Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
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| Genomic and proteomic characterization of the large Myoviridae bacteriophage ?TMA of the extreme thermophile Thermus thermophilus. | A lytic phage, designated as ?TMA, was isolated from a Japanese hot spring using Thermus thermophilus HB27 as an indicator strain. Electron microscopic examination showed that ?TMA had an icosahedral head and a contractile tail. The circular double-stranded DNA sequence of ?TMA was 151,483 bp in length, and its organization was essentially same as that of ?YS40 except that the ?TMA genome contained genes for a pair of transposase and resolvase, and a gene for a serine to asparagine substituted o ... | 2011 | 22164349 |
| rational design of an evolutionary precursor of glutaminyl-trna synthetase. | the specificity of most aminoacyl-trna synthetases for an amino acid and cognate trna pair evolved before the divergence of the three domains of life. glutaminyl-trna synthetase (glnrs) evolved later and is derived from the archaeal-type nondiscriminating glutamyl-trna synthetase (glurs), an enzyme with relaxed trna specificity capable of forming both glu-trna(glu) and glu-trna(gln). the archaea lack glnrs and use a specialized amidotransferase to convert glu-trna(gln) to gln-trna(gln) needed fo ... | 2011 | 22158897 |
| covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors. | evidence for an unusual catalysis of protonation/deprotonation by a reduced flavin mononucleotide cofactor is presented for type-2 isopentenyl diphosphate isomerase (idi-2), which catalyzes isomerization of the two fundamental building blocks of isoprenoid biosynthesis, isopentenyl diphosphate and dimethylallyl diphosphate. the covalent adducts formed between irreversible mechanism-based inhibitors, 3-methylene-4-penten-1-yl diphosphate or 3-oxiranyl-3-buten-1-yl diphosphate, and the flavin cofa ... | 2011 | 22158896 |
| isolation and characterization of the prochlorococcus carboxysome reveal the presence of the novel shell protein csos1d. | cyanobacteria, including members of the genus prochlorococcus, contain icosahedral protein microcompartments known as carboxysomes that encapsulate multiple copies of the co(2)-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) in a thin protein shell that enhances the catalytic performance of the enzyme in part through the action of a shell-associated carbonic anhydrase. however, the exact mechanism by which compartmentation provides a catalytic advantage to the enzyme is n ... | 2011 | 22155772 |
| 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 |
| epr-endor characterization of (17o, 1h, 2h) water in manganese catalase and its relevance to the oxygen-evolving complex of photosystem ii. | the synthesis of efficient water-oxidation catalysts demands insight into the only known, naturally occurring water-oxidation catalyst, the oxygen-evolving complex (oec) of photosystem ii (psii). understanding the water oxidation mechanism requires knowledge of where and when substrate water binds to the oec. mn catalase in its mn(iii)-mn(iv) state is a protein model of the oec's s(2) state. from (17)o-labeled water exchanged into the di-μ-oxo di-mn(iii,iv) coordination sphere of mn catalase, cw ... | 2012 | 22142421 |
| proline utilization by bacillus subtilis: uptake and catabolism. | l-proline can be used by bacillus subtilis as a sole source of carbon or nitrogen. we traced l-proline utilization genetically to the putbcp (ycgmno) locus. the putbcp gene cluster encodes a high-affinity proline transporter (putp) and two enzymes, the proline dehydrogenase putb and the δ(1)-pyrroline-5-carboxylate dehydrogenase putc, which jointly catabolize l-proline to l-glutamate. northern blotting, primer extension, and putb-trea reporter gene fusion analysis showed that the putbcp locus is ... | 2011 | 22139509 |
| seleno-detergent mad phasing of leukotriene c4 synthase in complex with dodecyl-β-d-selenomaltoside. | dodecyl-β-d-selenomaltoside (seddm) is a seleno-detergent with a β-glycosidic seleno-ether in place of the ether moiety in dodecyl-β-d-maltoside. seleno-detergents are candidates for heavy-atom agents in experimental phasing of membrane proteins in protein crystallography. crystals of a nuclear membrane-embedded enzyme, leukotriene c(4) synthase (ltc(4)s), in complex with seddm were prepared and a multiwavelength anomalous diffraction (mad) experiment was performed. the seddm in the ltc(4)s crys ... | 2011 | 22139193 |
| thermostable multicopper oxidase from thermus thermophilus hb27: crystallization and preliminary x-ray diffraction analysis of apo and holo forms. | a thermostable multicopper oxidase from thermus thermophilus hb27 (tth-mco) was successfully crystallized using the sitting-drop and hanging-drop vapour-diffusion methods. crystallization conditions and preliminary x-ray diffraction data to 1.5 å resolution obtained using synchrotron radiation at 100 k are reported. the crystals belonged to space group c222(1), with unit-cell parameters a = 93.6, b = 110.3, c = 96.3 å. a monomer in the asymmetric unit yielded a matthews coefficient (v(m)) of 2.6 ... | 2011 | 22139175 |
| crystallization and preliminary crystallographic analysis of a putative glucokinase/hexokinase from thermus thermophilus. | glucokinase/hexokinase catalyzes the phosphorylation of glucose to glucose 6-phosphate, which is the first step of glycolysis. the open reading frame ttha0299 of the extreme thermophile thermus thermophilus encodes a putative glucokinase/hexokinase which contains the consensus sequence for proteins from the repressors, open reading frames and sugar kinases family. in this study, the glucokinase/hexokinase from t. thermophilus was purified and crystallized using polyethylene glycol 8000 as a prec ... | 2011 | 22139166 |
| Overexpression, crystallization and preliminary X-ray crystallographic analysis of shikimate dehydrogenase from Archaeoglobus fulgidus. | Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Previous structural studies have shown that SDH exists in two conformations, an open and a closed form, and it is believed that the conformational state is crucial to understanding its catalytic mechanism. In order to facilitate further structural comparisons among SDHs, includ ... | 2011 | 22139165 |
| The rate-limiting step in O(2) reduction by cytochrome ba(3) from Thermus thermophilus. | Cytochrome ba(3) (ba(3)) of Thermus thermophilus (T. thermophilus) is a member of the heme-copper oxidase family, which has a binuclear catalytic center comprised of a heme (heme a(3)) and a copper (Cu(B)). The heme-copper oxidases generally catalyze the four electron reduction of molecular oxygen in a sequence involving several intermediates. We have investigated the reaction of the fully reduced ba(3) with O(2) using stopped-flow techniques. Transient visible absorption spectra indicated that ... | 2011 | 22138627 |
