Publications

biosynthesis of the rna polymerase inhibitor streptolydigin in streptomyces lydicus: tailoring modification of 3-methyl-aspartate.	the asparaginyl-trna synthetase-like slgz and methyltransferase slgm enzymes are involved in the biosynthesis of the tetramic acid streptolydigin in streptomyces lydicus. inactivation of slgz led to a novel streptolydigin derivative. overexpression of slgz, slgm, or both in s. lydicus led to a considerable increase in streptolydigin production.	2011	21398531
resolving stepping rotation in thermus thermophilus h(+)-atpase/synthase with an essentially drag-free probe.	vacuole-type atpases (v(o)v1) and f(o)f1 atp synthases couple atp hydrolysis/synthesis in the soluble v(1) or f1 portion with proton (or na(+)) flow in the membrane-embedded v(o) or f(o) portion through rotation of one common shaft. here we show at submillisecond resolutions the atp-driven rotation of isolated v1 and the whole v(o)v1 from thermus thermophilus, by attaching a 40-nm gold bead for which viscous drag is almost negligible. v1 made 120° steps, commensurate with the presence of three c ...	2011	21407199
genetic components of stringent response in vibrio cholerae.	nutritional stress elicits stringent response in bacteria involving modulation of expression of several genes. this is mainly triggered by the intracellular accumulation of two small molecules, namely, guanosine 3'-diphosphate 5'-triphosphate and guanosine 3',5'-bis(diphosphate), collectively called (p)ppgpp. like in other gram-negative bacteria, the cellular level of (p)ppgpp is maintained in vibrio cholerae, the causative bacterial pathogen of the disease cholera, by the products of two genes ...	2011	21415497
involvement of cara/litr and crp/fnr family transcriptional regulators in light-induced carotenoid production in thermus thermophilus.	members of the cara/litr family are merr-type transcriptional regulators that contain a c-terminal cobalamin-binding domain. they are thought to be involved in light-induced transcriptional regulation in a wide variety of nonphototrophic bacteria. based on the distribution of this kind of regulator, the current study examined carotenoid production in thermus thermophilus, and it was found to occur in a light-induced manner. litr and carotenoid and cobalamin biosynthesis genes were all located on ...	2011	21421762
substrate specificity of the bacillus licheniformis lyxose isomerase ydae and its application in in vitro catalysis for bioproduction of lyxose and glucose by two-step isomerization.	enzymatic processes are useful for industrially important sugar production, and in vitro two-step isomerization has proven to be an efficient process in utilizing readily available sugar sources. a hypothetical uncharacterized protein encoded by ydae of bacillus licheniformis was found to have broad substrate specificities and has shown high catalytic efficiency on d-lyxose, suggesting that the enzyme is d-lyxose isomerase. escherichia coli bl21 expressing the recombinant protein, of 19.5 kda, s ...	2011	21421786
insights into physiological and genetic mupirocin susceptibility in bifidobacteria.	mupirocin is an antibiotic commonly used in selective media for the isolation of bifidobacteria. however, little is known about the genetic traits responsible for bifidobacterial resistance to mupirocin. our investigation demonstrates that all of the bifidobacteria tested exhibit a phenotype of generally high resistance to this antibiotic. the genotypic reason for bifidobacterial mupirocin resistance was further characterized by sequencing of the isoleucyl-trna synthetase gene (iles) coupled wit ...	2011	21421794
a rigidifying salt-bridge favors the activity of thermophilic enzyme at high temperatures at the expense of low-temperature activity.	thermophilic enzymes are often less active than their mesophilic homologues at low temperatures. one hypothesis to explain this observation is that the extra stabilizing interactions increase the rigidity of thermophilic enzymes and hence reduce their activity. here we employed a thermophilic acylphosphatase from pyrococcus horikoshii and its homologous mesophilic acylphosphatase from human as a model to study how local rigidity of an active-site residue affects the enzymatic activity.	2011	21423654
the genetic architecture of branched-chain amino acid accumulation in tomato fruits.	previous studies of the genetic architecture of fruit metabolic composition have allowed us to identify four strongly conserved co-ordinate quantitative trait loci (qtl) for the branched-chain amino acids (bcaas). this study has been extended here to encompass the other 23 enzymes described to be involved in the pathways of bcaa synthesis and degradation. on coarse mapping the chromosomal location of these enzymes, it was possible to define the map position of 24 genes. of these genes eight co-l ...	2011	21436187
phylogenetic distribution and evolutionary history of bacterial dead-box proteins.	dead-box proteins are found in all domains of life and participate in almost all cellular processes that involve rna. the presence of dead and helicase_c conserved domains distinguish these proteins. dead-box proteins exhibit rna-dependent atpase activity in vitro, and several also show rna helicase activity. in this study, we analyzed the distribution and architecture of dead-box proteins among bacterial genomes to gain insight into the evolutionary pathways that have shaped their history. we i ...	2011	21437710
nmr structure of the c-terminal domain of a tyrosyl-trna synthetase that functions in group i intron splicing.	the mitochondrial tyrosyl-trna synthetases (mt tyrrss) of pezizomycotina fungi are bifunctional proteins that aminoacylate mitochondrial trna(tyr) and are structure-stabilizing splicing cofactors for group i introns. studies with the neurospora crassa synthetase (cyt-18 protein) showed that splicing activity is dependent upon pezizomycotina-specific structural adaptations that form a distinct group i intron-binding site in the n-terminal catalytic domain. although cyt-18's c-terminal domain also ...	2011	21438536
bacterial transcription terminators: the rna 3'-end chronicles.	the process of transcription termination is essential to proper expression of bacterial genes and, in many cases, to the regulation of bacterial gene expression. two types of bacterial transcriptional terminators are known to control gene expression. intrinsic terminators dissociate transcription complexes without the assistance of auxiliary factors. rho-dependent terminators are sites of dissociation mediated by an rna helicase called rho. despite decades of study, the molecular mechanisms of b ...	2011	21439297
unexpected diversity of chlorite dismutases: a catalytically efficient dimeric enzyme from nitrobacter winogradskyi.	chlorite dismutase (cld) is a unique heme enzyme catalyzing the conversion of clo(2)(-) to cl(-) and o(2). cld is usually found in perchlorate- or chlorate-reducing bacteria but was also recently identified in a nitrite-oxidizing bacterium of the genus nitrospira. here we characterized a novel cld-like protein from the chemolithoautotrophic nitrite oxidizer nitrobacter winogradskyi which is significantly smaller than all previously known chlorite dismutases. its three-dimensional (3d) crystal st ...	2011	21441524
