaryotic and other prokaryotic gtpases because they have a threonine (thr78) in place of the highly conserved aspartate residue of the consensus pm3 (phosphate-magnesium binding) region. to iden ...	2010	21083931
product-assisted catalysis as the basis of the reaction specificity of threonine synthase.	threonine synthase (ts), which is a pyridoxal 5'-phosphate (plp)-dependent enzyme, catalyzes the elimination of the γ-phosphate group from o-phospho-l-homoserine (ophs) and the subsequent addition of water at cβ to form l-threonine. the catalytic course of ts is the most complex among the plp enzymes, and it is an intriguing problem how the elementary steps are controlled in ts to carry out selective reactions. when l-vinylglycine was added to thermus thermophilus hb8 ts in the presence of phosp ...	2010	21084312
the role of oligomerization and cooperative regulation in protein function: the case of tryptophan synthase.	the oligomerization/co-localization of protein complexes and their cooperative regulation in protein function is a key feature in many biological systems. the synergistic regulation in different subunits often enhances the functional properties of the multi-enzyme complex. the present study used molecular dynamics and brownian dynamics simulations to study the effects of allostery, oligomerization and intermediate channeling on enhancing the protein function of tryptophan synthase (trps). trps u ...	2010	21085641
role of recj-like protein with 5'-3' exonuclease activity in oligo(deoxy)nucleotide degradation.	recj-like proteins belonging to the dhh family have been proposed to function as oligoribonucleases and 3'-phosphoadenosine 5'-phosphate (pap) phosphatases in bacteria and archaea, which do not have orn (oligoribonuclease) and cysq (pap phosphatase) homologs. in this study, we analyzed the biochemical and physiological characterization of the recj-like protein ttha0118 from thermus thermophilus hb8. ttha0118 had high enzymatic activity as an oligodeoxyribonucleotide- and oligoribonucleotide-spec ...	2010	21087930
carbon flux rerouting during mycobacterium tuberculosis growth arrest.	a hallmark of the mycobacterium tuberculosis life cycle is the pathogen's ability to switch between replicative and non-replicative states in response to host immunity. transcriptional profiling by qpcr of ∼ 50 m. tuberculosis genes involved in central and lipid metabolism revealed a re-routing of carbon flow associated with bacterial growth arrest during mouse lung infection. carbon rerouting was marked by a switch from metabolic pathways generating energy and biosynthetic precursors in growing ...	2010	21091505
assembling networks of microbial genomes using linear programming.	microbial genomes exhibit complex sets of genetic affinities due to lateral genetic transfer. assessing the relative contributions of parent-to-offspring inheritance and gene sharing is a vital step in understanding the evolutionary origins and modern-day function of an organism, but recovering and showing these relationships is a challenging problem.	2010	21092133
identification and characterization of a novel fumarase gene by metagenome expression cloning from marine microorganisms.	fumarase catalyzes the reversible hydration of fumarate to l-malate and is a key enzyme in the tricarboxylic acid (tca) cycle and in amino acid metabolism. fumarase is also used for the industrial production of l-malate from the substrate fumarate. thermostable and high-activity fumarases from organisms that inhabit extreme environments may have great potential in industry, biotechnology, and basic research. the marine environment is highly complex and considered one of the main reservoirs of mi ...	2010	21092234
pseudouridine at position 55 in trna controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium thermus thermophilus.	pseudouridine at position 55 (ψ55) in eubacterial trna is produced by trub. to clarify the role of the ψ55 modification, we constructed a trub gene disruptant (δtrub) strain of thermus thermophilus which is an extreme-thermophilic eubacterium. unexpectedly, the δtrub strain exhibited severe growth retardation at 50 °c. we assumed that these phenomena might be caused by lack of rna chaperone activity of trub, which was previously hypothetically proposed by others. to confirm this idea, we replace ...	2010	21097467
thermus thermophilus glycoside hydrolase family 57 branching enzyme: crystal structure, mechanism of action, and products formed.	branching enzyme (ec 2.4.1.18; glycogen branching enzyme; gbe) catalyzes the formation of α1,6-branching points in glycogen. until recently it was believed that all gbes belong to glycoside hydrolase family 13 (gh13). here we describe the cloning and expression of the thermus thermophilus family gh57-type gbe and report its biochemical properties and crystal structure at 1.35-å resolution. the enzyme has a central (β/α)(7)-fold catalytic domain a with an inserted domain b between β2 and α5 and a ...	2010	21097495