| crystal structure of the bacteriophage t4 late-transcription coactivator gp33 with the β-subunit flap domain of escherichia coli rna polymerase. | activated transcription of the bacteriophage t4 late genes, which is coupled to concurrent dna replication, is accomplished by an initiation complex containing the host rna polymerase associated with two phage-encoded proteins, gp55 (the basal promoter specificity factor) and gp33 (the coactivator), as well as the dna-mounted sliding-clamp processivity factor of the phage t4 replisome (gp45, the activator). we have determined the 3.0 å-resolution x-ray crystal structure of gp33 complexed with it ... | 2011 | 22135460 |
| mmdb: 3d structures and macromolecular interactions. | close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3d) structure by standard sequence similarity searches. potentially, a great deal can be learned about proteins or protein families of interest from considering 3d structure, and to this day 3d structure data may remain an underutilized resource. here we present enhancements in the molecular modeling database (mmdb) and its data presentation, specifically pertaining to biologically re ... | 2011 | 22135289 |
| mmdb: 3d structures and macromolecular interactions. | close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3d) structure by standard sequence similarity searches. potentially, a great deal can be learned about proteins or protein families of interest from considering 3d structure, and to this day 3d structure data may remain an underutilized resource. here we present enhancements in the molecular modeling database (mmdb) and its data presentation, specifically pertaining to biologically re ... | 2011 | 22135289 |
| Biochemical and structural studies of the uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed a NAD+-dependent L-serine dehydrogenase. | The ß-hydroxyacid dehydrogenases form a large family of ubiquitous enzymes that catalyze oxidation of various ß-hydroxyacid substrates to corresponding semialdehydes. Several known enzymes include ß-hydroxyisobutyrate dehydrogenase, 6-phosphogluconate dehydrogenase, 2-(hydroxymethyl)glutarate dehydrogenase, and phenylserine dehydrogenase, but the vast majority of ß-hydroxyacid dehydrogenases remain uncharacterized. Here, we demonstrate that the predicted ß-hydroxyisobutyrate dehydrogenase PA0743 ... | 2011 | 22128181 |
| Biochemical and structural studies of the uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed a NAD+-dependent L-serine dehydrogenase. | The ß-hydroxyacid dehydrogenases form a large family of ubiquitous enzymes that catalyze oxidation of various ß-hydroxyacid substrates to corresponding semialdehydes. Several known enzymes include ß-hydroxyisobutyrate dehydrogenase, 6-phosphogluconate dehydrogenase, 2-(hydroxymethyl)glutarate dehydrogenase, and phenylserine dehydrogenase, but the vast majority of ß-hydroxyacid dehydrogenases remain uncharacterized. Here, we demonstrate that the predicted ß-hydroxyisobutyrate dehydrogenase PA0743 ... | 2011 | 22128181 |
| 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 |
| Post-translational modification by ß-lysylation is required for the activity of E. coli Elongation Factor P (EF-P). | Bacterial elongation factor P (EF-P) is the ortholog of archaeal and eukaryotic initiation factor 5A (aIF5A and eIF5A). EF-P shares sequence homology and crystal structure with eIF5A, but unlike eIF5A, EF-P does not undergo hypusine modification. Recently, two bacterial genes, yjeA and yjeK, encoding truncated homologs of class II lysyl-tRNA synthetase and of lysine-2,3-aminomutase, respectively, have been implicated in the modification of EF-P to convert a specific lysine to a hypothetical ß- ... | 2011 | 22128152 |
| Post-translational modification by ß-lysylation is required for the activity of E. coli Elongation Factor P (EF-P). | Bacterial elongation factor P (EF-P) is the ortholog of archaeal and eukaryotic initiation factor 5A (aIF5A and eIF5A). EF-P shares sequence homology and crystal structure with eIF5A, but unlike eIF5A, EF-P does not undergo hypusine modification. Recently, two bacterial genes, yjeA and yjeK, encoding truncated homologs of class II lysyl-tRNA synthetase and of lysine-2,3-aminomutase, respectively, have been implicated in the modification of EF-P to convert a specific lysine to a hypothetical ß- ... | 2011 | 22128152 |
| substrate specificity of bacterial prolyl-trna synthetase editing domain is controlled by a tunable hydrophobic pocket. | aminoacyl-trna synthetases catalyze the covalent attachment of amino acids onto their cognate trnas. high fidelity in this reaction is crucial to the accurate decoding of genetic information and is ensured, in part, by proofreading of the newly synthesized aminoacyl-trnas. prolyl-trna synthetases (prors) mischarge trna(pro) with alanine or cysteine due to their smaller or similar sizes relative to cognate proline. mischarged ala-trna(pro) is hydrolyzed by an editing domain (ins) present in most ... | 2011 | 22128149 |
| substrate specificity of bacterial prolyl-trna synthetase editing domain is controlled by a tunable hydrophobic pocket. | aminoacyl-trna synthetases catalyze the covalent attachment of amino acids onto their cognate trnas. high fidelity in this reaction is crucial to the accurate decoding of genetic information and is ensured, in part, by proofreading of the newly synthesized aminoacyl-trnas. prolyl-trna synthetases (prors) mischarge trna(pro) with alanine or cysteine due to their smaller or similar sizes relative to cognate proline. mischarged ala-trna(pro) is hydrolyzed by an editing domain (ins) present in most ... | 2011 | 22128149 |
| the pfam protein families database. | pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. pfam is available via servers in the uk (http://pfam.sanger.ac.uk/), the usa (http://pfam.janelia.org/) and sweden (http://pfam.sbc.su.se/). here, we report on changes that have occurred since our 2010 nar paper (release 24.0). over the last 2 years, we have generated 1840 new families and increased coverage of the uniprot knowledgebase (uniprotkb) to ne ... | 2011 | 22127870 |
| the pfam protein families database. | pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. pfam is available via servers in the uk (http://pfam.sanger.ac.uk/), the usa (http://pfam.janelia.org/) and sweden (http://pfam.sbc.su.se/). here, we report on changes that have occurred since our 2010 nar paper (release 24.0). over the last 2 years, we have generated 1840 new families and increased coverage of the uniprot knowledgebase (uniprotkb) to ne ... | 2011 | 22127870 |
| directed molecular evolution to design advanced red fluorescent proteins. | fluorescent proteins have become indispensable imaging tools for biomedical research. continuing progress in fluorescence imaging, however, requires probes with additional colors and properties optimized for emerging techniques. here we summarize strategies for development of red-shifted fluorescent proteins. we discuss possibilities for knowledge-based rational design based on the photochemistry of fluorescent proteins and the position of the chromophore in protein structure. we consider advanc ... | 2011 | 22127219 |
| genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. | prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet earth with human beings (among others). however, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. an understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. the vast majorit ... | 2011 | 22126996 |
| effects of pressure and temperature on the binding of reca protein to single-stranded dna. | the binding and polymerization of reca protein to dna is required for recombination, which is an essential function of life. we study the pressure and temperature dependence of reca binding to single-stranded dna in the presence of adenosine 5'-[γ-thio]triphosphate (atp[γ-s]), in a temperature regulated high pressure cell using fluorescence anisotropy. measurements were possible at temperatures between 5-60 °c and pressures up to 300 mpa. experiments were performed on escherichia coli reca and r ... | 2011 | 22123983 |
| Molecular basis of dihydrouridine formation on tRNA. | Dihydrouridine (D) is a highly conserved modified base found in tRNAs from all domains of life. Dihydrouridine synthase (Dus) catalyzes the D formation of tRNA through reduction of uracil base with flavin mononucleotide (FMN) as a cofactor. Here, we report the crystal structures of Thermus thermophilus Dus (TthDus), which is responsible for D formation at positions 20 and 20a, in complex with tRNA and with a short fragment of tRNA (D-loop). Dus interacts extensively with the D-arm and recognizes ... | 2011 | 22123979 |
| Mössbauer Spectroscopy on Respiratory Complex I: The Iron-Sulfur Cluster Ensemble in the NADH-Reduced Enzyme Is Partially Oxidized. | In mitochondria, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. It contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters that transfer the electrons to quinone. Understanding electron transfer in complex I requires spectroscopic and structural data to be combined to reveal the properties of individual clusters and of the ensemble. EPR studies on complex I from ... | 2011 | 22122402 |
| Mössbauer Spectroscopy on Respiratory Complex I: The Iron-Sulfur Cluster Ensemble in the NADH-Reduced Enzyme Is Partially Oxidized. | In mitochondria, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. It contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters that transfer the electrons to quinone. Understanding electron transfer in complex I requires spectroscopic and structural data to be combined to reveal the properties of individual clusters and of the ensemble. EPR studies on complex I from ... | 2011 | 22122402 |
| Trimming down a protein structure to its bare foldons: spatial organisation of the cooperative unit. | Folding of the ribosomal protein S6 is a malleable process controlled by two competing, and partly overlapping, folding nuclei. Together, these nuclei extend over most of the S6 structure, save the edge strand ß2, which is consistently missing in the folding transition states: despite being part of the S6 four-stranded sheet, ß2 seems not to be part of the protein's cooperative unit. The question is then if ß2 can be removed from the S6 structure without compromising folding cooperativity or ... | 2011 | 22117065 |
| Trimming down a protein structure to its bare foldons: spatial organisation of the cooperative unit. | Folding of the ribosomal protein S6 is a malleable process controlled by two competing, and partly overlapping, folding nuclei. Together, these nuclei extend over most of the S6 structure, save the edge strand ß2, which is consistently missing in the folding transition states: despite being part of the S6 four-stranded sheet, ß2 seems not to be part of the protein's cooperative unit. The question is then if ß2 can be removed from the S6 structure without compromising folding cooperativity or ... | 2011 | 22117065 |
| sequence of the hyperplastic genome of the naturally competent thermus scotoductus sa-01. | many strains of thermus have been isolated from hot environments around the world. thermus scotoductus sa-01 was isolated from fissure water collected 3.2 km below surface in a south african gold mine. the isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. the genomes from two different thermus thermophilus strains have been com ... | 2011 | 22115438 |
| crystal structure of the central axis df complex of the prokaryotic v-atpase. | v-atpases function as atp-dependent ion pumps in various membrane systems of living organisms. atp hydrolysis causes rotation of the central rotor complex, which is composed of the central axis d subunit and a membrane c ring that are connected by f and d subunits. here we determined the crystal structure of the df complex of the prokaryotic v-atpase of enterococcus hirae at 2.0-å resolution. the structure of the d subunit comprised a long left-handed coiled coil with a unique short β-hairpin re ... | 2011 | 22114184 |
| francisella rna polymerase contains a heterodimer of non-identical alpha subunits. | abstract: background: all sequenced genomes of representatives of the francisella genus contain two rpoa genes, which encode non-identical rna polymerase (rnap) subunits, alpha1 and alpha2. in all other bacteria studied to date, a dimer of identical alpha subunits initiates the assembly of the catalytically proficient rnap core (subunit composition (alpha)2/beta/beta'). based on an observation that both alpha1 and alpha2 are incorporated into francisella rnap, charity et al. (2007) previously s ... | 2011 | 22108176 |
| terpene biosynthesis: modularity rules. | terpenes are the largest class of small-molecule natural products on earth, and the most abundant by mass. here, we summarize recent developments in elucidating the structure and function of the proteins involved in their biosynthesis. there are six main building blocks or modules (α, β, γ, δ, ε, and ζ) that make up the structures of these enzymes: the αα and αδ head-to-tail trans-prenyl transferases that produce trans-isoprenoid diphosphates from c(5) precursors; the ε head-to-head prenyl trans ... | 2011 | 22105807 |
| terpene biosynthesis: modularity rules. | terpenes are the largest class of small-molecule natural products on earth, and the most abundant by mass. here, we summarize recent developments in elucidating the structure and function of the proteins involved in their biosynthesis. there are six main building blocks or modules (α, β, γ, δ, ε, and ζ) that make up the structures of these enzymes: the αα and αδ head-to-tail trans-prenyl transferases that produce trans-isoprenoid diphosphates from c(5) precursors; the ε head-to-head prenyl trans ... | 2011 | 22105807 |
