Publications
| Title | Abstract | Year(sorted descending) Filter | PMID Filter |
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| mass spectrometry-based quantification of pseudouridine in rna. | direct detection of pseudouridine (ψ), an isomer of uridine, in rna is challenging. the most popular method requires chemical derivatization using n-cyclohexyl-n'-β-(4-methylmorpholinum ethyl) carbodiimide p-tosylate (cmct) followed by radiolabeled primer extension mediated by reverse transcriptase. more recently, mass spectrometry (ms)-based approaches for sequence placement of pseudouridine in rna have been developed. nearly all of these approaches, however, only yield qualitative information ... | 2011 | 21953190 |
| tagetitoxin inhibits rna polymerase through trapping of the trigger loop. | tagetitoxin (tgt) inhibits multisubunit chloroplast, bacterial, and some eukaryotic rna polymerases (rnaps). a crystallographic structure of tgt bound to bacterial rnap apoenzyme shows that tgt binds near the active site but does not explain why tgt acts only at certain sites. to understand the tgt mechanism, we constructed a structural model of tgt bound to the transcription elongation complex. in this model, tgt interacts with the β' subunit trigger loop (tl), stabilizing it in an inactive con ... | 2011 | 21976682 |
| massive multiplication of genome and ribosomes in dormant cells (akinetes) of aphanizomenon ovalisporum (cyanobacteria). | akinetes are dormancy cells commonly found among filamentous cyanobacteria, many of which are toxic and/or nuisance, bloom-forming species. development of akinetes from vegetative cells is a process that involves morphological and biochemical modifications. here, we applied a single-cell approach to quantify genome and ribosome content of akinetes and vegetative cells in aphanizomenon ovalisporum (cyanobacteria). vegetative cells of a. ovalisporum were naturally polyploid and contained, on avera ... | 2011 | 21975597 |
| massive multiplication of genome and ribosomes in dormant cells (akinetes) of aphanizomenon ovalisporum (cyanobacteria). | akinetes are dormancy cells commonly found among filamentous cyanobacteria, many of which are toxic and/or nuisance, bloom-forming species. development of akinetes from vegetative cells is a process that involves morphological and biochemical modifications. here, we applied a single-cell approach to quantify genome and ribosome content of akinetes and vegetative cells in aphanizomenon ovalisporum (cyanobacteria). vegetative cells of a. ovalisporum were naturally polyploid and contained, on avera ... | 2011 | 21975597 |
| structural and functional insights into the dna replication factor cdc45 reveal an evolutionary relationship to the dhh family of phosphoesterases. | cdc45 is an essential protein conserved in all eukaryotes and is involved both in the initiation of dna replication, as well as the progression of the replication fork. with gins, cdc45 is an essential co-factor of the mcm2-7 replicative helicase complex. despite its importance, no detailed information is available on either the structure or the biochemistry of the protein. intriguingly, whereas homologues of both gins and mcm proteins have been described in archaea, no counterpart for cdc45 is ... | 2011 | 22147708 |
| structural and functional insights into the dna replication factor cdc45 reveal an evolutionary relationship to the dhh family of phosphoesterases. | cdc45 is an essential protein conserved in all eukaryotes and is involved both in the initiation of dna replication, as well as the progression of the replication fork. with gins, cdc45 is an essential co-factor of the mcm2-7 replicative helicase complex. despite its importance, no detailed information is available on either the structure or the biochemistry of the protein. intriguingly, whereas homologues of both gins and mcm proteins have been described in archaea, no counterpart for cdc45 is ... | 2011 | 22147708 |
| crystal structure of human β-galactosidase: the structural basis of gm1 gangliosidosis and morquio b diseases. | gm1 gangliosidosis and morquio b are autosomal recessive lysosomal storage diseases associated with a neurodegenerative disorder or dwarfism and skeletal abnormalities, respectively. these diseases are caused by deficiencies in the lysosomal enzyme β-d-galactosidase (β-gal), which lead to accumulations of the β-gal substrates, gm1 ganglioside and keratan sulfate. β-gal is an exoglycosidase that catalyzes the hydrolysis of terminal β-linked galactose residues. the present study shows the crystal ... | 2011 | 22128166 |