rna in defense: crisprs protect prokaryotes against mobile genetic elements.	the crispr/cas system in prokaryotes provides resistance against invading viruses and plasmids. three distinct stages in the mechanism can be recognized. initially, fragments of invader dna are integrated as new spacers into the repetitive crispr locus. subsequently, the crispr is transcribed and the transcript is cleaved by a cas protein within the repeats, generating short rnas (crrnas) that contain the spacer sequence. finally, crrnas guide the cas protein machinery to a complementary invader ...	2012	21441598
solution structure of an alternate conformation of helix27 from escherichia coli16s rrna.	helix (h)27 of 16s ribosomal (r)rna from escherichia coli was dubbed the "switch helix" when mutagenesis suggested that two alternative base pair registers may have distinct functional roles in the bacterial ribosome. although more recent genetic analyses suggest that h27 conformational switching is not required for translation, previous solution studies demonstrated that the isolated e. coli h27 can dynamically convert between the 885 and 888 conformations. here, we have solved the nuclear magn ...	2011	21442607
identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks.	structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. while the conserved regions often superimpose well, the variable regions appear non superimposable. differences in homologous protein structures are thought to be due to evolutionary plasticity to accommodate diverged sequences during evolution. one of the kinds of differences between 3-d structures of homologou ...	2011	21445259
molecular evolution of urea amidolyase and urea carboxylase in fungi.	urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. urea amidolyase has been found only in some fungal species among eukaryotes. it contains two major domains: the amidase and urea carboxylase domains. a shorter form of urea amidolyase is known as urea carboxylase and has no amidase domain. eukaryotic urea carboxylase has been found only in several fungal species and green algae. in order to elucid ...	2011	21447149
a model of the proton translocation mechanism of complex i.	despite decades of speculation, the proton pumping mechanism of complex i (nadh-ubiquinone oxidoreductase) is unknown and continues to be controversial. recent descriptions of the architecture of the hydrophobic region of complex i have resolved one vital issue: this region appears to have multiple proton transporters that are mechanically interlinked. thus, transduction of conformational changes to drive the transmembrane transporters linked by a "connecting rod" during the reduction of ubiquin ...	2011	21454533
regulatory circuits of the aaa+ disaggregase hsp104.	yeast hsp104 is an aaa+ chaperone that rescues proteins from the aggregated state. six protomers associate to form the functional hexamer. each protomer contains two aaa+ modules, nbd1 and nbd2. hsp104 converts energy provided by atp into mechanical force used to thread polypeptides through its axial channel, thereby disrupting protein aggregates. but how the action of its 12 aaa+ domains is co-ordinated to catalyze disaggregation remained unexplained. here, we identify a sophisticated allosteri ...	2011	21454552
mutations in mitochondrial histidyl trna synthetase hars2 cause ovarian dysgenesis and sensorineural hearing loss of perrault syndrome.	perrault syndrome is a genetically heterogeneous recessive disorder characterized by ovarian dysgenesis and sensorineural hearing loss. in a nonconsanguineous family with five affected siblings, linkage analysis and genomic sequencing revealed the genetic basis of perrault syndrome to be compound heterozygosity for mutations in the mitochondrial histidyl trna synthetase hars2 at two highly conserved amino acids, l200v and v368l. the nucleotide substitution creating hars2 p.l200v also created an ...	2011	21464306
multifaceted roles of alkyltransferase and related proteins in dna repair, dna damage, resistance to chemotherapy, and research tools.	o(6)-alkylguanine-dna alkyltransferase (agt) is a widely distributed, unique dna repair protein that acts as a single agent to directly remove alkyl groups located on the o(6)-position of guanine from dna restoring the dna in one step. the protein acts only once, and its alkylated form is degraded rapidly. it is a major factor in counteracting the mutagenic, carcinogenic, and cytotoxic effects of agents that form such adducts including n-nitroso-compounds and a number of cancer chemotherapeutics ...	2011	21466232
isoflurane selectively inhibits distal mitochondrial complex i in caenorhabditis elegans.	complex i of the electron transport chain (etc) is a possible target of volatile anesthetics (vas). complex i enzymatic activities are inhibited by vas, and dysfunction of complex i can lead to hypersensitivity to vas in worms and in people. mutant analysis in caenorhabditis (c.) elegans suggests that vas may specifically interfere with complex i function at the binding site for its substrate ubiquinone. we hypothesized that isoflurane inhibits electron transport by competing with ubiquinone for ...	2011	21467554
clamping the clamp of rna polymerase.		2011	21468097
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
utilizing natural diversity to evolve protein function: applications towards thermostability.	protein evolution relies on designing a library of sequences that capture meaningful functional diversity in a limited number of protein variants. several approaches take advantage of the sequence space already explored through natural selection by incorporating sequence diversity available from modern genomes (and their ancestors) when designing these libraries. the success of these approaches is, partly, owing to the fact that modern sequence diversity has already been subjected to evolutionar ...	2011	21470898
a disulfide bridge network within the soluble periplasmic domain determines structure and function of the outer membrane protein rcsf.	rcsf, a proposed auxiliary regulator of the regulation of capsule synthesis (rcs) phosphorelay system, is a key element for understanding the rcsc-d-a/b signaling cascade, which is responsible for the regulation of more than 100 genes and is involved in cell division, motility, biofilm formation, and virulence. the rcsc-d-a/b system is one of the most complex bacterial signal transduction pathways, consisting of several membrane-bound and soluble proteins. rcsf is a lipoprotein attached to the o ...	2011	21471196
emerging structural themes in large rna molecules.	extensive networks of tertiary interactions give rise to unique, highly organized domain architectures that characterize the three-dimensional structure of large rna molecules. formed by stacked layers of a near-planar arrangement of contiguous coaxial helices, large rna molecules are relatively flat in overall shape. the functional core of these molecules is stabilized by a diverse set of tertiary interaction motifs that often bring together distant regions of conserved nucleotides. although ho ...	2011	21474301