| crystal structure of homoisocitrate dehydrogenase from schizosaccharomyces pombe. | homoisocitrate dehydrogenase (hicdh) catalyzes the conversion of homoisocitrate to 2-oxoadipate, the third enzymatic step in the α-aminoadipate pathway by which lysine is synthesized in fungi and certain archaebacteria. this enzyme represents a potential target for anti-fungal drug design. here, we describe the first crystal structures of a fungal hicdh, including structures of an apoenzyme and a binary complex with a glycine tri-peptide. the structures illustrate the homology of hicdh with othe ... | 2011 | 22105743 |
| crystal structure of homoisocitrate dehydrogenase from schizosaccharomyces pombe. | homoisocitrate dehydrogenase (hicdh) catalyzes the conversion of homoisocitrate to 2-oxoadipate, the third enzymatic step in the α-aminoadipate pathway by which lysine is synthesized in fungi and certain archaebacteria. this enzyme represents a potential target for anti-fungal drug design. here, we describe the first crystal structures of a fungal hicdh, including structures of an apoenzyme and a binary complex with a glycine tri-peptide. the structures illustrate the homology of hicdh with othe ... | 2011 | 22105743 |
| Histidine 66 in E. coli elongation factor Tu selectively stabilizes aminoacyl-tRNAs. | The universally conserved H66 of Elongation Factor Tu stacks on the side chain of the esterified Phe of Phe-tRNA(Phe). The affinities of eight aminoacyl-tRNAs were differentially destabilized by the introduction of the H66A mutation into E. coli EF-Tu while Ala-tRNA(Ala) and Gly-tRNA(Gly) were unaffected. The H66F and H66W proteins each show a different pattern of binding of ten different aa-tRNAs, clearly showing that this position is critical in establishing the specificity of EF-Tu for differ ... | 2011 | 22105070 |
| Histidine 66 in E. coli elongation factor Tu selectively stabilizes aminoacyl-tRNAs. | The universally conserved H66 of Elongation Factor Tu stacks on the side chain of the esterified Phe of Phe-tRNA(Phe). The affinities of eight aminoacyl-tRNAs were differentially destabilized by the introduction of the H66A mutation into E. coli EF-Tu while Ala-tRNA(Ala) and Gly-tRNA(Gly) were unaffected. The H66F and H66W proteins each show a different pattern of binding of ten different aa-tRNAs, clearly showing that this position is critical in establishing the specificity of EF-Tu for differ ... | 2011 | 22105070 |
| Crystallization and preliminary X-ray crystallographic analysis of putative tRNA-modification enzymes from Pyrococcus furiosus and Thermus thermophilus. | Methyltransferases form a major class of tRNA-modifying enzymes that are needed for the proper functioning of tRNA. Here, the expression, purification and crystallization of two related putative tRNA methyltransferases from two kingdoms of life are reported. The protein encoded by the gene pf1002 from the archaeon Pyrococcus furiosus was crystallized in the monoclinic space group P2(1). A complete data set was collected to 2.2 Å resolution. The protein encoded by the gene ttc1157 from the eubact ... | 2011 | 22102250 |
| crystallization and preliminary x-ray diffraction of the first periplasmic domain of secdf, a translocon-associated membrane protein, from thermus thermophilus. | a membrane-integrated sec component, secdf, associates with the secyeg protein-conducting channel and facilitates protein secretion and membrane-protein integration. secdf contains 12 transmembrane helices and two periplasmic domains. the first periplasmic domain (p1) plays an important role in protein translocation. here, the overexpression, purification and crystallization of the p1 domain of thermus thermophilus secdf are reported. the crystals diffracted x-rays to 2.3 å resolution and belong ... | 2011 | 22102233 |
| expression, purification, crystallization and preliminary x-ray analysis of ecgp123, an extremely stable monomeric green fluorescent protein with reversible photoswitching properties. | enhanced consensus green protein variant 123 (ecgp123) is an extremely thermostable green fluorescent protein (gfp) that exhibits useful negative reversible photoswitching properties. ecgp123 was derived by the application of both a consensus engineering approach and a recursive evolutionary process. diffraction-quality crystals of recombinant ecgp123 were obtained by the hanging-drop vapour-diffusion method using peg 3350 as the precipitant. the ecgp123 crystal diffracted x-rays to 2.10 å resol ... | 2011 | 22102044 |
| estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. | for many research questions in modern molecular and systems biology information about absolute protein quantities is imperative. these include, for example, kinetic modeling of processes, protein turnover determinations, stoichiometric investigations of protein complexes or quantitative comparisons of different proteins within one or across samples. to date, the vast majority of proteomic studies are limited to providing relative quantitative comparisons of protein levels between limited numbers ... | 2011 | 22101334 |
| estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. | for many research questions in modern molecular and systems biology information about absolute protein quantities is imperative. these include, for example, kinetic modeling of processes, protein turnover determinations, stoichiometric investigations of protein complexes or quantitative comparisons of different proteins within one or across samples. to date, the vast majority of proteomic studies are limited to providing relative quantitative comparisons of protein levels between limited numbers ... | 2011 | 22101334 |
| High-resolution structure of shikimate dehydrogenase from Thermotoga maritima reveals a tightly closed conformation. | Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Structural analysis of a SDH from Thermotoga maritima encoded by the Tm0346 gene was performed to facilitate further structural comparisons between the various shikimate dehydrogenases. The crystal structure of SDH from T. maritima was determined at 1.45 SDH from T. maritima sh ... | 2011 | 22095087 |
| High-resolution structure of shikimate dehydrogenase from Thermotoga maritima reveals a tightly closed conformation. | Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Structural analysis of a SDH from Thermotoga maritima encoded by the Tm0346 gene was performed to facilitate further structural comparisons between the various shikimate dehydrogenases. The crystal structure of SDH from T. maritima was determined at 1.45 SDH from T. maritima sh ... | 2011 | 22095087 |
| recent progress in bacillus subtilis sporulation. | the gram-positive bacterium bacillus subtilis can initiate the process of sporulation under conditions of nutrient limitation. here, we review some of the last 5 years of work in this area, with a particular focus on the decision to initiate sporulation, dna translocation, cell-cell communication, protein localization and spore morphogenesis. the progress we describe has implications not only just for the study of sporulation but also for other biological systems where homologs of sporulation-sp ... | 2012 | 22091839 |