| crystal structure of human β-galactosidase: the structural basis of gm1 gangliosidosis and morquio b diseases. | gm1 gangliosidosis and morquio b are autosomal recessive lysosomal storage diseases associated with a neurodegenerative disorder or dwarfism and skeletal abnormalities, respectively. these diseases are caused by deficiencies in the lysosomal enzyme β-d-galactosidase (β-gal), which lead to accumulations of the β-gal substrates, gm1 ganglioside and keratan sulfate. β-gal is an exoglycosidase that catalyzes the hydrolysis of terminal β-linked galactose residues. the present study shows the crystal ... | 2011 | 22128166 |
| peptides from aminoacyl-trna synthetases can cure the defects due to mutations in mt trna genes. | recent results from several laboratories have confirmed that human and yeast leucyl- and valyl-trna synthetases can rescue the respiratory defects due to mutations in mitochondrial trna genes. in this report we show that this effect cannot be ascribed to the catalytic activity per se and that isolated domains of aminoacyl-trna synthetases and even short peptides thereof have suppressing effects. | 2011 | 21903180 |
| characterization of family iv udg from aeropyrum pernix and its application in hot-start pcr by family b dna polymerase. | recombinant uracil-dna glycosylase (udg) from aeropyrum pernix (a. pernix) was expressed in e. coli. the biochemical characteristics of a. pernix udg (apeudg) were studied using oligonucleotides carrying a deoxyuracil (du) base. the optimal temperature range and ph value for du removal by apeudg were 55-65°c and ph 9.0, respectively. the removal of du was inhibited by the divalent ions of zn, cu, co, ni, and mn, as well as a high concentration of nacl. the opposite base in the complementary stra ... | 2011 | 22087273 |
| catalytic properties of the isolated diaphorase fragment of the nad-reducing [nife]-hydrogenase from ralstonia eutropha. | the nad+-reducing soluble hydrogenase (sh) from ralstonia eutropha h16 catalyzes the h₂-driven reduction of nad+, as well as reverse electron transfer from nadh to h+, in the presence of o₂. it comprises six subunits, hoxhyfui₂, and incorporates a [nife] h+/h₂ cycling catalytic centre, two non-covalently bound flavin mononucleotide (fmn) groups and an iron-sulfur cluster relay for electron transfer. this study provides the first characterization of the diaphorase sub-complex made up of hoxf and ... | 2011 | 22016788 |
| structures of the rna-guided surveillance complex from a bacterial immune system. | bacteria and archaea acquire resistance to viruses and plasmids by integrating short fragments of foreign dna into clustered regularly interspaced short palindromic repeats (crisprs). these repetitive loci maintain a genetic record of all prior encounters with foreign transgressors. crisprs are transcribed and the long primary transcript is processed into a library of short crispr-derived rnas (crrnas) that contain a unique sequence complementary to a foreign nucleic-acid challenger. in escheric ... | 2011 | 21938068 |
| novel base triples in rna structures revealed by graph theoretical searching methods. | highly hydrogen bonded base interactions play a major part in stabilizing the tertiary structures of complex rna molecules, such as transfer-rnas, ribozymes and ribosomal rnas. | 2011 | 22373013 |
| a computational study of elongation factor g (efg) duplicated genes: diverged nature underlying the innovation on the same structural template. | elongation factor g (efg) is a core translational protein that catalyzes the elongation and recycling phases of translation. a more complex picture of efg's evolution and function than previously accepted is emerging from analyzes of heterogeneous efg family members. whereas the gene duplication is postulated to be a prominent factor creating functional novelty, the striking divergence between efg paralogs can be interpreted in terms of innovation in gene function. | 2011 | 21829651 |
| 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 |
| defense islands in bacterial and archaeal genomes and prediction of novel defense systems. | the arms race between cellular life forms and viruses is a major driving force of evolution. a substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. we analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. the defense islands are enriched ... | 2011 | 21908672 |
| effect of lecithin on d-galactosamine induced hepatotoxicity through mitochondrial pathway involving bcl-2 and bax. | twenty four wistar strain albino rats were used for the investigations. lecithin 50 and 100 mg/kg b wt was administered for 1 week by oral route. liver damage was induced by intra peritoneal administration of 400 mg/kg b wt d-galactosamine on the last day. at the end of the study animals were sacrificed and liver enzyme levels, histopathology, mitochondrial integrity, expression of p53, bax and bcl-2 mrna levels were studied. increases in the liver enzyme levels by d-galn were significantly inhi ... | 2011 | 23024474 |