structural and functional characterization of rv2966c protein reveals an rsmd-like methyltransferase from mycobacterium tuberculosis and the role of its n-terminal domain in target recognition.	nine of ten methylated nucleotides of escherichia coli 16 s rrna are conserved in mycobacterium tuberculosis. all the 10 different methyltransferases are known in e. coli, whereas only tlya and gidb have been identified in mycobacteria. here we have identified rv2966c of m. tuberculosis as an ortholog of rsmd protein of e. coli. we have shown that rv2966c can complement rsmd-deleted e. coli cells. recombinant rv2966c can use 30 s ribosomes purified from rsmd-deleted e. coli as substrate and meth ...	2011	21474448
species-specific collaboration of heat shock proteins (hsp) 70 and 100 in thermotolerance and protein disaggregation.	yeast hsp104 and its bacterial homolog, clpb, are clp/hsp100 molecular chaperones and aaa+ atpases. hsp104 and clpb collaborate with the hsp70 and dnak chaperone systems, respectively, to retrieve and reactivate stress-denatured proteins from aggregates. the action of hsp104 and clpb in promoting cell survival following heat stress is species-specific: hsp104 cannot function in bacteria and clpb cannot act in yeast. to determine the regions of hsp104 and clpb necessary for this specificity, we t ...	2011	21474779
termination and antitermination: rna polymerase runs a stop sign.	termination signals induce rapid and irreversible dissociation of the nascent transcript from rna polymerase. terminators at the end of genes prevent unintended transcription into the downstream genes, whereas terminators in the upstream regulatory leader regions adjust expression of the structural genes in response to metabolic and environmental signals. premature termination within an operon leads to potentially deleterious defects in the expression of the downstream genes, but also provides a ...	2011	21478900
seca, a remarkable nanomachine.	biological cells harbor a variety of molecular machines that carry out mechanical work at the nanoscale. one of these nanomachines is the bacterial motor protein seca which translocates secretory proteins through the protein-conducting membrane channel secyeg. seca converts chemically stored energy in the form of atp into a mechanical force to drive polypeptide transport through secyeg and across the cytoplasmic membrane. in order to accommodate a translocating polypeptide chain and to release t ...	2011	21479870
synthesis of rare sugars with l-fuculose-1-phosphate aldolase (fuca) from thermus thermophilus hb8.	we report herein a one-pot four-enzyme approach for the synthesis of the rare sugars d-psicose, d-sorbose, l-tagatose, and l-fructose with aldolase fuca from a thermophilic source (thermus thermophilus hb8). importantly, the cheap starting material dl-gp (dl-glycerol 3-phosphate), was used to significantly reduce the synthetic cost.	2011	21482110
allosteric signal transmission in the nucleotide-binding domain of 70-kda heat shock protein (hsp70) molecular chaperones.	the 70-kda heat shock protein (hsp70) chaperones perform a wide array of cellular functions that all derive from the ability of their n-terminal nucleotide-binding domains (nbds) to allosterically regulate the substrate affinity of their c-terminal substrate-binding domains in a nucleotide-dependent mechanism. to explore the structural origins of hsp70 allostery, we performed nmr analysis on the nbd of dnak, the escherichia coli hsp70, in six different states (ligand-bound or apo) and in two con ...	2011	21482798
a chaperonin subunit with unique structures is essential for folding of a specific substrate.	type i chaperonins are large, double-ring complexes present in bacteria (groel), mitochondria (hsp60), and chloroplasts (cpn60), which are involved in mediating the folding of newly synthesized, translocated, or stress-denatured proteins. in escherichia coli, groel comprises 14 identical subunits and has been exquisitely optimized to fold its broad range of substrates. however, multiple cpn60 subunits with different expression profiles have evolved in chloroplasts. here, we show that, in arabido ...	2011	21483722
5'-methylthioadenosine nucleosidase is implicated in playing a key role in a modified futalosine pathway for menaquinone biosynthesis in campylobacter jejuni.	menaquinone (vitamin k(2)) serves as an electron carrier in the electron transport chain required for respiration in many pathogenic bacteria. most bacteria utilize a common menaquinone biosynthetic pathway as exemplified by escherichia coli. recently, a novel biosynthetic pathway, the futalosine pathway, was discovered in streptomyces. bioinformatic analysis strongly suggests that this pathway is also operative in the human pathogens campylobacter jejuni and helicobacter pylori. here, we provid ...	2011	21489995
structure of an archaeal-type phosphoenolpyruvate carboxylase sensitive to inhibition by aspartate.	the crystal structure of an archaeal-type phosphoenolpyruvate carboxylase from clostridium perfringens has been determined based on x-ray data extending to 3 å. the asymmetric unit of the structure includes two tetramers (each a dimer-of-dimers) of the enzyme. the precipitant, malonate, employed for the crystallization is itself a weak inhibitor of phosphoenolpyruvate carboxylase and a malonate molecule is seen in the active-site in the crystal structure. the allosteric binding sites for asparta ...	2011	21491491
structure-based identification of catalytic residues.	the identification of catalytic residues is an essential step in functional characterization of enzymes. we present a purely structural approach to this problem, which is motivated by the difficulty of evolution-based methods to annotate structural genomics targets that have few or no homologs in the databases. our approach combines a state-of-the-art support vector machine (svm) classifier with novel structural features that augment structural clues by spatial averaging and z scoring. special a ...	2011	21491495
quantum electron tunneling in respiratory complex i.	we have simulated the atomistic details of electronic wiring of all fe/s clusters in complex i, a key enzyme in the respiratory electron transport chain. the tunneling current theory of many-electron systems is applied to the broken-symmetry (bs) states of the protein at the zindo level. while the one-electron tunneling approximation is found to hold in electron tunneling between the antiferromagnetic binuclear and tetranuclear fe/s clusters without major orbital or spin rearrangement of the cor ...	2011	21495666
structural, mechanistic and coordination chemistry of relevance to the biosynthesis of iron-sulfur and related iron cofactors.	iron-sulfur clusters are an important class of protein-bound prosthetic center that find wide utility in nature. roles include electron transfer, enzyme catalysis, protein structure stabilization, and regulation of gene expression as transcriptional and translational sensors. in eukaryotes their biosynthesis requires a complex molecular machinery that is located within the mitochondrion, while bacteria exhibit up to three independent cluster assembly pathways. all of these paths share common the ...	2011	21499539