| recent progress in bacillus subtilis sporulation. | the gram-positive bacterium bacillus subtilis can initiate the process of sporulation under conditions of nutrient limitation. here, we review some of the last 5 years of work in this area, with a particular focus on the decision to initiate sporulation, dna translocation, cell-cell communication, protein localization and spore morphogenesis. the progress we describe has implications not only just for the study of sporulation but also for other biological systems where homologs of sporulation-sp ... | 2012 | 22091839 |
| Structure and Function of the Small MutS-Related Domain. | MutS family proteins are widely distributed in almost all organisms from bacteria to human and play central roles in various DNA transactions such as DNA mismatch repair and recombinational events. The small MutS-related (Smr) domain was originally found in the C-terminal domain of an antirecombination protein, MutS2, a member of the MutS family. MutS2 is thought to suppress homologous recombination by endonucleolytic resolution of early intermediates in the process. The endonuclease activity of ... | 2011 | 22091410 |
| bioinformatic analysis of leishmania donovani long-chain fatty acid-coa ligase as a novel drug target. | fatty acyl-coa synthetase (fatty acid: coa ligase, amp-forming; (ec 6.2.1.3)) catalyzes the formation of fatty acyl-coa by a two-step process that proceeds through the hydrolysis of pyrophosphate. fatty acyl-coa represents bioactive compounds that are involved in protein transport, enzyme activation, protein acylation, cell signaling, and transcriptional control in addition to serving as substrates for beta oxidation and phospholipid biosynthesis. fatty acyl-coa synthetase occupies a pivotal rol ... | 2011 | 22091399 |
| 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 |
| neutrons, magnets, and photons: a career in structural biology. | the purpose of reflections articles, it seems, is to give elderly scientists a chance to write about the "good old days," when everyone walked to school in the snow. they enjoy this activity so much that your editor, martha fedor, must have known that i would accept her invitation to write such an article, no matter how much i demurred at first. as everyone knows, flattery will get you everywhere. it may comfort the apprehensive reader to learn that there is not going to be much walking to schoo ... | 2011 | 22086921 |
| neutrons, magnets, and photons: a career in structural biology. | the purpose of reflections articles, it seems, is to give elderly scientists a chance to write about the "good old days," when everyone walked to school in the snow. they enjoy this activity so much that your editor, martha fedor, must have known that i would accept her invitation to write such an article, no matter how much i demurred at first. as everyone knows, flattery will get you everywhere. it may comfort the apprehensive reader to learn that there is not going to be much walking to schoo ... | 2011 | 22086921 |
| a temperature-dependent conformational change of nadh oxidase from thermus thermophilus hb8. | using molecular dynamics simulations and steady-state fluorescence spectroscopy, we have identified a conformational change in the active site of a thermophilic flavoenzyme, nadh oxidase from thermus thermophilus hb8 (nox). the enzyme's far-uv circular dichroism spectrum, intrinsic tryptophan fluorescence, and apparent molecular weight measured by dynamic light scattering varied little between 25 and 75°c. however, the fluorescence of the tightly bound fad cofactor increased approximately fourfo ... | 2011 | 22081476 |
| Loss of elongation factor p disrupts bacterial outer membrane integrity. | Elongation factor P (EF-P) is posttranslationally modified at a conserved lysyl residue by the coordinated action of two enzymes, PoxA and YjeK. We have previously established the importance of this modification in Salmonella stress resistance. Here we report that, like poxA and yjeK mutants, Salmonella strains lacking EF-P display increased susceptibility to hypoosmotic conditions, antibiotics, and detergents and enhanced resistance to the compound S-nitrosoglutathione. The susceptibility pheno ... | 2012 | 22081389 |
| membrane proteins in four acts: function precedes structure determination. | studies on four membrane protein systems, which combine information derived from crystal structures and biophysical studies have emphasized, as a precursor to crystallization, demonstration of functional activity. these assays have relied on sensitive spectrophotometric, electrophysiological, and microbiological assays of activity to select purification procedures that lead to functional complexes and with greater likelihood to successful crystallization: (i), hetero-oligomeric proteins involved ... | 2011 | 22079407 |
| the structure of aquifex aeolicus ribosomal protein s8 reveals a unique subdomain that contributes to an extremely tight association with 16s rrna. | the assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. the ribosomal protein s8 from aquifex aeolicus (as8) is unique in that there is a 41-residue insertion in the consensus s8 sequence. in addition, as8 exhibits an unusually high affinity for the 16s ribosomal rna, characterized by a picomolar dissociation constant that is approximately 26,000-fold tighter than ... | 2011 | 22079365 |
| the structure of aquifex aeolicus ribosomal protein s8 reveals a unique subdomain that contributes to an extremely tight association with 16s rrna. | the assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. the ribosomal protein s8 from aquifex aeolicus (as8) is unique in that there is a 41-residue insertion in the consensus s8 sequence. in addition, as8 exhibits an unusually high affinity for the 16s ribosomal rna, characterized by a picomolar dissociation constant that is approximately 26,000-fold tighter than ... | 2011 | 22079365 |
| Biogenesis of cbb(3)-type cytochrome c oxidase in Rhodobacter capsulatus. | The cbb(3)-type cytochrome c oxidases (cbb(3)-Cox) constitute the second most abundant cytochrome c oxidase (Cox) group after the mitochondrial-like aa(3)-type Cox. They are present in bacteria only, and are considered to represent a primordial innovation in the domain of Eubacteria due to their phylogenetic distribution and their similarity to nitric oxide (NO) reductases. They are crucial for the onset of many anaerobic biological processes, such as anoxygenic photosynthesis or nitrogen fixati ... | 2011 | 22079199 |
| Biogenesis of cbb(3)-type cytochrome c oxidase in Rhodobacter capsulatus. | The cbb(3)-type cytochrome c oxidases (cbb(3)-Cox) constitute the second most abundant cytochrome c oxidase (Cox) group after the mitochondrial-like aa(3)-type Cox. They are present in bacteria only, and are considered to represent a primordial innovation in the domain of Eubacteria due to their phylogenetic distribution and their similarity to nitric oxide (NO) reductases. They are crucial for the onset of many anaerobic biological processes, such as anoxygenic photosynthesis or nitrogen fixati ... | 2011 | 22079199 |