| a universal method for the identification of bacteria based on general pcr primers. | the universal method (um) described here will allow the detection of any bacterial rdna leading to the identification of that bacterium. the method should allow prompt and accurate identification of bacteria. the principle of the method is simple; when a pure pcr product of the 16s gene is obtained, sequenced, and aligned against bacterial dna data base, then the bacterium can be identified. confirmation of identity may follow. in this work, several general 16s primers were designed, mixed and a ... | 2011 | 23024404 |
| structure of the pilus assembly protein tadz from eubacterium rectale: implications for polar localization. | the tad (tight adherence) locus encodes a protein translocation system that produces a novel variant of type iv pili. the pilus assembly protein tadz (called cpae in caulobacter crescentus) is ubiquitous in tad loci, but is absent in other type iv pilus biogenesis systems. the crystal structure of tadz from eubacterium rectale (ertadz), in complex with atp and mg(2+) , was determined to 2.1 å resolution. ertadz contains an atypical atpase domain with a variant of a deviant walker-a motif that re ... | 2011 | 22211578 |
| annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. | the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ... | 2011 | 24710297 |
| structural biology of redox partner interactions in p450cam monooxygenase: a fresh look at an old system. | the p450cam monooxygenase system consists of three separate proteins: the fad-containing, nadh-dependent oxidoreductase (putidaredoxin reductase or pdr), cytochrome p450cam and the 2fe2s ferredoxin (putidaredoxin or pdx), which transfers electrons from pdr to p450cam. over the past few years our lab has focused on the interaction between these redox components. it has been known for some time that pdx can serve as an effector in addition to its electron shuttle role. the binding of pdx to p450ca ... | 2011 | 20816746 |
| structural biology of redox partner interactions in p450cam monooxygenase: a fresh look at an old system. | the p450cam monooxygenase system consists of three separate proteins: the fad-containing, nadh-dependent oxidoreductase (putidaredoxin reductase or pdr), cytochrome p450cam and the 2fe2s ferredoxin (putidaredoxin or pdx), which transfers electrons from pdr to p450cam. over the past few years our lab has focused on the interaction between these redox components. it has been known for some time that pdx can serve as an effector in addition to its electron shuttle role. the binding of pdx to p450ca ... | 2011 | 20816746 |
| biochemical and structural characterization of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-iv. | mammalian maspat (mitochondrial aspartate aminotransferase) is recently reported to have kat (kynurenine aminotransferase) activity and plays a role in the biosynthesis of kyna (kynurenic acid) in rat, mouse and human brains. this study concerns the biochemical and structural characterization of mouse maspat. in this study, mouse maspat cdna was amplified from mouse brain first stand cdna and its recombinant protein was expressed in an escherichia coli expression system. sixteen oxo acids were t ... | 2011 | 20977429 |
| idiosyncrasy and identity in the prokaryotic phe-system: crystal structure of e. coli phenylalanyl-trna synthetase complexed with phenylalanine and amp. | the crystal structure of phenylalanyl-trna synthetase from e. coli (ecphers), a class ii aminoacyl-trna synthetase, complexed with phenylalanine and amp was determined at 3.05 å resolution. ecphers is a (αβ)₂ heterotetramer: the αβ heterodimer of ecphers consists of 11 structural domains. three of them: the n-terminus, a1 and a2 belong to the α-subunit and b1-b8 domains to the β subunit. the structure of ecphers revealed that architecture of four helix-bundle interface, characteristic of class i ... | 2011 | 21082706 |
| idiosyncrasy and identity in the prokaryotic phe-system: crystal structure of e. coli phenylalanyl-trna synthetase complexed with phenylalanine and amp. | the crystal structure of phenylalanyl-trna synthetase from e. coli (ecphers), a class ii aminoacyl-trna synthetase, complexed with phenylalanine and amp was determined at 3.05 å resolution. ecphers is a (αβ)₂ heterotetramer: the αβ heterodimer of ecphers consists of 11 structural domains. three of them: the n-terminus, a1 and a2 belong to the α-subunit and b1-b8 domains to the β subunit. the structure of ecphers revealed that architecture of four helix-bundle interface, characteristic of class i ... | 2011 | 21082706 |