light-dependent gene regulation by a coenzyme b12-based photoreceptor.	cobalamin (b(12)) typically functions as an enzyme cofactor but can also regulate gene expression via rna-based riboswitches. b(12)-directed gene regulatory mechanisms via protein factors have, however, remained elusive. recently, we reported down-regulation of a light-inducible promoter in the bacterium myxococcus xanthus by two paralogous transcriptional repressors, of which one, carh, but not the other, cara, absolutely requires b(12) for activity even though both have a canonical b(12)-bindi ...	2011	21502508
an src homology 3 domain-like fold protein forms a ferredoxin binding site for the chloroplast nadh dehydrogenase-like complex in arabidopsis.	some subunits of chloroplast nad(p)h dehydrogenase (ndh) are related to those of the respiratory complex i, and ndh mediates photosystem i (psi) cyclic electron flow. despite extensive surveys, the electron donor and its binding subunits have not been identified. here, we identified three novel components required for ndh activity. crrj and crrl are j- and j-like proteins, respectively, and are components of ndh subcomplex a. crr31 is an src homology 3 domain-like fold protein, and its c-termina ...	2011	21505067
structural basis of defects in the sacsin hepn domain responsible for autosomal recessive spastic ataxia of charlevoix-saguenay (arsacs).	sacsin is a 520-kda protein mutated in the early-onset neurodevelopmental and neurodegenerative disease autosomal recessive spastic ataxia of charlevoix-saguenay (arsacs). the c terminus of the protein contains an hepn (higher eukaryotes and prokaryotes nucleotide-binding) domain of unknown function. here, we determined the high-resolution 1.9-å crystal structure of the hepn domain from human sacsin. the structure is composed of five parallel α-helices with a large loop of several short helical ...	2011	21507954
reca proteins from deinococcus geothermalis and deinococcus murrayi - cloning, purification and biochemical characterisation.	abstract:	2011	21513512
bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.	trimeric intracellular cation-specific (tric) channels are integral to muscle excitation-contraction coupling. tric channels provide counter-ionic flux when calcium is rapidly transported from intracellular stores to the cell cytoplasm. until recently, knowledge of the presence of these proteins was limited to animals. we analyzed the tric family and identified a profusion of prokaryotic family members with topologies and motifs similar to those of their eukaryotic counterparts. prokaryotic memb ...	2011	21519847
the central core region of yeast ribosomal protein l11 is important for subunit joining and translational fidelity.	yeast ribosomal protein l11 is positioned at the intersubunit cleft of the large subunit central protuberance, forming an intersubunit bridge with the small subunit protein s18. mutants were engineered in the central core region of l11 which interacts with helix 84 of the 25s rrna. numerous mutants in this region conferred 60s subunit biogenesis defects. specifically, many mutations of f96 and the a66d mutant promoted formation of halfmers as assayed by sucrose density ultracentrifugation. halfm ...	2011	21519857
functional consequences of t-stem mutations in e. coli trnathrugu in vitro and in vivo.	the binding affinities between escherichia coli ef-tu and 34 single and double base-pair changes in the t stem of e. coli trna(thr)(ugu) were compared with similar data obtained previously for several aa-trnas binding to thermus thermophilus ef-tu. with a single exception, the two proteins bound to mutations in three t-stem base pairs in a quantitatively identical manner. however, trna(thr) differs from other trnas by also using its rare a52-c62 pair as a negative specificity determinant. using ...	2011	21527672
the history of the discovery of the molybdenum cofactor and novel aspects of its biosynthesis in bacteria.	biosynthesis of the molybdenum cofactor in bacteria is described with a detailed analysis of each individual reaction leading to the formation of stable intermediates during the synthesis of molybdopterin from gtp. as a starting point, the discovery of molybdopterin and the elucidation of its structure through the study of stable degradation products are described. subsequent to molybdopterin synthesis, the molybdenum atom is added to the molybdopterin dithiolene group to form the molybdenum cof ...	2011	21528011
a central interdomain protein joint in ef-g regulates antibiotic sensitivity, gtp hydrolysis, and ribosome translocation.	the antibiotic fusidic acid potently inhibits bacterial translation (and cellular growth) by lodging between domains i and iii of elongation factor g (ef-g), and preventing release of ef-g from the ribosome. we have examined the functions of key amino acid residues near the active site of ef-g, which interact with fusidic acid and regulate hydrolysis of guanosine 5'-triphosphate (gtp). alanine mutants of these residues spontaneously hydrolyze gtp in solution, bypassing the ribosome's normal acti ...	2011	21531717
formation of a stable ruva double tetramer is required for efficient branch migration in vitro and for replication fork reversal in vivo.	in bacteria, ruvabc is required for the resolution of holliday junctions (hj) made during homologous recombination. the ruvab complex catalyzes hj branch migration and replication fork reversal (rfr). during rfr, a stalled fork is reversed to form a hj adjacent to a dna double-strand end, a reaction that requires ruvab in certain e. coli replication mutants. the exact structure of active ruvab complexes remains elusive as it is still unknown whether one or two tetramers of ruva support ruvb duri ...	2011	21531731
parb binding and spreading on dna determine its biological function in pseudomonas aeruginosa.	parb protein of pseudomonas aeruginosa belongs to a widely represented parb family of chromosomally and plasmid-encoded partitioning type ia proteins. ten putative pars sites are dispersed in the p. aeruginosa chromosome with eight of them localizing in the oric domain. after binding to pars parb spreads on the dna causing transcriptional silencing of nearby genes (5). we have studied parb derivatives impaired in spreading either due to loss of dna binding ability or oligomerization. we defined ...	2011	21531806
crystal structure of a metal-dependent phosphoesterase (yp_910028.1) from bifidobacterium adolescentis: computational prediction and experimental validation of phosphoesterase activity.	the crystal structures of an unliganded and adenosine 5'-monophosphate (amp) bound, metal-dependent phosphoesterase (yp_910028.1) from bifidobacterium adolescentis are reported at 2.4 and 1.94 å, respectively. functional characterization of this enzyme was guided by computational analysis and then confirmed by experiment. the structure consists of a polymerase and histidinol phosphatase (php, pfam: pf02811) domain with a second domain (residues 105-178) inserted in the middle of the php sequence ...	2011	21538547