co impedes superfast o2 binding in ba3 cytochrome oxidase from thermus thermophilus.	kinetic studies of heme-copper terminal oxidases using the co flow-flash method are potentially compromised by the fate of the photodissociated co. in this time-resolved optical absorption study, we compared the kinetics of dioxygen reduction by ba(3) cytochrome c oxidase from thermus thermophilus in the absence and presence of co using a photolabile o(2)-carrier. a novel double-laser excitation is introduced in which dioxygen is generated by photolyzing the o(2)-carrier with a 355 nm laser puls ...	2010	21097703
diversity of the early step of the futalosine pathway.	we recently demonstrated that the futalosine pathway was operating in some bacteria for the biosynthesis of menaquinone and that futalosine was converted into dehypoxanthinyl futalosine (dhfl) by an mqnb of thermus thermophilus. in this study, we found that aminodeoxyfutalosine, which has adenine instead of hypoxanthine in futalosine, was directly converted into dhfl by an mqnb of helicobacter pylori. therefore, this step is potentially an attractive target for the development of specific anti-h ...	2010	21098241
rsga releases rbfa from 30s ribosome during a late stage of ribosome biosynthesis.	rsga is a 30s ribosomal subunit-binding gtpase with an unknown function, shortage of which impairs maturation of the 30s subunit. we identified multiple gain-of-function mutants of escherichia coli rbfa, the gene for a ribosome-binding factor, that suppress defects in growth and maturation of the 30s subunit of an rsga-null strain. these mutations promote spontaneous release of rbfa from the 30s subunit, indicating that cellular disorders upon depletion of rsga are due to prolonged retention of ...	2010	21102555
rsga releases rbfa from 30s ribosome during a late stage of ribosome biosynthesis.	rsga is a 30s ribosomal subunit-binding gtpase with an unknown function, shortage of which impairs maturation of the 30s subunit. we identified multiple gain-of-function mutants of escherichia coli rbfa, the gene for a ribosome-binding factor, that suppress defects in growth and maturation of the 30s subunit of an rsga-null strain. these mutations promote spontaneous release of rbfa from the 30s subunit, indicating that cellular disorders upon depletion of rsga are due to prolonged retention of ...	2010	21102555
structural basis of molecular recognition of the leishmania small hydrophilic endoplasmic reticulum-associated protein (sherp) at membrane surfaces.	the 57-residue small hydrophilic endoplasmic reticulum-associated protein (sherp) shows highly specific, stage-regulated expression in the non-replicative vector-transmitted stages of the kinetoplastid parasite, leishmania major, the causative agent of human cutaneous leishmaniasis. previous studies have demonstrated that sherp localizes as a peripheral membrane protein on the cytosolic face of the endoplasmic reticulum and on outer mitochondrial membranes, whereas its high copy number suggests ...	2010	21106528
structural basis of molecular recognition of the leishmania small hydrophilic endoplasmic reticulum-associated protein (sherp) at membrane surfaces.	the 57-residue small hydrophilic endoplasmic reticulum-associated protein (sherp) shows highly specific, stage-regulated expression in the non-replicative vector-transmitted stages of the kinetoplastid parasite, leishmania major, the causative agent of human cutaneous leishmaniasis. previous studies have demonstrated that sherp localizes as a peripheral membrane protein on the cytosolic face of the endoplasmic reticulum and on outer mitochondrial membranes, whereas its high copy number suggests ...	2010	21106528
an assessment of mechanisms underlying peripheral axonal degeneration caused by aminoacyl-trna synthetase mutations.	mutations in glycyl-, tyrosyl-, and alanyl-trna synthetases (gars, yars and aars respectively) cause autosomal dominant charcot-marie-tooth disease, and mutations in gars cause a similar peripheral neuropathy in mice. aminoacyl-trna synthetases (arss) charge amino acids onto their cognate trnas during translation; however, the pathological mechanism(s) of ars mutations remains unclear. to address this, we tested possible mechanisms using mouse models. first, amino acid mischarging was discounted ...	2010	21115117