| structural insights into pre-translocation ribosome motions. | subsequent to the peptidyl transfer step of the translation elongation cycle, the initially formed pre-translocation ribosome, which we refer to here as r(1), undergoes a ratchet-like intersubunit rotation in order to sample a rotated conformation, referred to here as r(f), that is an obligatory intermediate in the translocation of trnas and mrna through the ribosome during the translocation step of the translation elongation cycle. r(f) and the r(1) to r(f) transition are currently the subject ... | 2011 | 21121048 |
| a combined global and local approach to elucidate spatial organization of the mycobacterial parb-pars partition assembly. | combining diverse sets of data at global (size, shape) and local (residue) scales is an emerging trend for elucidating the organization and function of the cellular assemblies. we used such a strategy, combining data from x-ray and neutron scattering with h/d-contrast variation and x-ray footprinting with mass spectrometry, to elucidate the spatial organization of the parb-pars assembly from mycobacterium tuberculosis. the parb-pars participates in plasmid and chromosome segregation and condensa ... | 2011 | 21142182 |
| structures of domains i and iv from ybbr are representative of a widely distributed protein family. | ybbr domains are widespread throughout eubacteria and are expressed as monomeric units, linked in tandem repeats or cotranslated with other domains. although the precise role of these domains remains undefined, the location of the multiple ybbr domain-encoding ybbr gene in the bacillus subtilis glmm operon and its previous identification as a substrate for a surfactin-type phosphopantetheinyl transferase suggests a role in cell growth, division, and virulence. to further characterize the ybbr do ... | 2011 | 21154411 |
| structures of domains i and iv from ybbr are representative of a widely distributed protein family. | ybbr domains are widespread throughout eubacteria and are expressed as monomeric units, linked in tandem repeats or cotranslated with other domains. although the precise role of these domains remains undefined, the location of the multiple ybbr domain-encoding ybbr gene in the bacillus subtilis glmm operon and its previous identification as a substrate for a surfactin-type phosphopantetheinyl transferase suggests a role in cell growth, division, and virulence. to further characterize the ybbr do ... | 2011 | 21154411 |
| proline dehydrogenase contributes to pathogen defense in arabidopsis. | l-proline (pro) catabolism is activated in plants recovering from abiotic stresses associated with water deprivation. in this catabolic pathway, pro is converted to glutamate by two reactions catalyzed by proline dehydrogenase (prodh) and ?(1)-pyrroline-5-carboxylate dehydrogenase (p5cdh), with ?(1)-pyrroline-5-carboxylate (p5c) as the intermediate. alternatively, under certain conditions, the p5c derived from pro is converted back to pro by p5c reductase, thus stimulating the pro-p5c cycle, whi ... | 2011 | 21311034 |
| energetics of seca dimerization. | transport of many proteins to extracytoplasmic locations occurs via the general secretion (sec) pathway. in escherichia coli, this pathway is composed of the secyeg protein-conducting channel and the seca atpase. seca plays a central role in binding the signal peptide region of preproteins, directing preproteins to membrane-bound secyeg and promoting translocation coupled with atp hydrolysis. although it is well established that seca is crucial for preprotein transport and thus cell viability, i ... | 2011 | 21315086 |
| natural competence in the hyperthermophilic archaeon pyrococcus furiosus facilitates genetic manipulation: construction of markerless deletions of genes encoding the two cytoplasmic hydrogenases. | in attempts to develop a method of introducing dna into pyrococcus furiosus, we discovered a variant within the wild-type population that is naturally and efficiently competent for dna uptake. a pyrf gene deletion mutant was constructed in the genome, and the combined transformation and recombination frequencies of this strain allowed marker replacement by direct selection using linear dna. we have demonstrated the use of this strain, designated com1, for genetic manipulation. using genetic sele ... | 2011 | 21317259 |
| il-10 expression by primary tumor cells correlates with melanoma progression from radial to vertical growth phase and development of metastatic competence. | downregulation of the immune system facilitates tumor progression at different stages of cutaneous melanoma. sentinel nodes, the first lymph nodes on lymphatics draining directly from a primary melanoma, are immune downregulated by tumor-generated immunosuppressive cytokines, including interleukin-10 (il-10). to better understand the kinetics of sentinel node suppression, we investigated il-10 expression by melanoma cells and tumor-associated macrophages and lymphocytes at different stages of pr ... | 2011 | 21317876 |