structure of mycobacterium tuberculosisphosphopantetheine adenylyltransferase in complex with the feedback inhibitor coa reveals only one active-site conformation.	phosphopantetheine adenylyltransferase (ppat) catalyzes the penultimate step in the coenzyme a (coa) biosynthetic pathway, reversibly transferring an adenylyl group from atp to 4'-phosphopantetheine to form dephosphocoenzyme a (dpcoa). to complement recent biochemical and structural studies on mycobacterium tuberculosis ppat (mtppat) and to provide further insight into the feedback regulation of mtppat by coa, the x-ray crystal structure of the mtppat enzyme in complex with coa was determined to ...	2011	21543857
crystallization and preliminary x-ray diffraction analysis of transaldolase from thermoplasma acidophilum.	the metabolic enzyme transaldolase from thermoplasma acidophilum was recombinantly expressed in escherichia coli and could be crystallized in two polymorphic forms. crystals were grown by the hanging-drop vapour-diffusion method using peg 6000 as precipitant. native data sets for crystal forms 1 and 2 were collected in-house to resolutions of 3.0 and 2.7 å, respectively. crystal form 1 belonged to the orthorhombic space group c222(1) with five monomers per asymmetric unit and crystal form 2 belo ...	2011	21543867
isolation of xylose isomerases by sequence- and function-based screening from a soil metagenome library.	abstract: background: xylose isomerase (xi) catalyses the isomerization of xylose to xylulose in bacteria and some fungi. currently, only a limited number of xi genes have been functionally expressed in saccharomyces cerevisiae, the microorganism of choice for lignocellulosic ethanol production. the objective of the present study was to search for novel xi genes in the vastly diverse microbial habitat present in soil. as the exploitation of microbial diversity is impaired by the ability to culti ...	2011	21545702
mitochondrial targeting of human nadh dehydrogenase (ubiquinone) flavoprotein 2 (ndufv2) and its association with early-onset hypertrophic cardiomyopathy and encephalopathy.	abstract: background: nadh dehydrogenase (ubiquinone) flavoprotein 2 (ndufv2), containing one iron sulfur cluster ([2fe-2s] binuclear cluster n1a), is one of the core nuclear-encoded subunits existing in human mitochondrial complex i. defects in this subunit have been associated with parkinson's disease, alzheimer's disease, bipolar disorder, and schizophrenia. the aim of this study is to examine the mitochondrial targeting of ndufv2 and dissect the pathogenetic mechanism of one human deletion m ...	2011	21548921
the 2'-oh group of the peptidyl-trna stabilizes an active conformation of the ribosomal ptc.	the ribosome accelerates the rate of peptidyl transfer by >10(6)-fold relative to the background rate. a widely accepted model for this rate enhancement invokes entropic effects whereby the ribosome and the 2'-oh of the peptidyl-trna substrate precisely position the reactive moieties through an extensive network of hydrogen bonds that allows proton movement through them. some studies, however, have called this model into question because they find the 2'-oh of the peptidyl-trna to be dispensable ...	2011	21552203
inactivation of the dna repair genes muts, mutl or the anti-recombination gene muts2 leads to activation of vitamin b(1) biosynthesis genes.	oxidative stress generates harmful reactive oxygen species (ros) that attack biomolecules including dna. in living cells, there are several mechanisms for detoxifying ros and repairing oxidatively-damaged dna. in this study, transcriptomic analyses clarified that disruption of dna repair genes muts and mutl, or the anti-recombination gene muts2, in thermus thermophilus hb8, induces the biosynthesis pathway for vitamin b(1), which can serve as an ros scavenger. in addition, disruption of muts, mu ...	2011	21552516
crystal structures of burkholderia cenocepacia dihydropteroate synthase in the apo-form and complexed with the product 7,8-dihydropteroate.	abstract:	2011	21554707
a bioinformatics classifier and database for heme-copper oxygen reductases.	heme-copper oxygen reductases (hcos) are the last enzymatic complexes of most aerobic respiratory chains, reducing dioxygen to water and translocating up to four protons across the inner mitochondrial membrane (eukaryotes) or cytoplasmatic membrane (prokaryotes). the number of completely sequenced genomes is expanding exponentially, and concomitantly, the number and taxonomic distribution of hco sequences. these enzymes were initially classified into three different types being this classificati ...	2011	21559461
structure and function of a membrane component secdf that enhances protein export.	protein translocation across the bacterial membrane, mediated by the secretory translocon secyeg and the seca atpase, is enhanced by proton motive force and membrane-integrated secdf, which associates with secyeg. the role of secdf has remained unclear, although it is proposed to function in later stages of translocation as well as in membrane protein biogenesis. here, we determined the crystal structure of thermus thermophilus secdf at 3.3 å resolution, revealing a pseudo-symmetrical, 12-helix ...	2011	21562494
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
secretins: dynamic channels for protein transport across membranes.	secretins form megadalton bacterial-membrane channels in at least four sophisticated multiprotein systems that are crucial for translocation of proteins and assembled fibers across the outer membrane of many species of bacteria. secretin subunits contain multiple domains, which interact with numerous other proteins, including pilotins, secretion-system partner proteins, and exoproteins. our understanding of the structure of secretins is rapidly progressing, and it is now recognized that features ...	2011	21565514
structure and activity of a novel archaeal β-casp protein with n-terminal kh domains.	mth1203, a β-casp metallo-β-lactamase family nuclease from the archaeon methanothermobacter thermautotrophicus, was identified as a putative nuclease that might contribute to rna processing. the crystal structure of mth1203 reveals that, in addition to the metallo-β-lactamase nuclease and the β-casp domains, it contains two contiguous kh domains that are unique to mth1203 and its orthologs. rna-binding experiments indicate that mth1203 preferentially binds u-rich sequences with a dissociation co ...	2011	21565697
in medicago truncatula, water deficit modulates the transcript accumulation of components of small rna pathways.	small rnas (srnas) are 20-24 nucleotide (nt) rnas and are involved in plant development and response to abiotic stresses. plants have several srna pathways implicated in the transcriptional and post-transcriptional silencing of gene expression. two key enzyme families common to all pathways are the dicer-like (dcl) proteins involved in srnas maturation and the argonautes (agos) involved in the targeting and functional action of srnas. post-transcriptional silencing mediated by agos may occur by ...	2011	21569262