| The structure and allosteric regulation of mammalian glutamate dehydrogenase. | Glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of l-glutamate to 2-oxoglutarate. Only in the animal kingdom is this enzyme heavily allosterically regulated by a wide array of metabolites. The major activators are ADP and leucine, while the most important inhibitors include GTP, palmitoyl CoA, and ATP. Recently, spontaneous mutations in the GTP inhibitory site that lead to the hyperinsulinism/hyperammonemia (HHS) syndrome have shed ligh ... | 2011 | 22079166 |
| The structure and allosteric regulation of mammalian glutamate dehydrogenase. | Glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of l-glutamate to 2-oxoglutarate. Only in the animal kingdom is this enzyme heavily allosterically regulated by a wide array of metabolites. The major activators are ADP and leucine, while the most important inhibitors include GTP, palmitoyl CoA, and ATP. Recently, spontaneous mutations in the GTP inhibitory site that lead to the hyperinsulinism/hyperammonemia (HHS) syndrome have shed ligh ... | 2011 | 22079166 |
| comparison of two yeast mnsods: mitochondrial saccharomyces cerevisiae versus cytosolic candida albicans. | human mnsod is significantly more product-inhibited than bacterial mnsods at high concentrations of superoxide (o(2)(-)). this behavior limits the amount of h(2)o(2) produced at high [o(2)(-)]; its desirability can be explained by the multiple roles of h(2)o(2) in mammalian cells, particularly its role in signaling. to investigate the mechanism of product inhibition in mnsod, two yeast mnsods, one from saccharomyces cerevisiae mitochondria (scmnsod) and the other from candida albicans cytoso ... | 2011 | 22077216 |
| dehydratase mediated 1-propanol production in metabolically engineered escherichia coli. | with the increasing consumption of fossil fuels, the question of meeting the global energy demand is of great importance in the near future. as an effective solution, production of higher alcohols from renewable sources by microorganisms has been proposed to address both energy crisis and environmental concerns. higher alcohols contain more than two carbon atoms and have better physiochemical properties than ethanol as fuel substitutes. | 2011 | 22074179 |
| multistrand rna secondary structure prediction and nanostructure design including pseudoknots. | we are presenting nanofolder, a method for the prediction of the base pairing of potentially pseudoknotted multistrand rna nanostructures. we show that the method outperforms several other structure prediction methods when applied to rna complexes with non-nested base pairs. we extended this secondary structure prediction capability to allow rna sequence design. using native page, we experimentally confirm that four in silico designed rna strands corresponding to a triangular rna structure form ... | 2011 | 22067111 |
| heme ligand identification and redox properties of the cytochrome c synthetase, ccmf. | cytochrome c maturation in many bacteria, archaea, and plant mitochondria involves the integral membrane protein ccmf, which is thought to function as a cytochrome c synthetase by facilitating the final covalent attachment of heme to the apocytochrome c. we previously reported that the e. coli ccmf protein contains a b-type heme that is stably and stoichiometrically associated with the protein and is not the heme attached to apocytochrome c. here, we show that mutation of either of two conserved ... | 2011 | 22066495 |
| a photolyase-like protein from agrobacterium tumefaciens with an iron-sulfur cluster. | photolyases and cryptochromes are evolutionarily related flavoproteins with distinct functions. while photolyases can repair uv-induced dna lesions in a light-dependent manner, cryptochromes regulate growth, development and the circadian clock in plants and animals. here we report about two photolyase-related proteins, named phra and phrb, found in the phytopathogen agrobacterium tumefaciens. phra belongs to the class iii cyclobutane pyrimidine dimer (cpd) photolyases, the sister class of plant ... | 2011 | 22066008 |
| Crystal structure of the NurA-dAMP-Mn2+ complex. | Generation of the 3' overhang is a critical event during homologous recombination (HR) repair of DNA double strand breaks. A 5'-3' nuclease, NurA, plays an important role in generating 3' single-stranded DNA during archaeal HR, together with Mre11-Rad50 and HerA. We have determined the crystal structures of apo- and dAMP-Mn(2)(+)-bound NurA from Pyrococcus furiousus (Pf?NurA) to provide the basis for its cleavage mechanism. Pf?NurA forms a pyramid-shaped dimer containing a large central channel ... | 2011 | 22064858 |
| Crystal structure of the NurA-dAMP-Mn2+ complex. | Generation of the 3' overhang is a critical event during homologous recombination (HR) repair of DNA double strand breaks. A 5'-3' nuclease, NurA, plays an important role in generating 3' single-stranded DNA during archaeal HR, together with Mre11-Rad50 and HerA. We have determined the crystal structures of apo- and dAMP-Mn(2)(+)-bound NurA from Pyrococcus furiousus (Pf?NurA) to provide the basis for its cleavage mechanism. Pf?NurA forms a pyramid-shaped dimer containing a large central channel ... | 2011 | 22064858 |
| Probing the mechanistic role of the long a-helix in subunit L of respiratory Complex I from Escherichia coli by site-directed mutagenesis. | The C-terminus of the NuoL subunit of Complex I includes a long amphipathic a-helix positioned parallel to the membrane, which has been considered to function as a piston in the proton pumping machinery. Here, we have introduced three types of mutations into the nuoL gene to test the piston-like function. First, NuoL was truncated at its C- and N-termini, which resulted in low production of a fragile Complex I with negligible activity. Second, we mutated three partially conserved residues of the ... | 2011 | 22060017 |
| structural basis of initial rna polymerase ii transcription. | during transcription initiation by rna polymerase (pol) ii, a transient open promoter complex (oc) is converted to an initially transcribing complex (itc) containing short rnas, and to a stable elongation complex (ec). we report structures of a pol ii-dna complex mimicking part of the oc, and of complexes representing minimal itcs with 2, 4, 5, 6, and 7 nucleotide (nt) rnas, with and without a non-hydrolyzable nucleoside triphosphate (ntp) in the insertion site +1. the partial oc structure revea ... | 2011 | 22056778 |
| new biotechnological perspectives of a nadh oxidase variant from thermus thermophilus hb27 as nad+-recycling enzyme. | the number of biotransformations that use nicotinamide recycling systems is exponentially growing. for this reason one of the current challenges in biocatalysis is to develop and optimize more simple and efficient cofactor recycling systems. one promising approach to regenerate nad+ pools is the use of nadh-oxidases that reduce oxygen to hydrogen peroxide while oxidizing nadh to nad+. this class of enzymes may be applied to asymmetric reduction of prochiral substrates in order to obtain enantiop ... | 2011 | 22053761 |