| unusual outer membrane lipid composition of the gram-negative, lipopolysaccharide-lacking myxobacterium sorangium cellulosum so ce56. | the gram-negative myxobacterium sorangium cellulosum so ce56 bears the largest bacterial genome published so far, coding for nearly 10,000 genes. careful analysis of this genome data revealed that part of the genes coding for the very well conserved biosynthesis of lipopolysaccharides (lps) are missing in this microbe. biochemical analysis gave no evidence for the presence of lps in the membranes of so ce56. by analyzing the lipid composition of its outer membrane sphingolipids were identified a ... | 2011 | 21321121 |
| activity of and development of resistance to corallopyronin a, an inhibitor of rna polymerase. | we explored the properties of corallopyronin a (cora), a poorly characterized inhibitor of bacterial rna polymerase (rnap). it displayed a 50% inhibitory concentration of 0.73 µm against rnap, compared with 11.5 nm for rifampin. the antibacterial activity of cora was also inferior to rifampin, and resistant mutants of staphylococcus aureus were easily selected. the mutations conferring resistance resided in the rpob and rpoc subunits of rnap. we conclude that cora is not a promising antibacteria ... | 2011 | 21321139 |
| bacterial toxin rele mediates frequent codon-independent mrna cleavage from the 5' end of coding regions in vivo. | the enzymatic activity of the rele bacterial toxin component of the escherichia coli relbe toxin-antitoxin system has been extensively studied in vitro and to a lesser extent in vivo. these earlier reports revealed that 1) rele alone does not exhibit mrna cleavage activity, 2) rele mediates mrna cleavage through its association with the ribosome, 3) rele-mediated mrna cleavage occurs at the ribosomal a site and, 4) cleavage of mrna by rele exhibits high codon specificity. more specifically, rele ... | 2011 | 21324908 |
| a highly conserved protein of unknown function in sinorhizobium meliloti affects srna regulation similar to hfq. | the smc01113/ybey protein, belonging to the upf0054 family, is highly conserved in nearly every bacterium. however, the function of these proteins still remains elusive. our results show that smc01113/ybey proteins share structural similarities with the mid domain of the argonaute (ago) proteins, and might similarly bind to a small-rna (srna) seed, making a special interaction with the phosphate on the 5'-side of the seed, suggesting they may form a component of the bacterial srna pathway. indee ... | 2011 | 21325267 |
| avoiding premature oxidation during the binding of cu(ii) to a dithiolate site in bssco. a rapid freeze-quench epr study. | the bacillus subtilis version of sco1 (bssco) is required for assembly of cu(a) in cytochrome c oxidase and may function in thiol-disulfide exchange and/or copper delivery. bssco binds cu(ii) with ligation by two cysteines, one histidine and one water. however, copper is a catalyst of cysteine oxidation and bssco must avoid this reaction to remain functional. time resolved, rapid freeze-quench (rfq) electron paramagnetic resonance of apo-bssco reacting with cu(ii) reveals an initial cu(ii) speci ... | 2011 | 21333651 |
| organic hydroperoxide resistance protein and ergothioneine compensate for loss of mycothiol in mycobacterium smegmatis mutants. | the msha::tn5 mutant of mycobacterium smegmatis does not produce mycothiol (msh) and was found to markedly overproduce both ergothioneine and an ~15-kda protein determined to be organic hydroperoxide resistance protein (ohr). an msha(g32d) mutant lacking msh overproduced ergothioneine but not ohr. comparison of the mutant phenotypes with those of the wild-type strain indicated the following: ohr protects against organic hydroperoxide toxicity, whereas ergothioneine does not; an additional msh-de ... | 2011 | 21335456 |
| chlorite dismutases, dyps, and efeb: 3 microbial heme enzyme families comprise the cde structural superfamily. | heme proteins are extremely diverse, widespread, and versatile biocatalysts, sensors, and molecular transporters. the chlorite dismutase family of hemoproteins received its name due to the ability of the first-isolated members to detoxify anthropogenic clo(2)(-), a function believed to have evolved only in the last few decades. family members have since been found in 15 bacterial and archaeal genera, suggesting ancient roots. a structure- and sequence-based examination of the family is presented ... | 2011 | 21354424 |