unsuspected diversity of arsenite-oxidizing bacteria as revealed by widespread distribution of the aoxb gene in prokaryotes.	in this study, new strains were isolated from an environment with elevated arsenic levels, sainte-marie-aux-mines (france), and the diversity of aoxb genes encoding the arsenite oxidase large subunit was investigated. the distribution of bacterial aoxb genes is wider than what was previously thought. aoxb subfamilies characterized by specific signatures were identified. an exhaustive analysis of aoxb sequences from this study and from public databases shows that horizontal gene transfer has like ...	2011	21571879
bis{μ-4,4'-dimeth-oxy-2,2'-[propane-1,2-diylbis(nitrilo-methyl-idyne)]diphenolato}bis-({4,4'-dimeth-oxy-2,2'-[propane-1,2-diylbis(nitrilo-methyl-idyne)]diphenol}manganese(iii)) bis-(hexa-fluorido-phosphate).	in the title complex, [mn(2)(c(19)h(20)n(2)o(4))(2)(c(19)h(22)n(2)o(4))(2)](pf(6))(2), the mn(iii) ion is coordinated by two o [mn-o = 1.855 (2) and 1.887 (2) å] and two n [mn-n = 1.982 (3) and 1.977 (3) å] atoms from the tetra-dentate schiff base ligand and a coordinated axial ligand [mn-o = 2.129 (2) å]. the centrosymmetric dimer contains two jahn-teller-distorted mn(iii) ions, each in a nearly octa-hedral geometry, connected through two phenolate bridges from two ligands. there are two stereo ...	2009	21583304
tmrna on its way through the ribosome: two steps of resume, and what next?	trans-translation is a universal quality-control process eubacteria use to degrade incompletely synthesized proteins and rescue ribosome stalled on defective mrnas. this process is facilitated by a ribonucleoprotein complex composed of transfer-messenger rna (tmrna)-a chimera made of a trna-like molecule and a short open reading frame (orf) -and small protein b (smpb). determination of the structure of tmrna and smpb in complex with the ribosome, at the stage when translation has resumed on tmrn ...	2011	21593606
structure of the pilm-piln inner membrane type iv pilus biogenesis complex from thermus thermophilus.	type iv pili are surface-exposed filaments which extend from a variety of bacterial pathogens and play a major role in pathogenesis, motility and dna uptake. here we present the crystal structure of a complex between a cytoplasmic component of the type iv pilus biogenesis system from thermus thermophilus, pilm, in complex with a peptide derived from the cytoplasmic portion of the inner membrane protein piln. pilm also binds atp, and its structure is most similar to the actin-like protein ftsa. p ...	2011	21596754
the evolution of respiratory chain complex i from a smaller last common ancestor consisting of 11 protein subunits.	the nadh:quinone oxidoreductase (complex i) has evolved from a combination of smaller functional building blocks. chloroplasts and cyanobacteria contain a complex i-like enzyme having only 11 subunits. this enzyme lacks the n-module which harbors the nadh binding site and the flavin and iron-sulfur cluster prosthetic groups. a complex i-homologous enzyme found in some archaea contains an f(420) dehydrogenase subunit denoted as fpof rather than the n-module. in the present study, all currently av ...	2011	21597881
expression, purification, and characterisation of dehydroquinate synthase from pyrococcus furiosus.	dehydroquinate synthase (dhqs) catalyses the second step of the shikimate pathway to aromatic compounds. dhqs from the archaeal hyperthermophile pyrococcus furiosus was insoluble when expressed in escherichia coli but was partially solubilised when kcl was included in the cell lysis buffer. a purification procedure was developed, involving lysis by sonication at 30°c followed by a heat treatment at 70°c and anion exchange chromatography. purified recombinant p. furiosus dhqs is a dimer with a su ...	2011	21603259
hcv ires domain iib affects the configuration of coding rna in the 40s subunit's decoding groove.	hepatitis c virus (hcv) uses a structured internal ribosome entry site (ires) rna to recruit the translation machinery to the viral rna and begin protein synthesis without the ribosomal scanning process required for canonical translation initiation. different ires structural domains are used in this process, which begins with direct binding of the 40s ribosomal subunit to the ires rna and involves specific manipulation of the translational machinery. we have found that upon initial 40s subunit b ...	2011	21606179
insights into the composition and assembly of the membrane arm of plant complex i through analysis of subcomplexes in arabidopsis mutant lines.	nadh-ubiquinone oxidoreductase (complex i, ec 1.6.5.3) is the largest complex of the mitochondrial respiratory chain. in eukaryotes, it is composed of more than 40 subunits that are encoded by both the nuclear and mitochondrial genomes. plant complex i differs from the enzyme described in other eukaryotes, most notably due to the large number of plant-specific subunits in the membrane arm of the complex. the elucidation of the assembly pathway of complex i has been a long-standing research aim i ...	2011	21606486
the role of the precursor structure in the biogenesis of microrna.	the human genome contains more than 1,000 microrna (mirna) genes, which are transcribed mainly by rna polymerase ii. the canonical pathway of mirna biogenesis includes the nuclear processing of primary transcripts (pri-mirnas) by the ribonuclease drosha and further cytoplasmic processing of pre-mirnas by the ribonuclease dicer. this review discusses the issue of mirna end heterogeneity generated primarily by drosha and dicer cleavage and focuses on the structural aspects of the dicer step of mir ...	2011	21607569
cross-linking, ligation, and sequencing of hybrids reveals rna-rna interactions in yeast.	many protein-protein and protein-nucleic acid interactions have been experimentally characterized, whereas rna-rna interactions have generally only been predicted computationally. here, we describe a high-throughput method to identify intramolecular and intermolecular rna-rna interactions experimentally by cross-linking, ligation, and sequencing of hybrids (clash). as validation, we identified 39 known target sites for box c/d modification-guide small nucleolar rnas (snornas) on the yeast pre-rr ...	2011	21610164
crystal structure of alkyl hydroperoxidase d like protein pa0269 from pseudomonas aeruginosa: homology of the ahpd-like structural family.	abstract: background: alkyl hydroperoxidase activity provides an important antioxidant defense for bacterial cells. the catalytic mechanism requires two peroxidases, ahpc and ahpd, where ahpd plays the role of an essential adaptor protein. results: the crystal structure of a putative ahpd from pseudomonas aeruginosa has been determined at 1.9 a. the protein has an all-helical fold with a chain topology similar to a known ahpd from mycobacterium tuberculosis despite a low overall sequence identit ...	2011	21615954
converting structural information into an allosteric-energy-based picture for elongation factor tu activation by the ribosome.	the crucial process of aminoacyl-trna delivery to the ribosome is energized by the gtpase reaction of the elongation factor tu (ef-tu). advances in the elucidation of the structure of the ef-tu/ribosome complex provide the rare opportunity of gaining a detailed understanding of the activation process of this system. here, we use quantitative simulation approaches and reproduce the energetics of the gtpase reaction of ef-tu with and without the ribosome and with several key mutants. our study pro ...	2011	21617092