| comprehensive survey and geometric classification of base triples in rna structures. | base triples are recurrent clusters of three rna nucleobases interacting edge-to-edge by hydrogen bonding. we find that the central base in almost all triples forms base pairs with the other two bases of the triple, providing a natural way to geometrically classify base triples. given 12 geometric base pair families defined by the leontis-westhof nomenclature, combinatoric enumeration predicts 108 potential geometric base triple families. we searched representative atomic-resolution rna 3d struc ... | 2011 | 22053086 |
| comprehensive survey and geometric classification of base triples in rna structures. | base triples are recurrent clusters of three rna nucleobases interacting edge-to-edge by hydrogen bonding. we find that the central base in almost all triples forms base pairs with the other two bases of the triple, providing a natural way to geometrically classify base triples. given 12 geometric base pair families defined by the leontis-westhof nomenclature, combinatoric enumeration predicts 108 potential geometric base triple families. we searched representative atomic-resolution rna 3d struc ... | 2011 | 22053086 |
| structural basis of free reduced flavin generation by flavin reductase from thermus thermophilus hb8. | free reduced flavins are involved in a variety of biological functions. they are generated from nad(p)h by flavin reductase via co-factor flavin bound to the enzyme. although recent findings on the structure and function of flavin reductase provide new information about co-factor fad and substrate nad, there have been no reports on the substrate flavin binding site. here we report the structure of ttha0420 from thermus thermophilus hb8, which belongs to flavin reductase, and describe the dual bi ... | 2011 | 22052907 |
| interactions with the substrate phenolic group are essential for hydroxylation by the oxygenase component of p-hydroxyphenylacetate 3-hydroxylase. | p-hydroxyphenylacetate (hpa) 3-hydroxylase is a two-component flavoprotein monooxygenase that catalyzes the hydroxylation of p-hydroxyphenylacetate to form 3,4-dihydroxyphenylacetate. based on structures of the oxygenase component (c(2)), both his-120 and ser-146 are located ~2.8 å from the hydroxyl group of hpa. the variants h120n, h120q, h120y, h120d, and h120e can form c4a-hydroperoxy-fmn (a reactive intermediate necessary for hydroxylation) but cannot hydroxylate hpa. the impairment of h120n ... | 2011 | 22052902 |
| type-2 isopentenyl diphosphate isomerase: evidence for a stepwise mechanism. | isopentenyl diphosphate isomerase (idi) catalyzes the interconversion of isopentenyl diphosphate (ipp) and dimethylallyl diphosphate (dmapp). these two molecules are the building blocks for construction of isoprenoid carbon skeletons in nature. two structurally unrelated forms of idi are known. a variety of studies support a proton addition/proton elimination mechanism for both enzymes. during studies with thermus thermophilus idi-2, we discovered that the olefinic hydrogens of a vinyl thiomethy ... | 2011 | 22047048 |
| a novel metagenomic short-chain dehydrogenase/reductase attenuates pseudomonas aeruginosa biofilm formation and virulence on caenorhabditis elegans. | in pseudomonas aeruginosa, the expression of a number of virulence factors, as well as biofilm formation, are controlled by quorum sensing (qs). n-acylhomoserine lactones (ahls) are an important class of signaling molecules involved in bacterial qs and in many pathogenic bacteria infection and host colonization are ahl-dependent. the ahl signaling molecules are subject to inactivation mainly by hydrolases (enzyme commission class number ec 3) (i.e. n-acyl-homoserine lactonases and n-acyl-homoser ... | 2011 | 22046268 |
| Multifaceted SlyD from Helicobacter pylori: implication in [NiFe] hydrogenase maturation. | SlyD belongs to the FK506-binding protein (FKBP) family with both peptidylprolyl isomerase (PPIase) and chaperone activities, and is considered to be a ubiquitous cytosolic protein-folding facilitator in bacteria. It possesses a histidine- and cysteine-rich C-terminus binding to selected divalent metal ions (e.g., Ni(2+), Zn(2+)), which is important for its involvement in the maturation processes of metalloenzymes. We have determined the solution structure of C-terminus-truncated SlyD from Helic ... | 2011 | 22045417 |
| Multifaceted SlyD from Helicobacter pylori: implication in [NiFe] hydrogenase maturation. | SlyD belongs to the FK506-binding protein (FKBP) family with both peptidylprolyl isomerase (PPIase) and chaperone activities, and is considered to be a ubiquitous cytosolic protein-folding facilitator in bacteria. It possesses a histidine- and cysteine-rich C-terminus binding to selected divalent metal ions (e.g., Ni(2+), Zn(2+)), which is important for its involvement in the maturation processes of metalloenzymes. We have determined the solution structure of C-terminus-truncated SlyD from Helic ... | 2011 | 22045417 |
| in vivo and in silico determination of essential genes of campylobacter jejuni. | in the united kingdom, the thermophilic campylobacter species c. jejuni and c. coli are the most frequent causes of food-borne gastroenteritis in humans. while campylobacteriosis is usually a relatively mild infection, it has a significant public health and economic impact, and possible complications include reactive arthritis and the autoimmune diseases guillain-barré syndrome. the rapid developments in "omics" technologies have resulted in the availability of diverse datasets allowing predicti ... | 2011 | 22044676 |
| minimal functional sites allow a classification of zinc sites in proteins. | zinc is indispensable to all forms of life as it is an essential component of many different proteins involved in a wide range of biological processes. not differently from other metals, zinc in proteins can play different roles that depend on the features of the metal-binding site. in this work, we describe zinc sites in proteins with known structure by means of three-dimensional templates that can be automatically extracted from pdb files and consist of the protein structure around the metal, ... | 2011 | 22043316 |
| conformational dynamics of the plug domain of the secyeg protein-conducting channel. | the central pore of the secyeg preprotein-conducting channel is closed at the periplasmic face of the membrane by a plug domain. to study its conformational dynamics, the plug was labeled site-specifically with an environment-sensitive fluorophore. in the presence of a stable preprotein translocation inter-mediate, the secy plug showed an enhanced solvent exposure consistent with a displacement from the hydrophobic central pore region. in contrast, binding and insertion of a ribosome-bound nasce ... | 2011 | 22033919 |
| insights into the molecular determinants of ef-g catalyzed translocation. | translocation, the directional movement of transfer rna (trna) and messenger rna (mrna) substrates on the ribosome during protein synthesis, is regulated by dynamic processes intrinsic to the translating particle. using single-molecule fluorescence resonance energy transfer (smfret) imaging, in combination with site-directed mutagenesis of the ribosome and trna substrates, we show that peptidyl-trna within the aminoacyl site of the bacterial pretranslocation complex can adopt distinct hybrid trn ... | 2011 | 22033333 |
| Chloroplast RNase J compensates for inefficient transcription termination by removal of antisense RNA. | Ribonuclease J is an essential enzyme, and the Bacillus subtilis ortholog possesses both endoribonuclease and 5' ? 3' exoribonuclease activities. Chloroplasts also contain RNase J, which has been postulated to participate, as both an exo- and endonuclease, in the maturation of polycistronic mRNAs. Here we have examined recombinant Arabidopsis RNase J and found both 5' ? 3' exoribonuclease and endonucleolytic activities. Virus-induced gene silencing was used to reduce RNase J expression in Arabid ... | 2011 | 22033332 |
| mitochondrial complex i and cell death: a semi-automatic shotgun model. | mitochondrial dysfunction often leads to cell death and disease. we can now draw correlations between the dysfunction of one of the most important mitochondrial enzymes, nadh:ubiquinone reductase or complex i, and its structural organization thanks to the recent advances in the x-ray structure of its bacterial homologs. the new structural information on bacterial complex i provide essential clues to finally understand how complex i may work. however, the same information remains difficult to int ... | 2011 | 22030538 |
| the histone database: an integrated resource for histones and histone fold-containing proteins. | eukaryotic chromatin is composed of dna and protein components-core histones-that act to compactly pack the dna into nucleosomes, the fundamental building blocks of chromatin. these nucleosomes are connected to adjacent nucleosomes by linker histones. nucleosomes are highly dynamic and, through various core histone post-translational modifications and incorporation of diverse histone variants, can serve as epigenetic marks to control processes such as gene expression and recombination. the histo ... | 2011 | 22025671 |
| bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes. | fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within bacteria. in this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and fou ... | 2011 | 22022440 |
| mass spectrometry of intact v-type atpases reveals bound lipids and the effects of nucleotide binding. | the ability of electrospray to propel large viruses into a mass spectrometer is established and is rationalized by analogy to the atmospheric transmission of the common cold. much less clear is the fate of membrane-embedded molecular machines in the gas phase. here we show that rotary adenosine triphosphatases (atpases)/synthases from thermus thermophilus and enterococcus hirae can be maintained intact with membrane and soluble subunit interactions preserved in vacuum. mass spectra reveal subuni ... | 2011 | 22021858 |
| enzymatic synthesis of d-sorbose and d-psicose with aldolase rhad: effect of acceptor configuration on enzyme stereoselectivity. | it was previously reported that dhap-dependent aldolase rhad selectively chooses l-glyceraldehyde from racemic glyceraldehyde to produce l-fructose exclusively. contrastingly, we discovered that d-glyceraldehyde is also tolerated as an acceptor and the stereoselectivity of the enzyme is lost in the corresponding aldol addition. furthermore, we applied this property to efficiently synthesize two rare sugars d-sorbose and d-psicose. | 2011 | 22018788 |
| 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 |
| Small-angle X-ray Scattering Studies of the Oligomeric State and Quaternary Structure of the Trifunctional Proline Utilization A (PutA) Flavoprotein from Escherichia coli. | The trifunctional flavoprotein proline utilization A (PutA) links metabolism and gene regulation in Gram-negative bacteria by catalyzing the two-step oxidation of proline to glutamate and repressing transcription of the proline utilization regulon. Small-angle x-ray scattering (SAXS) and domain deletion analysis were used to obtain solution structural information for the 1320-residue PutA from Escherichia coli. Shape reconstructions show that PutA is a symmetric V-shaped dimer having dimensions ... | 2011 | 22013066 |
| the darc site: a database of aligned ribosomal complexes. | the ribosome is a highly dynamic machine responsible for protein synthesis within the cell. cryo-electron microscopy (cryo-em) and x-ray crystallography structures of ribosomal particles, alone and in complex with diverse ligands (protein factors, rnas and small molecules), have revealed the dynamic nature of the ribosome and provided much needed insight into translation and its regulation. in the past years, there has been exponential growth in the deposition of cryo-em maps into the electron m ... | 2011 | 22009674 |
| the darc site: a database of aligned ribosomal complexes. | the ribosome is a highly dynamic machine responsible for protein synthesis within the cell. cryo-electron microscopy (cryo-em) and x-ray crystallography structures of ribosomal particles, alone and in complex with diverse ligands (protein factors, rnas and small molecules), have revealed the dynamic nature of the ribosome and provided much needed insight into translation and its regulation. in the past years, there has been exponential growth in the deposition of cryo-em maps into the electron m ... | 2011 | 22009674 |
| structure and activity of the cas3 hd nuclease mj0384, an effector enzyme of the crispr interference. | clustered regularly interspaced short palindromic repeats (crisprs) and cas proteins represent an adaptive microbial immunity system against viruses and plasmids. cas3 proteins have been proposed to play a key role in the crispr mechanism through the direct cleavage of invasive dna. here, we show that the cas3 hd domain protein mj0384 from methanocaldococcus jannaschii cleaves endonucleolytically and exonucleolytically (3'-5') single-stranded dnas and rnas, as well as 3'-flaps, splayed arms, and ... | 2011 | 22009198 |
| Ratiometric pulse-chase amidination mass spectrometry as a probe of biomolecular complex formation. | Selective chemical modification of protein side chains coupled with mass spectrometry is often most informative when used to compare residue-specific reactivities in a number of functional states or macromolecular complexes. Herein, we develop ratiometric pulse-chase amidination mass spectrometry (rPAm-MS) as a site-specific probe of lysine reactivities at equilibrium using the Cu(I)-sensing repressor CsoR from Bacillus subtilis as a model system. CsoR in various allosteric states was reacted ... | 2011 | 22007758 |