| activity map of the escherichia coli rna polymerase bridge helix. | transcription, the synthesis of rna from a dna template, is performed by multisubunit rna polymerases (rnaps) in all cellular organisms. the bridge helix (bh) is a distinct feature of all multisubunit rnaps and makes direct interactions with several active site-associated mobile features implicated in the nucleotide addition cycle and rna and dna binding. because the bh has been captured in both kinked and straight conformations in different crystals structures of rnap, recently supported by mol ... | 2011 | 21357417 |
| correct assembly of iron-sulfur cluster fs0 into escherichia coli dimethyl sulfoxide reductase (dmsabc) is a prerequisite for molybdenum cofactor insertion. | the fs0 [4fe-4s] cluster of the catalytic subunit (dmsa) of escherichia coli dimethyl sulfoxide reductase (dmsabc) plays a key role in the electron transfer relay. we have now established an additional role for the cluster in directing molybdenum cofactor assembly during enzyme maturation. epr spectroscopy indicates that fs0 has a high spin ground state (s = 3/2) in its reduced form, resulting in an epr spectrum with a peak at g ~ 5.0. the cluster is predicted to be in close proximity to the mol ... | 2011 | 21357619 |
| an expanded collection and refined consensus model of glms ribozymes. | self-cleaving glms ribozymes selectively bind glucosamine-6-phosphate (glcn6p) and use this metabolite as a cofactor to promote self-cleavage by internal phosphoester transfer. representatives of the glms ribozyme class are found in gram-positive bacteria where they reside in the 5' untranslated regions (utrs) of glms messenger rnas that code for the essential enzyme l-glutamine:d-fructose-6-phosphate aminotransferase. by using comparative sequence analyses, we have expanded the number of glms r ... | 2011 | 21367971 |
| insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1. | mitochondria have their own translational machineries for the synthesis of thirteen polypeptide chains that are components of the complexes that participate in the process of oxidative phosphorylation (or atp generation). translation initiation in mammalian mitochondria requires two initiation factors, if2(mt) and if3(mt), instead of the three that are present in eubacteria. the mammalian if2(mt) possesses a unique 37 amino acid insertion domain, which is known to be important for the formation ... | 2011 | 21368145 |
| two rotary motors in f-atp synthase are elastically coupled by a flexible rotor and a stiff stator stalk. | atp is synthesized by atp synthase (f(o)f(1)-atpase). its rotary electromotor (f(o)) translocates protons (in some organisms sodium cations) and generates torque to drive the rotary chemical generator (f(1)). elastic power transmission between f(o) and f(1) is essential for smoothing the cooperation of these stepping motors, thereby increasing their kinetic efficiency. a particularly compliant elastic domain is located on the central rotor (c(10-15)/e/?), right between the two sites of torque ge ... | 2011 | 21368147 |
| e1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea. | based on our recent work with haloferax volcanii, ubiquitin-like (ubl) proteins (samp1 and samp2) are known to be covalently attached to proteins in archaea. here, we investigated the enzymes required for the formation of these ubl-protein conjugates (sampylation) and whether this system is linked to sulfur transfer. markerless in-frame deletions were generated in h. volcanii target genes. the mutants were examined for: (i) the formation of ubl protein conjugates, (ii) growth under various condi ... | 2011 | 21368171 |
| oxidative stress resistance in deinococcus radiodurans. | deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive dna damage efficiently and accurately. it is extremely resistant to many dna-damaging agents, including ionizing radiation and uv radiation (100 to 295 nm), desiccation, and mitomycin c, which induce oxidative damage not only to dna but also to all cellular macromolecules via the production of reactive oxygen species. the extreme resilience of d. radiodurans to oxidative stress is imparted synergistically ... | 2011 | 21372322 |
| partial functional replacement of cyma by sircd in shewanella oneidensis mr-1. | the gammaproteobacterium shewanella oneidensis mr-1 utilizes a complex electron transfer network composed primarily of c-type cytochromes to respire under anoxic conditions a variety of compounds, including fumarate, nitrate, and dimethyl sulfoxide (dmso), in addition to the minerals fe(iii) and mn(iv). central to several respiratory pathways is cyma, a cytoplasmic membrane-bound tetraheme c-type cytochrome that functions as the major hydroquinone dehydrogenase. to investigate functional redunda ... | 2011 | 21378180 |