isoprenoid precursor biosynthesis offers potential targets for drug discovery against diseases caused by apicomplexan parasites.	two, simple, c5 compounds, dimethylally diphosphate and isopentenyl diphosphate, are the universal precursors of isoprenoids, a large family of natural products involved in numerous important biological processes. two distinct biosynthetic pathways have evolved to supply these precursors. humans use the mevalonate route whilst many species of bacteria including important pathogens, plant chloroplasts and apicomplexan parasites exploit the non-mevalonate pathway. the absence from humans, combined ...	2011	21619509
allosteric nucleotide-binding site in the mitochondrial nadh:ubiquinone oxidoreductase (respiratory complex i).	the rotenone-insensitive nadh:hexaammineruthenium iii (har) oxidoreductase reactions catalyzed by bovine heart and yarrowia lipolytica submitochondrial particles or purified bovine complex i are stimulated by atp and other purine nucleotides. the soluble fraction of mammalian complex i (fp) and prokaryotic complex i homolog ndh-1 in paracoccus denitrificans plasma membrane lack stimulation of their activities by atp. the stimulation appears as a decrease in apparent k(m) values for nadh and har. ...	2011	21624365
an extensive network of information flow through the b1b/c intersubunit bridge of the yeast ribosome.	yeast ribosomal proteins l11 and s18 form a dynamic intersubunit interaction called the b1b/c bridge. recent high resolution images of the ribosome have enabled targeting of specific residues in this bridge to address how distantly separated regions within the large and small subunits of the ribosome communicate with each other. mutations were generated in the l11 side of the b1b/c bridge with a particular focus on disrupting the opposing charge motifs that have previously been proposed to be in ...	2011	21625514
the influence of the local sequence environment on rna loop structures.	rna folding is assumed to be a hierarchical process. the secondary structure of an rna molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. subsequently, the rna molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). to what extent the backbone conformation of rna loops also r ...	2011	21628431
crystal structure of the heme d1 biosynthesis enzyme nire in complex with its substrate reveals new insights into the catalytic mechanism of s-adenosyl-l-methionine dependent uroporphyrinogen iii methyltransferases.	during the biosynthesis of heme d(1), the essential cofactor of cytochrome cd(1) nitrite reductase, the nire protein catalyzes the methylation of uroporphyrinogen iii to precorrin-2 using s-adenosyl-l-methionine (sam) as the methyl group donor. the crystal structure of pseudomonas aeruginosa nire in complex with its substrate uroporphyrinogen iii and the reaction by-product s-adenosyl-l-homocysteine (sah) was solved to 2.0 angstrom resolution. this represents the first enzyme-substrate complex s ...	2011	21632530
the yeast rapid trna decay pathway primarily monitors the structural integrity of the acceptor and t-stems of mature trna.	trnas, like other rnas, are subject to quality control steps during and after biosynthesis. we previously described a rapid trna degradation (rtd) pathway in which the 5'-3' exonucleases rat1 and xrn1 degrade mature trna(val(aac)) in yeast mutants lacking m(7)g and m(5)c, and mature trna(ser(cga)) in mutants lacking um and ac(4)c. to understand how the rtd pathway selects substrate trnas among different trnas lacking the same modifications, we used a genetic screen to examine trna(ser(cga)) vari ...	2011	21632824
differences in dinucleotide frequencies of thermophilic genes encoding water soluble and membrane proteins.	the occurrence frequencies of the dinucleotides of genes of three thermophilic and three mesophilic species from both archaea and eubacteria were investigated in this study. the genes encoding water soluble proteins were rich in the dinucleotides of purine dimers, whereas the genes encoding membrane proteins were rich in pyrimidine dimers. the dinucleotides of purine dimers are the counterparts of pyrimidine dimers in a double-stranded dna. the purine/pyrimidine dimers were favored in the thermo ...	2011	21634034
crystallization and preliminary x-ray analysis of argininosuccinate lyase from streptococcus mutans.	argininosuccinate lyase (asl) is an important enzyme in arginine synthesis and the urea cycle, which are highly conserved from bacteria to eukaryotes. the gene encoding streptococcus mutans asl (smasl) was amplified and cloned into expression vector pet28a. the recombinant smasl protein was expressed in a soluble form in escherichia coli strain bl21 (de3) and purified to homogeneity by two-step column chromatography. crystals suitable for x-ray analysis were obtained and x-ray diffraction data w ...	2011	21636911
crystallization and preliminary x-ray crystallographic analysis of dihydrouridine synthase from thermus thermophilus and its complex with trna.	dihydrouridine synthase (dus) is responsible for catalyzing dihydrouridine formation in rna by the reduction of uridine. to elucidate its rna-recognition mechanism, dus from thermus thermophilus (tthdus) and its complex with trna were crystallized. diffraction data sets were collected from crystals of native and selenomethionine-substituted tthdus to resolutions of 1.70 and 2.30 å, respectively. these crystals belonged to space group p1. preliminary x-ray crystallographic analysis showed that tw ...	2011	21636912
expression, crystallization and preliminary x-ray analysis of a ferric binding protein from thermus thermophilus hb8.	a ferric binding protein from thermus thermophilus hb8 (ttfbpa) was expressed, purified and crystallized using the hanging-drop vapour-diffusion method. four different crystal forms were obtained and characterized by x-ray diffraction. two crystal forms with ttfbpa in the apo state belonged to the orthorhombic space group p2(1)2(1)2(1) (unit-cell parameters a = 42.1, b = 139.3, c = 326.5 å and a = 42.1, b = 139.3, c = 218.9 å). the third form with ttfbpa also in the apo state belonged to the mon ...	2011	21636922
allosteric communication between the nucleotide binding domains of caseinolytic peptidase b(clpb).	clpb is a hexameric chaperone that solubilizes and reactivates protein aggregates in cooperation with the hsp70/dnak chaperone system. each of the identical protein monomer contains two nucleotide binding domains (nbd), whose atpase activity must be coupled to exert on the substrate the mechanical work required for its reactivation. however, how communication between these sites occurs is at present poorly understood. we have studied herein the affinity of each of the nbds for nucleotides in wt ...	2011	21642426
a new family of deamination repair enzymes in the uracil dna glycosylase superfamily.	dna glycoyslases play a major role in the repair of deaminated dna damage. previous investigations identified five families within the uracil dna glycosylase (udg) superfamily. all enzymes within the superfamily studied thus far exhibit uracil dna glycosylase activity. here we identify a new class of dna glycosylases in the udg superfamily that lacks udg activity. instead, these enzymes act as hypoxanthine dna glycosylases in vitro and in vivo. molecular modeling and structure-guided mutational ...	2011	21642431
microbial ecology of the dark ocean above, at, and below the seafloor.	the majority of life on earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. ...	2011	21646433
crystal structure of the mid-piwi lobe of a eukaryotic argonaute protein.	argonaute proteins (agos) are essential effectors in rna-mediated gene silencing pathways. they are characterized by a bilobal architecture, in which one lobe contains the n-terminal and paz domains and the other contains the mid and piwi domains. here, we present the first crystal structure of the mid-piwi lobe from a eukaryotic ago, the neurospora crassa qde-2 protein. compared to prokaryotic agos, the domain orientation is conserved, indicating a conserved mode of nucleic acid binding. the pi ...	2011	21646546
uracil-dna glycosylase of thermoplasma acidophilumdirects long-patch base excision repair, which is promoted by deoxynucleoside triphosphates and atp/adp, into short-patch repair.	hydrolytic deamination of cytosine to uracil in dna is increased in organisms adapted to high temperatures. hitherto, the uracil base excision repair (ber) pathway has only been described in two archaeons, the crenarchaeon pyrobaculum aerophilumand the euryarchaeon archaeoglobus fulgidus, which are hyperthermophiles and use single-nucleotide replacement. in the former the apurinic/apyrimidinic (ap) site intermediate is removed by the sequential action of a 5'-acting ap endonuclease and a 5'-deox ...	2011	21665970
a sulfite respiration pathway from thermus thermophilus and the key role of newly identified cytochrome côéàôéàôéç.	sulfite, produced for instance during amino acid metabolism, is a very reactive and toxic compound. various detoxification mechanisms exist, but sulfite oxidoreductases (sors) are one of the major actors in sulfite remediation in bacteria and animals. here we describe the existence of an operon in the extreme thermophilic bacterium thermus thermophilus hb8 encoding both a sor and a diheme c-type cytochrome. the in vitro analysis clearly showed that the newly identified cytochrome côéàôéàôéç acts ...	2011	21665981
high tolerance to mutations in a chlamydia trachomatis peptide deformylase loop.	to determine if and how a loop region in the peptide deformylase (pdf) of chlamydia trachomatis regulates enzyme function.	2011	21666811
small noncoding rnas in the germline.	small noncoding rnas have emerged as potent regulators of gene expression, especially in the germline. we review the biogenesis and regulatory function of three major small noncoding rna pathways in the germline: the small interfering rna (sirna) pathway that leads to the degradation of target mrnas, the microrna (mirna) pathway that mostly represses the translation of target mrnas, and the newly discovered piwi-interacting rna (pirna) pathway that appears to have diverse functions in epigenetic ...	2011	21669983
the rpb2 flap loop of human rna polymerase ii is dispensable for transcription initiation and elongation.	the flap domain of multisubunit rna polymerases (rnaps), also called the wall, forms one side of the rna exit channel. in bacterial rnap, the mobile part of the flap is called the flap tip and makes essential contacts with initiation and elongation factors. cocrystal structures suggest that the orthologous part of eukaryotic rnapii, called the flap loop, contacts transcription factor iib (tfiib), but the function of the flap loop has not been assessed. we constructed and tested a deletion of the ...	2011	21670157
structural and kinetic mapping of side-chain exposure onto the protein energy landscape.	identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. native-state hydrogen exchange (nshx) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating t ...	2011	21670244
markus: a server to navigate sequence-structure-function space.	we describe markus, a web server for analysis and comparison of the structural and functional properties of proteins. in contrast to a 'structure in/function out' approach to protein function annotation, the server is designed to be highly interactive and to allow flexibility in the examination of possible functions, suggested either automatically by various similarity measures or specified by a user directly. this is combined with tools that allow a user to assess independently whether or not a ...	2011	21672961
a pilot study of bacterial genes with disrupted orfs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment.	bacterial genome annotations contain a number of coding sequences (cdss) that, in spite of reading frame disruptions, encode a single continuous polypeptide. such disruptions have different origins: sequencing errors, frameshift, or stop codon mutations, as well as instances of utilization of nontriplet decoding. we have extracted over 1,000 cdss with annotated disruptions and found that about 75% of them can be clustered into 64 groups based on sequence similarity. analysis of the clusters reve ...	2011	21673094
carotenoid ╬▓-ring hydroxylase and ketolase from marine bacteria-promiscuous enzymes for synthesizing functional xanthophylls.	marine bacteria belonging to genera paracoccus and brevundimonas of the ╬▒-proteobacteria class can produce côéäôéç-type dicyclic carotenoids containing two ╬▓-end groups (╬▓ rings) that are modified with keto and hydroxyl groups. these bacteria produce astaxanthin, adonixanthin, and their derivatives, which are ketolated by carotenoid ╬▓-ring 4(4')-ketolase (4(4')-oxygenase; crtw) and hydroxylated by carotenoid ╬▓-ring 3(3')-hydroxylase (crtz). in addition, the genus brevundimonas possesses a g ...	2011	21673887
stabilization of c4a-hydroperoxyflavin in a two-component flavin-dependent monooxygenase is achieved through interactions at flavin n5 and c4a atoms.	p-hydroxyphenylacetate (hpa) 3-hydroxylase is a two-component flavin-dependent monooxygenase. based on the crystal structure of the oxygenase component (c(2)), his-396 is 4.5 å from the flavin c4a locus, whereas ser-171 is 2.9 å from the flavin n5 locus. we investigated the roles of these two residues in the stability of the c4a-hydroperoxy-fmn intermediate. the results indicated that the rate constant for c4a-hydroperoxy-fmn formation decreased ~30-fold in h396n, 100-fold in h396a, and 300-fold ...	2011	21680741
alterations in the {beta} flap and {beta}' dock domains of the rna polymerase abolish nusa-mediated feedback regulation of the mety-nusa-infb operon.	the rimm protein in escherichia coli is important for the in vivo maturation of 30s ribosomal subunits and a +örimm mutant grows poorly due to assembly and translational defects. these deficiencies are suppressed partially by mutations that increase the synthesis of another assembly protein, rbfa, encoded by the mety-nusa-infb operon. among these suppressors are mutations in nusa that impair the nusa-mediated negative-feedback regulation at internal intrinsic transcriptional terminators of the m ...	2011	21685293