an assessment of mechanisms underlying peripheral axonal degeneration caused by aminoacyl-trna synthetase mutations.	mutations in glycyl-, tyrosyl-, and alanyl-trna synthetases (gars, yars and aars respectively) cause autosomal dominant charcot-marie-tooth disease, and mutations in gars cause a similar peripheral neuropathy in mice. aminoacyl-trna synthetases (arss) charge amino acids onto their cognate trnas during translation; however, the pathological mechanism(s) of ars mutations remains unclear. to address this, we tested possible mechanisms using mouse models. first, amino acid mischarging was discounted ...	2010	21115117
evolution of respiratory complex i: "supernumerary" subunits are present in the alpha-proteobacterial enzyme.	modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. respiratory complex i from α-proteobacteria and mitochondria is well conserved at the level of the 14 "core" subunits, consistent with that notion. mitochondrial complex i contains the core subunits, present in all species, and up to 31 "supernumerary" subunits, generally thought to have originated only within eukaryotic lineages. however, the full protein composition of ...	2010	21115482
evolution of respiratory complex i: "supernumerary" subunits are present in the alpha-proteobacterial enzyme.	modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. respiratory complex i from α-proteobacteria and mitochondria is well conserved at the level of the 14 "core" subunits, consistent with that notion. mitochondrial complex i contains the core subunits, present in all species, and up to 31 "supernumerary" subunits, generally thought to have originated only within eukaryotic lineages. however, the full protein composition of ...	2010	21115482
identification of an rnase j ortholog in sulfolobus solfataricus: implications for 5'-to-3' directional decay and 5'-end protection of mrna in crenarchaeota.	in both bacteria and eukaryotes, degradation is known to start at the 5' and at the 3' extremities of mrnas. until the recent discovery of 5'-to-3' exoribonucleases in hyperthermophilic euryarchaeota, the exosome was assumed to be the key enzyme in mrna degradation in archaea. by means of zymogram assays and bioinformatics, we have identified a 5'-to-3' exoribonuclease activity in the crenarchaeum sulfolobus solfataricus (sso), which is affected by the phosphorylation state of the 5'-end of the ...	2010	21115637
characterization of a mannose-6-phosphate isomerase from thermus thermophilus and increased l-ribose production by its r142n mutant.	an uncharacterized gene from thermus thermophilus, thought to encode a mannose-6-phosphate isomerase, was cloned and expressed in escherichia coli. the maximal activity of the recombinant enzyme for l-ribulose isomerization was observed at ph 7.0 and 75°c in the presence of 0.5 mm cu(2+). among all of the pentoses and hexoses evaluated, the enzyme exhibited the highest activity for the conversion of l-ribulose to l-ribose, a potential starting material for many l-nucleoside-based pharmaceutical ...	2010	21115698
n-acetyl-d-glucosaminylphosphatidylinositol de-n-acetylase from entamoeba histolytica: metal alters catalytic rates but not substrate affinity.	pig-l/gpi12 proteins are endoplasmic reticulum-resident membrane proteins involved in the second step of glycosylphosphatidylinositol anchor biosynthesis in eukaryotes. we show that the entamoeba histolytica pig-l protein is optimally active in the acidic ph range. the enzyme has an intrinsic low level of de-n-acetylase activity in the absence of metal and is significantly stimulated by divalent cations. metal binding induces a large conformational change in the protein that appears to improve c ...	2010	21118807
n-acetyl-d-glucosaminylphosphatidylinositol de-n-acetylase from entamoeba histolytica: metal alters catalytic rates but not substrate affinity.	pig-l/gpi12 proteins are endoplasmic reticulum-resident membrane proteins involved in the second step of glycosylphosphatidylinositol anchor biosynthesis in eukaryotes. we show that the entamoeba histolytica pig-l protein is optimally active in the acidic ph range. the enzyme has an intrinsic low level of de-n-acetylase activity in the absence of metal and is significantly stimulated by divalent cations. metal binding induces a large conformational change in the protein that appears to improve c ...	2010	21118807
mutation in subdomain g' of mitochondrial elongation factor g1 is associated with combined oxphos deficiency in fibroblasts but not in muscle.	the mitochondrial translation system is responsible for the synthesis of 13 proteins required for oxidative phosphorylation (oxphos), the major energy-generating process of our cells. mitochondrial translation is controlled by various nuclear encoded proteins. in 27 patients with combined oxphos deficiencies, in whom complex ii (the only complex that is entirely encoded by the nuclear dna) showed normal activities, and mutations in the mitochondrial genome as well as polymerase gamma were exclud ...	2010	21119709
mutation in subdomain g' of mitochondrial elongation factor g1 is associated with combined oxphos deficiency in fibroblasts but not in muscle.	the mitochondrial translation system is responsible for the synthesis of 13 proteins required for oxidative phosphorylation (oxphos), the major energy-generating process of our cells. mitochondrial translation is controlled by various nuclear encoded proteins. in 27 patients with combined oxphos deficiencies, in whom complex ii (the only complex that is entirely encoded by the nuclear dna) showed normal activities, and mutations in the mitochondrial genome as well as polymerase gamma were exclud ...	2010	21119709
pivotal roles of three conserved carboxyl residues of the nuoc (30k) segment in the structural integrity of proton-translocating nadh-quinone oxidoreductase from escherichia coli.	the prokaryotic proton-translocating nadh-quinone oxidoreductase (ndh-1) is an l-shaped membrane-bound enzyme that contains 14 subunits (nuoa-nuon or nqo1-nqo14). all subunits have their counterparts in the eukaryotic enzyme (complex i). ndh-1 consists of two domains: the peripheral arm (nuob, -c, -d, -e, -f, -g, and -i) and the membrane arm (nuoa, -h, -j, -k, -l, -m, and -n). in escherichia coli ndh-1, the hydrophilic subunits nuoc/nqo5/30k and nuod/nqo4/49k are fused together in a single polyp ...	2010	20979355
cryo-em structure and rrna model of a translating eukaryotic 80s ribosome at 5.5-a resolution.	protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. although x-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80s ribosomes are lacking. using cryoelectron microscopy and single-particle reconstruction, we have determined the structure of a translating plant (triticum aestivum) 80s ribosome at 5.5-å resolution. this map, together with a 6.1-å map of a saccharomyces cere ...	2010	20980660
molecular mechanisms of the whole dna repair system: a comparison of bacterial and eukaryotic systems.	dna is subjected to many endogenous and exogenous damages. all organisms have developed a complex network of dna repair mechanisms. a variety of different dna repair pathways have been reported: direct reversal, base excision repair, nucleotide excision repair, mismatch repair, and recombination repair pathways. recent studies of the fundamental mechanisms for dna repair processes have revealed a complexity beyond that initially expected, with inter- and intrapathway complementation as well as f ...	2010	20981145
ph-dependent studies reveal an efficient hydroxylation mechanism of the oxygenase component of p-hydroxyphenylacetate 3-hydroxylase.	p-hydroxyphenylacetate (hpa) 3-hydroxylase (hpah) catalyzes the hydroxylation of hpa at the ortho-position to yield 3,4-dihydroxyphenylacetate. the enzyme is a flavin-dependent two-component monooxygenase that consists of a reductase component and an oxygenase component (c(2)). c(2) catalyzes the hydroxylation of hpa using oxygen and reduced fmn as co-substrates. to date, the effects of ph on the oxygenation of the two-component monooxygenases have never been reported. here, we report the reacti ...	2010	21030590
ph-dependent studies reveal an efficient hydroxylation mechanism of the oxygenase component of p-hydroxyphenylacetate 3-hydroxylase.	p-hydroxyphenylacetate (hpa) 3-hydroxylase (hpah) catalyzes the hydroxylation of hpa at the ortho-position to yield 3,4-dihydroxyphenylacetate. the enzyme is a flavin-dependent two-component monooxygenase that consists of a reductase component and an oxygenase component (c(2)). c(2) catalyzes the hydroxylation of hpa using oxygen and reduced fmn as co-substrates. to date, the effects of ph on the oxygenation of the two-component monooxygenases have never been reported. here, we report the reacti ...	2010	21030590
inactivation of the rlud pseudouridine synthase has minimal effects on growth and ribosome function in wild-type escherichia coli and salmonella enterica.	the escherichia coli rlud gene encodes a pseudouridine synthase responsible for the pseudouridine (ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23s rrna. it has been reported that deletion of rlud in k-12 strains of e. coli is associated with extremely slow growth, increased readthrough of stop codons, and defects in 50s ribosomal subunit assembly and 30s-50s subunit association. suppressor mutations in the prfb and prfc genes encoding release factor 2 (rf2) and rf3 that res ...	2010	21037010