| structural insights into cognate versus near-cognate discrimination during decoding. | the structural basis of the trna selection process is investigated by cryo-electron microscopy of ribosomes programmed with uga codons and incubated with ternary complex (tc) containing the near-cognate trp-trna(trp) in the presence of kirromycin. going through more than 350 000 images and employing image classification procedures, we find ~8% in which the tc is bound to the ribosome. the reconstructed 3d map provides a means to characterize the arrangement of the near-cognate aa-trna with respe ... | 2011 | 21378755 |
| architecture of the rna polymerase-spt4/5 complex and basis of universal transcription processivity. | related rna polymerases (rnaps) carry out cellular gene transcription in all three kingdoms of life. the universal conservation of the transcription machinery extends to a single rnap-associated factor, spt5 (or nusg in bacteria), which renders rnap processive and may have arisen early to permit evolution of long genes. spt5 associates with spt4 to form the spt4/5 heterodimer. here, we present the crystal structure of archaeal spt4/5 bound to the rnap clamp domain, which forms one side of the rn ... | 2011 | 21386817 |
| mutagenesis of the l, m, and n subunits of complex i from escherichia coli indicates a common role in function. | the membrane arm of complex i (nadh:ubiquinone oxidoreductase) contains three large, and closely related subunits, which are called l, m, and n in e. coli. these subunits are homologous to components of multi-subunit na(+)/h(+) antiporters, and so are implicated in proton translocation. | 2011 | 21387012 |
| susceptibility and mode of binding of the mycobacterium tuberculosis cysteinyl transferase mycothiol ligase to trna synthetase inhibitors. | the cysteinyl transferase mycothiol ligase, or mshc, catalyzes the fourth step in the biosynthesis of the small molecular weight thiol mycothiol. mshc is essential for growth of mycobacterium tuberculosis. two groups of known aminoacyl trna synthetase inhibitors were evaluated for inhibition of m. tuberculosis mshc including aminoacyl adenosine analogs and natural products. using enzyme assays, isothermal titration calorimetry and nmr, we show that mshc is selectively inhibited by cysteinyl sulf ... | 2011 | 21392992 |
| cloning, expression, purification, crystallization and preliminary x-ray diffraction analysis of the regulatory domain of aspartokinase (rv3709c) from mycobacterium tuberculosis. | the regulatory domain of mycobacterium tuberculosis aspartokinase (mtb-ak, mtb-ask, rv3709c) has been cloned, heterologously expressed in escherichia coli and purified using standard chromatographic techniques. screening for initial crystallization conditions using the regulatory domain (ak-+¦) in the presence of the potential feedback inhibitor threonine identified four conditions which yielded crystals suitable for x-ray diffraction analysis. from these four conditions five different crystal f ... | 2011 | 21393848 |
| crystallization and preliminary x-ray analysis of mannosyl-3-phosphoglycerate phosphatase from thermus thermophilus hb27. | mannosylglycerate (mg) is primarily known as an osmolyte and is widely distributed among (hyper)thermophilic marine microorganisms. the synthesis of mg via mannosyl-3-phosphoglycerate synthase (mpgs) and mannosyl-3-phosphoglycerate phosphatase (mpgp), the so-called two-step pathway, is the most prevalent route among these organisms. the phosphorylated intermediate mannosyl-3-phosphoglycerate is synthesized by the first enzyme and is subsequently dephosphorylated by the second. the structure of m ... | 2011 | 21393850 |
| purification and biochemical properties of a cytochrome bc complex from the aerobic hyperthermophilic archaeon aeropyrum pernix. | the bioenergetics of archaea with respect to the evolution of electron transfer systems is very interesting. in contrast to terminal oxidases, a canonical bc1 complex has not yet been isolated from archaea. in particular, c-type cytochromes have been reported only for a limited number of species. | 2011 | 21396131 |
| the antibacterial threaded-lasso peptide capistruin inhibits bacterial rna polymerase. | capistruin, a ribosomally synthesized, post-translationally modified peptide produced by burkholderia thailandensis e264, efficiently inhibits growth of burkholderia and closely related pseudomonas strains. the functional target of capistruin is not known. capistruin is a threaded-lasso peptide (lariat peptide) consisting of an n-terminal ring of nine amino acids and a c-terminal tail of 10 amino acids threaded through the ring. the structure of capistruin is similar to that of microcin j25 (mcc ... | 2011 | 21396375 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| clamping the clamp of rna polymerase. | 2011 | 21468097 | |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |