| crystal structure of the atpase domain of the human aaa+ protein paraplegin/spg7. | paraplegin is an m-aaa protease of the mitochondrial inner membrane that is linked to hereditary spastic paraplegias. the gene encodes an ftsh-homology protease domain in tandem with an aaa+ homology atpase domain. the protein is believed to form a hexamer that uses atpase-driven conformational changes in its aaa-domain to deliver substrate peptides to its protease domain. we present the crystal structure of the aaa-domain of human paraplegin bound to adp at 2.2 a. this enables assignment of the ... | 2009 | 19841671 |
| yeast aep3p is an accessory factor in initiation of mitochondrial translation. | initiation of protein synthesis in mitochondria and chloroplasts normally uses a formylated initiator methionyl-trna (fmet-trna(f)(met)). however, mitochondrial protein synthesis in saccharomyces cerevisiae can initiate with nonformylated met-trna(f)(met), as demonstrated in yeast mutants in which the nuclear gene encoding mitochondrial methionyl-trna formyltransferase (fmt1) has been deleted. the role of formylation of the initiator trna is not known, but in vitro formylation increases binding ... | 2009 | 19843529 |
| the structure of staphylococcus aureus phosphopantetheine adenylyltransferase in complex with 3'-phosphoadenosine 5'-phosphosulfate reveals a new ligand-binding mode. | bacterial phosphopantetheine adenylyltransferase (ppat) catalyzes the penultimate step in the coenzyme a (coa) biosynthetic pathway. it catalyzes the reversible transfer of an adenylyl group from atp to 4'-phosphopantetheine (ppant) to form dephospho-coa (dpcoa) and pyrophosphate. previous structural studies have revealed how several ligands are recognized by bacterial ppats. atp, adp, ppant and dpcoa bind to the same binding site in a highly similar manner, while coa binds to a partially overla ... | 2009 | 19851003 |
| crystallization and preliminary x-ray analysis of mannosyl-3-phosphoglycerate synthase from thermus thermophilus hb27. | mannosylglycerate (mg) is a compatible solute that is widespread in marine organisms that are adapted to hot environments, with its intracellular pool generally increasing in response to osmotic stress. these observations suggest that mg plays a relevant role in osmoadaptation and thermoadaptation. the pathways for the synthesis of mg have been characterized in a number of thermophilic and hyperthermophilic organisms. mannosyl-3-phosphoglycerate synthase (mpgs) is a key enzyme in the biosynthesi ... | 2009 | 19851010 |
| allosteric control of catalysis by the f loop of rna polymerase. | bacterial rna polymerases (rnaps) undergo coordinated conformational changes during catalysis. in particular, concerted folding of the trigger loop and rearrangements of the bridge helix at the rnap active center have been implicated in nucleotide addition and rnap translocation. at moderate temperatures, the rate of catalysis by rnap from thermophilic thermus aquaticus is dramatically reduced compared with its closest mesophilic relative, deinococcus radiodurans. here, we show that a part of th ... | 2009 | 19855007 |
| the crystal structure of the novobiocin biosynthetic enzyme novp: the first representative structure for the tylf o-methyltransferase superfamily. | novp is an s-adenosyl-l-methionine-dependent o-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. specifically, it methylates at 4-oh of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic: previous crystallographic studies have shown that this group interacts directly with the target enzyme dna gyrase, which is a validated drug target. we have determined the high-resolution c ... | 2010 | 19857499 |
| the crystal structure of the novobiocin biosynthetic enzyme novp: the first representative structure for the tylf o-methyltransferase superfamily. | novp is an s-adenosyl-l-methionine-dependent o-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. specifically, it methylates at 4-oh of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic: previous crystallographic studies have shown that this group interacts directly with the target enzyme dna gyrase, which is a validated drug target. we have determined the high-resolution c ... | 2010 | 19857499 |
| spermine synthase. | spermine is present in many organisms including animals, plants, some fungi, some archaea, and some bacteria. it is synthesized by spermine synthase, a highly specific aminopropyltransferase. this review describes spermine synthase structure, genetics, and function. structural and biochemical studies reveal that human spermine synthase is an obligate dimer. each monomer contains a c-terminal domain where the active site is located, a central linking domain that also forms the lid of the catalyti ... | 2010 | 19859664 |
| spermine synthase. | spermine is present in many organisms including animals, plants, some fungi, some archaea, and some bacteria. it is synthesized by spermine synthase, a highly specific aminopropyltransferase. this review describes spermine synthase structure, genetics, and function. structural and biochemical studies reveal that human spermine synthase is an obligate dimer. each monomer contains a c-terminal domain where the active site is located, a central linking domain that also forms the lid of the catalyti ... | 2010 | 19859664 |
| structural and dynamic features of the mutt protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base. | escherichia coli mutt hydrolyzes 8-oxo-dgtp to 8-oxo-dgmp, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in dna. of the several enzymes that recognize 8-oxoguanine, mutt exhibits high substrate specificity for 8-oxoguanine nucleotides; however, the structural basis for this specificity is unknown. the crystal structures of mutt in the apo and holo forms and in the binary and ternary forms complexed with the product 8-oxo-dgmp and 8-oxo-dgmp plus mn(2+), respecti ... | 2010 | 19864691 |
| structural and dynamic features of the mutt protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base. | escherichia coli mutt hydrolyzes 8-oxo-dgtp to 8-oxo-dgmp, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in dna. of the several enzymes that recognize 8-oxoguanine, mutt exhibits high substrate specificity for 8-oxoguanine nucleotides; however, the structural basis for this specificity is unknown. the crystal structures of mutt in the apo and holo forms and in the binary and ternary forms complexed with the product 8-oxo-dgmp and 8-oxo-dgmp plus mn(2+), respecti ... | 2010 | 19864691 |
| crystal structure of the aspartyl-trna synthetase from entamoeba histolytica. | the crystal structure of the aspartyl-trna synthetase from the eukaryotic parasite entamoeba histolytica has been determined at 2.8aresolution. relative to homologous sequences, the e. histolytica protein contains a 43-residue insertion between the n-terminal anticodon binding domain and the c-terminal catalytic domain. the present structure reveals that this insertion extends an arm of the hinge region that has previously been shown to mediate interaction of aspartyl-trna synthetase with the co ... | 2010 | 19874856 |
| crystal structure of the aspartyl-trna synthetase from entamoeba histolytica. | the crystal structure of the aspartyl-trna synthetase from the eukaryotic parasite entamoeba histolytica has been determined at 2.8aresolution. relative to homologous sequences, the e. histolytica protein contains a 43-residue insertion between the n-terminal anticodon binding domain and the c-terminal catalytic domain. the present structure reveals that this insertion extends an arm of the hinge region that has previously been shown to mediate interaction of aspartyl-trna synthetase with the co ... | 2010 | 19874856 |
| proteomics-based refinement of deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. | deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. to achieve a comprehensive and accurate annotation of the deinococcus deserti genome, we performed an n terminus-oriented characterization of its proteome. for this, we used a labeling reagent, n-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein n termini. the larg ... | 2010 | 19875382 |
| proteomics-based refinement of deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. | deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. to achieve a comprehensive and accurate annotation of the deinococcus deserti genome, we performed an n terminus-oriented characterization of its proteome. for this, we used a labeling reagent, n-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein n termini. the larg ... | 2010 | 19875382 |
| the role of upf0157 in the folding of m. tuberculosis dephosphocoenzyme a kinase and the regulation of the latter by ctp. | targeting the biosynthetic pathway of coenzyme a (coa) for drug development will compromise multiple cellular functions of the tubercular pathogen simultaneously. structural divergence in the organization of the penultimate and final enzymes of coa biosynthesis in the host and pathogen and the differences in their regulation mark out the final enzyme, dephosphocoenzyme a kinase (coae) as a potential drug target. | 2009 | 19876400 |
| isolation and characterization of tirandamycins from a marine-derived streptomyces sp. | the novel dienoyl tetramic acids tirandamycin c (1) and tirandamycin d (2) with activity against vancomycin-resistant enterococcus faecalis were isolated from the marine environmental isolate streptomyces sp. 307-9, which also produces the previously identified compounds tirandamycins a (3) and b (4). spectroscopic analysis of 1 and 2 indicated structural similarity to 3 and 4, with differences only in the pattern of pendant oxygenation on the bicyclic ketal system. the isolation of these putati ... | 2009 | 19883065 |
| atp-induced conformational changes in hsp70: molecular dynamics and experimental validation of an in silico predicted conformation. | the 70 kda heat shock proteins (hsp70s) play important roles in preventing the misfolding of proteins and repairing damage under stress by coupling atp binding and hydrolysis to protein substrate release and binding, respectively. atp binding is believed to induce closing of the hsp70 nucleotide binding domain (nbd) around the nucleotide. we report here a combined computational-experimental study of this open-closed transition. all-atom molecular dynamics simulations were performed for isolated ... | 2009 | 19883127 |
| direct evidence for nitrogen ligation to the high stability semiquinone intermediate in escherichia coli nitrate reductase a. | the membrane-bound heterotrimeric nitrate reductase a (narghi) catalyzes the oxidation of quinols in the cytoplasmic membrane of escherichia coli and reduces nitrate to nitrite in the cytoplasm. the enzyme strongly stabilizes a menasemiquinone intermediate at a quinol oxidation site (q(d)) located in the vicinity of the distal heme b(d). here molecular details of the interaction between the semiquinone radical and the protein environment have been provided using advanced multifrequency pulsed ep ... | 2010 | 19892705 |
| direct evidence for nitrogen ligation to the high stability semiquinone intermediate in escherichia coli nitrate reductase a. | the membrane-bound heterotrimeric nitrate reductase a (narghi) catalyzes the oxidation of quinols in the cytoplasmic membrane of escherichia coli and reduces nitrate to nitrite in the cytoplasm. the enzyme strongly stabilizes a menasemiquinone intermediate at a quinol oxidation site (q(d)) located in the vicinity of the distal heme b(d). here molecular details of the interaction between the semiquinone radical and the protein environment have been provided using advanced multifrequency pulsed ep ... | 2010 | 19892705 |
| molecular evolution of multisubunit rna polymerases: structural analysis. | comprehensive multiple sequence alignments of the multisubunit dna-dependent rna polymerase (rnap) large subunits, including the bacterial beta and beta' subunits and their homologs from archaebacterial rnaps, eukaryotic rnaps i-iii, nuclear-cytoplasmic large double-stranded dna virus rnaps, and plant plastid rnaps, were created [lane, w. j. and darst, s. a. (2009). molecular evolution of multisubunit rna polymerases: sequence analysis. in press]. the alignments were used to delineate sequence r ... | 2010 | 19895816 |
| molecular evolution of multisubunit rna polymerases: structural analysis. | comprehensive multiple sequence alignments of the multisubunit dna-dependent rna polymerase (rnap) large subunits, including the bacterial beta and beta' subunits and their homologs from archaebacterial rnaps, eukaryotic rnaps i-iii, nuclear-cytoplasmic large double-stranded dna virus rnaps, and plant plastid rnaps, were created [lane, w. j. and darst, s. a. (2009). molecular evolution of multisubunit rna polymerases: sequence analysis. in press]. the alignments were used to delineate sequence r ... | 2010 | 19895816 |
| function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase pa5185 from pseudomonas aeruginosa pao1. | the crystal structure of pa5185, a putative thioesterase from pseudomonas aeruginosa strain pao1, was solved using multi-wavelength anomalous diffraction to 2.4 a. analysis of the structure and information about the putative function of the protein were used to optimize crystallization conditions. the crystal growth was optimized by applying additives with chemical similarity to a fragment of a putative pa5185 substrate (coa or its derivative). using new crystallization conditions containing thi ... | 2008 | 19898606 |
| two distinct regions in staphylococcus aureus gatcab guarantee accurate trna recognition. | in many prokaryotes the biosynthesis of the amide aminoacyl-trnas, gln-trna(gln) and asn-trna(asn), proceeds by an indirect route in which mischarged glu-trna(gln) or asp-trna(asn) is amidated to the correct aminoacyl-trna catalyzed by a trna-dependent amidotransferase (adt). two types of adts exist: bacteria, archaea and organelles possess heterotrimeric gatcab, while heterodimeric gatde occurs exclusively in archaea. bacterial gatcab and gatde recognize the first base pair of the acceptor stem ... | 2010 | 19906721 |
| two distinct regions in staphylococcus aureus gatcab guarantee accurate trna recognition. | in many prokaryotes the biosynthesis of the amide aminoacyl-trnas, gln-trna(gln) and asn-trna(asn), proceeds by an indirect route in which mischarged glu-trna(gln) or asp-trna(asn) is amidated to the correct aminoacyl-trna catalyzed by a trna-dependent amidotransferase (adt). two types of adts exist: bacteria, archaea and organelles possess heterotrimeric gatcab, while heterodimeric gatde occurs exclusively in archaea. bacterial gatcab and gatde recognize the first base pair of the acceptor stem ... | 2010 | 19906721 |
| crystal and solution structures of a prokaryotic m16b peptidase: an open and shut case. | the m16 family of zinc peptidases comprises a pair of homologous domains that form two halves of a "clam-shell" surrounding the active site. the m16a and m16c subfamilies form one class ("peptidasomes"): they degrade 30-70 residue peptides, and adopt both open and closed conformations. the eukaryotic m16b subfamily forms a second class ("processing proteases"): they adopt a single partly-open conformation that enables them to cleave signal sequences from larger proteins. here, we report the solu ... | 2009 | 19913481 |
| characterization of chlorophenol 4-monooxygenase (tftd) and nadh:fad oxidoreductase (tftc) of burkholderia cepacia ac1100. | burkholderia cepacia ac1100 completely degrades 2,4,5-trichlorophenol, in which an fadh(2)-dependent monooxygenase (tftd) and an nadh:fad oxidoreductase (tftc) catalyze the initial steps. tftd oxidizes 2,4,5-trichlorophenol (2,4,5-tcp) to 2,5-dichloro-p-benzoquinone, which is chemically reduced to 2,5-dichloro-p-hydroquinone (2,5-dichq). then, tftd oxidizes the latter to 5-chloro-2-hydroxy-p-benzoquinone. in those processes, tftc provides all the required fadh(2). we have determined the crystal ... | 2010 | 19915006 |
| characterization of chlorophenol 4-monooxygenase (tftd) and nadh:fad oxidoreductase (tftc) of burkholderia cepacia ac1100. | burkholderia cepacia ac1100 completely degrades 2,4,5-trichlorophenol, in which an fadh(2)-dependent monooxygenase (tftd) and an nadh:fad oxidoreductase (tftc) catalyze the initial steps. tftd oxidizes 2,4,5-trichlorophenol (2,4,5-tcp) to 2,5-dichloro-p-benzoquinone, which is chemically reduced to 2,5-dichloro-p-hydroquinone (2,5-dichq). then, tftd oxidizes the latter to 5-chloro-2-hydroxy-p-benzoquinone. in those processes, tftc provides all the required fadh(2). we have determined the crystal ... | 2010 | 19915006 |
| the conserved lysine69 residue plays a catalytic role in mycobacterium tuberculosis shikimate dehydrogenase. | the shikimate pathway is an attractive target for the development of antitubercular agents because it is essential in mycobacterium tuberculosis, the causative agent of tuberculosis, but absent in humans. m. tuberculosis aroe-encoded shikimate dehydrogenase catalyzes the forth reaction in the shikimate pathway. structural and functional studies indicate that lysine69 may be involved in catalysis and/or substrate binding in m. tuberculosis shikimate dehydrogenase. investigation of the kinetic pro ... | 2009 | 19917104 |
| unusual diheme conformation of the heme-degrading protein from mycobacterium tuberculosis. | heme degradation plays a pivotal role in the availability of the essential nutrient, iron, in pathogenic bacteria. a previously unannotated protein from mycobacterium tuberculosis, rv3592, which shares homology to heme-degrading enzymes, has been identified. biochemical analyses confirm that rv3592, which we have termed mhud (mycobacterial heme utilization, degrader), is able to bind and degrade heme. interestingly, contrary to previously reported stoichiometry for the staphylococcus aureus heme ... | 2010 | 19917297 |
| unusual diheme conformation of the heme-degrading protein from mycobacterium tuberculosis. | heme degradation plays a pivotal role in the availability of the essential nutrient, iron, in pathogenic bacteria. a previously unannotated protein from mycobacterium tuberculosis, rv3592, which shares homology to heme-degrading enzymes, has been identified. biochemical analyses confirm that rv3592, which we have termed mhud (mycobacterial heme utilization, degrader), is able to bind and degrade heme. interestingly, contrary to previously reported stoichiometry for the staphylococcus aureus heme ... | 2010 | 19917297 |
| analysis of acyclic nucleoside modifications in sirnas finds sensitivity at position 1 that is restored by 5'-terminal phosphorylation both in vitro and in vivo. | small interfering rnas (sirnas) are short, double-stranded rnas that use the endogenous rnai pathway to mediate gene silencing. phosphorylation facilitates loading of a sirna into the ago2 complex and subsequent cleavage of the target mrna. in this study, 2', 3' seco nucleoside modifications, which contain an acylic ribose ring and are commonly called unlocked nucleic acids (unas), were evaluated at all positions along the guide strand of a sirna targeting apolipoprotein b (apob). una modificati ... | 2010 | 19917641 |
| analysis of acyclic nucleoside modifications in sirnas finds sensitivity at position 1 that is restored by 5'-terminal phosphorylation both in vitro and in vivo. | small interfering rnas (sirnas) are short, double-stranded rnas that use the endogenous rnai pathway to mediate gene silencing. phosphorylation facilitates loading of a sirna into the ago2 complex and subsequent cleavage of the target mrna. in this study, 2', 3' seco nucleoside modifications, which contain an acylic ribose ring and are commonly called unlocked nucleic acids (unas), were evaluated at all positions along the guide strand of a sirna targeting apolipoprotein b (apob). una modificati ... | 2010 | 19917641 |
| molecular modeling of the bifunctional enzyme udp-glcnac 2-epimerase/mannac kinase and predictions of structural effects of mutations associated with hibm and sialuria. | the bifunctional enzyme udp-glcnac 2-epimerase/ mannac kinase (gne/mnk), encoded by the gne gene, catalyzes the first two committed, rate-limiting steps in the biosynthesis of n-acetylneuraminic acid (sialic acid). gne/mnk is feedback inhibited by binding of the downstream product, cmp-sialic acid in its allosteric site. gne mutations can result in two human disorders, hereditary inclusion body myopathy (hibm) or sialuria. so far, no active site geometry predictions or conformational transitions ... | 2010 | 19917666 |
| molecular modeling of the bifunctional enzyme udp-glcnac 2-epimerase/mannac kinase and predictions of structural effects of mutations associated with hibm and sialuria. | the bifunctional enzyme udp-glcnac 2-epimerase/ mannac kinase (gne/mnk), encoded by the gne gene, catalyzes the first two committed, rate-limiting steps in the biosynthesis of n-acetylneuraminic acid (sialic acid). gne/mnk is feedback inhibited by binding of the downstream product, cmp-sialic acid in its allosteric site. gne mutations can result in two human disorders, hereditary inclusion body myopathy (hibm) or sialuria. so far, no active site geometry predictions or conformational transitions ... | 2010 | 19917666 |
| h135a controls the redox activity of the sco copper center. kinetic and spectroscopic studies of the his135ala variant of bacillus subtilis sco. | sco-like proteins contain copper bound by two cysteines and a histidine residue. although their function is still incompletely understood, there is a clear involvement with the assembly of cytochrome oxidases that contain the cu(a) center in subunit 2, possibly mediating the transfer of copper into the cu(a) binuclear site. we are investigating the reaction chemistry of bsco, the homologue from bacillus subtilis. our studies have revealed that bsco behaves more like a redox protein than a metall ... | 2009 | 19921776 |
| solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase. | due to its potential as an antibiotic target, e. coli peptide deformylase (pdf(ec)) serves as a model enzyme system for inhibitor design. while investigating the structural-functional and inhibitory features of this enzyme, we unexpectedly discovered that 2-amino-5-mercapto-1,3,4-thiadiazole (amt) served as a slow-binding inhibitor of pdf(ec) when the above compound was dissolved only in dimethylformamide (dmf), but not in any other solvent, and allowed to age. the time dependent inhibitory pote ... | 2010 | 19922819 |
| solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase. | due to its potential as an antibiotic target, e. coli peptide deformylase (pdf(ec)) serves as a model enzyme system for inhibitor design. while investigating the structural-functional and inhibitory features of this enzyme, we unexpectedly discovered that 2-amino-5-mercapto-1,3,4-thiadiazole (amt) served as a slow-binding inhibitor of pdf(ec) when the above compound was dissolved only in dimethylformamide (dmf), but not in any other solvent, and allowed to age. the time dependent inhibitory pote ... | 2010 | 19922819 |
| structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis. | nonribosomal peptide synthetases (nrpss) are large, multidomain proteins that are involved in the biosynthesis of an array of secondary metabolites. we report the structure of the third adenylation domain from the siderophore-synthesizing nrps, sidn, from the endophytic fungus neotyphodium lolii. this is the first structure of a eukaryotic nrps domain, and it reveals a large binding pocket required to accommodate the unusual amino acid substrate, n(delta)-cis-anhydromevalonyl-n(delta)-hydroxy-l- ... | 2010 | 19923209 |
| structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis. | nonribosomal peptide synthetases (nrpss) are large, multidomain proteins that are involved in the biosynthesis of an array of secondary metabolites. we report the structure of the third adenylation domain from the siderophore-synthesizing nrps, sidn, from the endophytic fungus neotyphodium lolii. this is the first structure of a eukaryotic nrps domain, and it reveals a large binding pocket required to accommodate the unusual amino acid substrate, n(delta)-cis-anhydromevalonyl-n(delta)-hydroxy-l- ... | 2010 | 19923209 |
| structure of an n-terminally truncated nudix hydrolase dr2204 from deinococcus radiodurans. | nudix pyrophosphatases are a well represented protein family in the deinococcus radiodurans genome. these hydrolases, which are known to be enzymatically active towards nucleoside diphosphate derivatives, play a role in cleansing the cell pool of potentially deleterious damage products. here, the structure of dr2204, the only adp-ribose pyrophosphatase in the d. radiodurans genome that is known to be active towards flavin adenosine dinucleotide (fad), is presented at 2.0 angstrom resolution. | 2009 | 19923723 |
| expression, purification and crystallization of an archaeal-type phosphoenolpyruvate carboxylase. | an archaeal-type phosphoenolpyruvate carboxylase (pepca) from clostridium perfringens has been expressed in escherichia coli in a soluble form with an amino-terminal his tag. the recombinant protein is enzymatically active and two crystal forms have been obtained. complete diffraction data extending to 3.13 angstrom resolution have been measured from a crystal soaked in kau(cn)(2), using radiation at a wavelength just above the au l(iii) edge. the asymmetric unit contains two tetramers of pepca. | 2009 | 19923749 |
| solution nmr structures of proteins vpa0419 from vibrio parahaemolyticus and yiis from shigella flexneri provide structural coverage for protein domain family pfam 04175. | | 2010 | 19927321 |
| solution nmr structures of proteins vpa0419 from vibrio parahaemolyticus and yiis from shigella flexneri provide structural coverage for protein domain family pfam 04175. | | 2010 | 19927321 |
| communication between r481 and cu(b) in cytochrome bo(3) ubiquinol oxidase from escherichia coli. | the r481 residue of cytochrome bo(3) ubiquinol oxidase from e. coli is highly conserved in the heme-copper oxidase superfamily. it has been postulated to serve as part of a proton loading site that regulates proton translocation across the protein matrix of the enzyme. along these lines, proton pumping efficiency has been demonstrated to be abolished in many r481 mutants. however, r481q in bo(3) from e. coli has been shown to be fully functional, implying that the positive charge of the arginine ... | 2009 | 19928831 |
| protein-precursor trna contact leads to sequence-specific recognition of 5' leaders by bacterial ribonuclease p. | bacterial ribonuclease p (rnase p) catalyzes the cleavage of 5' leader sequences from precursor trnas (pre-trnas). previously, all known substrate nucleotide specificities in this system are derived from rna-rna interactions with the rnase p rna subunit. here, we demonstrate that pre-trna binding affinities for bacillus subtilis and escherichia coli rnase p are enhanced by sequence-specific contacts between the fourth pre-trna nucleotide on the 5' side of the cleavage site (n(-4)) and the rnase ... | 2010 | 19932118 |
| protein-precursor trna contact leads to sequence-specific recognition of 5' leaders by bacterial ribonuclease p. | bacterial ribonuclease p (rnase p) catalyzes the cleavage of 5' leader sequences from precursor trnas (pre-trnas). previously, all known substrate nucleotide specificities in this system are derived from rna-rna interactions with the rnase p rna subunit. here, we demonstrate that pre-trna binding affinities for bacillus subtilis and escherichia coli rnase p are enhanced by sequence-specific contacts between the fourth pre-trna nucleotide on the 5' side of the cleavage site (n(-4)) and the rnase ... | 2010 | 19932118 |
| n7-methylguanine at position 46 (m7g46) in trna from thermus thermophilus is required for cell viability at high temperatures through a trna modification network. | n(7)-methylguanine at position 46 (m(7)g46) in trna is produced by trna (m(7)g46) methyltransferase (trmb). to clarify the role of this modification, we made a trmb gene disruptant (deltatrmb) of thermus thermophilus, an extreme thermophilic eubacterium. the absence of trmb activity in cell extract from the deltatrmb strain and the lack of the m(7)g46 modification in trna(phe) were confirmed by enzyme assay, nucleoside analysis and rna sequencing. when the deltatrmb strain was cultured at high t ... | 2010 | 19934251 |
| solution structures and backbone dynamics of the ribosomal protein s6 and its permutant p(54-55). | the ribosomal protein s6 from thermus thermophilus has served as a model system for the study of protein folding, especially for understanding the effects of circular permutations of secondary structure elements. this study presents the structure of a permutant protein, the 96-residue p(54-55), and the structure of its 101-residue parent protein s6(wt) in solution. the data also characterizes the effects of circular permutation on the backbone dynamics of s6. consistent with crystallographic dat ... | 2010 | 19937661 |
| catalytic mechanism of human alpha-galactosidase. | the enzyme alpha-galactosidase (alpha-gal, also known as alpha-gal a; e.c. 3.2.1.22) is responsible for the breakdown of alpha-galactosides in the lysosome. defects in human alpha-gal lead to the development of fabry disease, a lysosomal storage disorder characterized by the buildup of alpha-galactosylated substrates in the tissues. alpha-gal is an active target of clinical research: there are currently two treatment options for fabry disease, recombinant enzyme replacement therapy (approved in ... | 2010 | 19940122 |
| catalytic mechanism of human alpha-galactosidase. | the enzyme alpha-galactosidase (alpha-gal, also known as alpha-gal a; e.c. 3.2.1.22) is responsible for the breakdown of alpha-galactosides in the lysosome. defects in human alpha-gal lead to the development of fabry disease, a lysosomal storage disorder characterized by the buildup of alpha-galactosylated substrates in the tissues. alpha-gal is an active target of clinical research: there are currently two treatment options for fabry disease, recombinant enzyme replacement therapy (approved in ... | 2010 | 19940122 |
| trna-dependent pre-transfer editing by prokaryotic leucyl-trna synthetase. | to prevent genetic code ambiguity due to misincorporation of amino acids into proteins, aminoacyl-trna synthetases have evolved editing activities to eliminate intermediate or final non-cognate products. in this work we studied the different editing pathways of class ia leucyl-trna synthetase (leurs). different mutations and experimental conditions were used to decipher the editing mechanism, including the recently developed compound an2690 that targets the post-transfer editing site of leurs. t ... | 2010 | 19940155 |
| trna-dependent pre-transfer editing by prokaryotic leucyl-trna synthetase. | to prevent genetic code ambiguity due to misincorporation of amino acids into proteins, aminoacyl-trna synthetases have evolved editing activities to eliminate intermediate or final non-cognate products. in this work we studied the different editing pathways of class ia leucyl-trna synthetase (leurs). different mutations and experimental conditions were used to decipher the editing mechanism, including the recently developed compound an2690 that targets the post-transfer editing site of leurs. t ... | 2010 | 19940155 |
| peptide-based antibodies against glutathione-binding domains suppress superoxide production mediated by mitochondrial complex i. | complex i (nqr) is a critical site of superoxide (o2-*) production and the major host of redox protein thiols in mitochondria. in response to oxidative stress, nqr-derived protein thiols at the 51- and 75-kda subunits are known to be reversibly s-glutathionylated. although several glutathionylated domains from nqr 51 and 75 kda have been identified, their roles in the regulatory functions remain to be explored. to gain further insights into protein s-glutathionylation of complex i, we used two p ... | 2010 | 19940158 |
| peptide-based antibodies against glutathione-binding domains suppress superoxide production mediated by mitochondrial complex i. | complex i (nqr) is a critical site of superoxide (o2-*) production and the major host of redox protein thiols in mitochondria. in response to oxidative stress, nqr-derived protein thiols at the 51- and 75-kda subunits are known to be reversibly s-glutathionylated. although several glutathionylated domains from nqr 51 and 75 kda have been identified, their roles in the regulatory functions remain to be explored. to gain further insights into protein s-glutathionylation of complex i, we used two p ... | 2010 | 19940158 |
| coupling atp utilization to protein remodeling by clpb, a hexameric aaa+ protein. | clpb and hsp104 are members of the aaa+ (atpases associated with various cellular activities) family of proteins and are molecular machines involved in thermotolerance. they are hexameric proteins containing 12 atp binding sites with two sites per protomer. clpb and hsp104 possess some innate protein remodeling activities; however, they require the collaboration of the dnak/hsp70 chaperone system to disaggregate and reactivate insoluble aggregated proteins. we investigated the mechanism by which ... | 2009 | 19940245 |
| crystal structure of pyrococcus horikoshii tryptophanyl-trna synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-trna synthetase. | the ancient and ubiquitous aminoacyl-trna synthetases constitute a valuable model system for studying early evolutionary events. so far, the evolutionary relationship of tryptophanyl- and tyrosyl-trna synthetase (trprs and tyrrs) remains controversial. as trprs and tyrrs share low sequence homology but high structural similarity, a structure-based method would be advantageous for phylogenetic analysis of the enzymes. here, we present the first crystal structure of an archaeal trprs, the structur ... | 2010 | 19942682 |
| crystal structure of pyrococcus horikoshii tryptophanyl-trna synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-trna synthetase. | the ancient and ubiquitous aminoacyl-trna synthetases constitute a valuable model system for studying early evolutionary events. so far, the evolutionary relationship of tryptophanyl- and tyrosyl-trna synthetase (trprs and tyrrs) remains controversial. as trprs and tyrrs share low sequence homology but high structural similarity, a structure-based method would be advantageous for phylogenetic analysis of the enzymes. here, we present the first crystal structure of an archaeal trprs, the structur ... | 2010 | 19942682 |
| stereochemical mechanisms of trna methyltransferases. | methylation of trna on the four canonical bases adds structural complexity to the molecule, and improves decoding specificity and efficiency. while many trna methylases are known, detailed insight into the catalytic mechanism is only available in a few cases. of interest among all trna methylases is the structural basis for nucleotide selection, by which the specificity is limited to a single site, or broadened to multiple sites. general themes in catalysis include the basis for rate acceleratio ... | 2010 | 19944101 |
| cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. | aspartokinase (ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ask network or from alternative pathways. ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. two subhomology divisions, ask(alpha) and ask(beta), have been recognize ... | 2009 | 19946135 |
| the effect of primer-template mismatches on the detection and quantification of nucleic acids using the 5' nuclease assay. | real-time polymerase chain reaction (pcr) is the current method of choice for detection and quantification of nucleic acids, especially for molecular diagnostics. complementarity between primers and template is often crucial for pcr applications, as mismatches can severely reduce priming efficiency. however, little quantitative data on the effect of these mismatches is available. we quantitatively investigated the effects of primer-template mismatches within the 3'-end primer region on real-time ... | 2010 | 19948821 |
| dynamics of the base of ribosomal a-site finger revealed by molecular dynamics simulations and cryo-em. | helix 38 (h38) of the large ribosomal subunit, with a length of 110 a, reaches the small subunit through intersubunit bridge b1a. previous cryo-em studies revealed that the tip of h38 moves by more than 10 a from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible h38 in attenuation of translocation and in dynamical signaling between ribosomal functional centers. we investigate a region including the elbow-shaped kink-turn (kt-38) i ... | 2010 | 19952067 |
| dynamics of the base of ribosomal a-site finger revealed by molecular dynamics simulations and cryo-em. | helix 38 (h38) of the large ribosomal subunit, with a length of 110 a, reaches the small subunit through intersubunit bridge b1a. previous cryo-em studies revealed that the tip of h38 moves by more than 10 a from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible h38 in attenuation of translocation and in dynamical signaling between ribosomal functional centers. we investigate a region including the elbow-shaped kink-turn (kt-38) i ... | 2010 | 19952067 |
| posttranslational control of transcription factor fixk2, a key regulator for the bradyrhizobium japonicum-soybean symbiosis. | rhizobial fixk-like proteins play essential roles in activating genes for endosymbiotic life in legume root nodules, such as genes for micro-oxic respiration. in the facultative soybean symbiont, bradyrhizobium japonicum, the fixk(2) protein is the key player in a complex regulatory network. the fixk(2) gene itself is activated by the 2-component regulatory system fixlj in response to a moderate decrease of the oxygen tension, and the fixk(2) protein distributes and amplifies this response to th ... | 2009 | 19955406 |
| the crystal structure of apo-ftsh reveals domain movements necessary for substrate unfolding and translocation. | the hexameric membrane-spanning atp-dependent metalloprotease ftsh is universally conserved in eubacteria, mitochondria, and chloroplasts, where it fulfills key functions in quality control and signaling. as a member of the self-compartmentalizing atpases associated with various cellular activities (aaa+ proteases), ftsh converts the chemical energy stored in atp via conformational rearrangements into a mechanical force that is used for substrate unfolding and translocation into the proteolytic ... | 2009 | 19955424 |
| tissue inhibitor of metalloproteinase 1 expression associated with gene demethylation confers anoikis resistance in early phases of melanocyte malignant transformation. | although anoikis resistance has been considered a hallmark of malignant phenotype, the causal relation between neoplastic transformation and anchorage-independent growth remains undefined. we developed an experimental model of murine melanocyte malignant transformation, where a melanocyte lineage (melan-a) was submitted to sequential cycles of anchorage blockade, resulting in progressive morphologic alterations, and malignant transformation. throughout this process, cells corresponding to premal ... | 2009 | 19956395 |
| synergistic cooperation between two clpb isoforms in aggregate reactivation. | bacterial aaa+ atpase clpb cooperates with dnak during reactivation of aggregated proteins. the clpb-mediated disaggregation is linked to translocation of polypeptides through the channel in the oligomeric clpb. two isoforms of clpb are produced in vivo: the full-length clpb95 and clpb80, which does not contain the substrate-interacting n-terminal domain. the biological role of the truncated isoform clpb80 is unknown. we found that resolubilization of aggregated proteins in escherichia coli afte ... | 2010 | 19961856 |
| synergistic cooperation between two clpb isoforms in aggregate reactivation. | bacterial aaa+ atpase clpb cooperates with dnak during reactivation of aggregated proteins. the clpb-mediated disaggregation is linked to translocation of polypeptides through the channel in the oligomeric clpb. two isoforms of clpb are produced in vivo: the full-length clpb95 and clpb80, which does not contain the substrate-interacting n-terminal domain. the biological role of the truncated isoform clpb80 is unknown. we found that resolubilization of aggregated proteins in escherichia coli afte ... | 2010 | 19961856 |
| the effect of spermine on the initiation of mitochondrial protein synthesis. | polyamines are important in both prokaryotic and eukaryotic translational systems. spermine is a quaternary aliphatic amine that is cationic under physiological conditions. in this paper, we demonstrate that spermine stimulates fmet-trna binding to mammalian mitochondrial 55s ribosomes. the stimulatory effect of spermine is independent of the identity of the mrna. the degree of stimulation of spermine is the same at all concentrations of mitochondrial initiation factor 2 (if2(mt)) and mitochondr ... | 2010 | 19962967 |
| the effect of spermine on the initiation of mitochondrial protein synthesis. | polyamines are important in both prokaryotic and eukaryotic translational systems. spermine is a quaternary aliphatic amine that is cationic under physiological conditions. in this paper, we demonstrate that spermine stimulates fmet-trna binding to mammalian mitochondrial 55s ribosomes. the stimulatory effect of spermine is independent of the identity of the mrna. the degree of stimulation of spermine is the same at all concentrations of mitochondrial initiation factor 2 (if2(mt)) and mitochondr ... | 2010 | 19962967 |
| lcca, an archaeal laccase secreted as a highly stable glycoprotein into the extracellular medium by haloferax volcanii. | laccases couple the oxidation of phenolic compounds to the reduction of molecular oxygen and thus span a wide variety of applications. while laccases of eukaryotes and bacteria are well characterized, these enzymes have not been described in archaea. here, we report the purification and characterization of a laccase (lcca) from the halophilic archaeon haloferax volcanii. lcca was secreted at high levels into the culture supernatant of a recombinant h. volcanii strain, with peak activity (170 +/- ... | 2010 | 19966030 |
| lcca, an archaeal laccase secreted as a highly stable glycoprotein into the extracellular medium by haloferax volcanii. | laccases couple the oxidation of phenolic compounds to the reduction of molecular oxygen and thus span a wide variety of applications. while laccases of eukaryotes and bacteria are well characterized, these enzymes have not been described in archaea. here, we report the purification and characterization of a laccase (lcca) from the halophilic archaeon haloferax volcanii. lcca was secreted at high levels into the culture supernatant of a recombinant h. volcanii strain, with peak activity (170 +/- ... | 2010 | 19966030 |
| the structure of the proline utilization a proline dehydrogenase domain inactivated by n-propargylglycine provides insight into conformational changes induced by substrate binding and flavin reduction. | proline utilization a (puta) from escherichia coli is a flavoprotein that has mutually exclusive roles as a transcriptional repressor of the put regulon and a membrane-associated enzyme that catalyzes the oxidation of proline to glutamate. previous studies have shown that the binding of proline in the proline dehydrogenase (prodh) active site and subsequent reduction of the fad trigger global conformational changes that enhance puta-membrane affinity. these events cause puta to switch from its r ... | 2010 | 19994913 |
| expression of reck and matrix metalloproteinase-2 in ameloblastoma. | ameloblastoma is a frequent odontogenic benign tumor characterized by local invasiveness, high risk of recurrence and occasional metastasis and malignant transformation. matrix metalloproteinase-2 (mmp-2) promotes tumor invasion and progression by destroying the extracellular matrix (ecm) and basement membrane. for this proteolytic activity, the endogenous inhibitor is reversion-inducing cysteine rich protein with kazal motifs (reck). the aim of this study was to characterize the relationship be ... | 2009 | 19995435 |
| mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from thermus thermophilus. | homocitrate synthase (hcs) catalyzes aldol-type condensation of acetyl coenzyme a (acetyl-coa) and alpha-ketoglutarate (alpha-kg) to synthesize homocitrate (hc), which is the first and committed step in the lysine biosynthetic pathway through alpha-aminoadipate. as known in most enzymes catalyzing the first reactions in amino acid biosynthetic pathways, hcs is regulated via feedback inhibition by the end product, lysine. here, we determined the crystal structures of hcs from thermus thermophilus ... | 2010 | 19996101 |
| functional significance of eif5a and its hypusine modification in eukaryotes. | the unusual basic amino acid, hypusine [n(epsilon)-(4-amino-2-hydroxybutyl)-lysine], is a modified lysine with the addition of the 4-aminobutyl moiety from the polyamine spermidine. this naturally occurring amino acid is a product of a unique posttranslational modification that occurs in only one cellular protein, eukaryotic translation initiation factor 5a (eif5a, eif-5a). hypusine is synthesized exclusively in this protein by two sequential enzymatic steps involving deoxyhypusine synthase (dhs ... | 2010 | 19997760 |
| functional significance of eif5a and its hypusine modification in eukaryotes. | the unusual basic amino acid, hypusine [n(epsilon)-(4-amino-2-hydroxybutyl)-lysine], is a modified lysine with the addition of the 4-aminobutyl moiety from the polyamine spermidine. this naturally occurring amino acid is a product of a unique posttranslational modification that occurs in only one cellular protein, eukaryotic translation initiation factor 5a (eif5a, eif-5a). hypusine is synthesized exclusively in this protein by two sequential enzymatic steps involving deoxyhypusine synthase (dhs ... | 2010 | 19997760 |
| studies on the mechanism of p-hydroxyphenylacetate 3-hydroxylase from pseudomonas aeruginosa: a system composed of a small flavin reductase and a large flavin-dependent oxygenase. | there are two known types of microbial two-component flavin-dependent monooxygenases that catalyze oxygenation of p-hydroxyphenylacetate (hpa), and they are distinguished by having structurally distinct reductases and oxygenases. this paper presents a detailed analysis of the properties of the enzyme from pseudomonas aeruginosa, an example of one group, and compares its properties to those published for the acinetobacter baumannii enzyme, an example of the alternative group. the reductase and ox ... | 2010 | 20000468 |
| the structural basis for mrna recognition and cleavage by the ribosome-dependent endonuclease rele. | translational control is widely used to adjust gene expression levels. during the stringent response in bacteria, mrna is degraded on the ribosome by the ribosome-dependent endonuclease, rele. the molecular basis for recognition of the ribosome and mrna by rele and the mechanism of cleavage are unknown. here, we present crystal structures of e. coli rele in isolation (2.5 a) and bound to programmed thermus thermophilus 70s ribosomes before (3.3 a) and after (3.6 a) cleavage. rele occupies the a ... | 2009 | 20005802 |
| measurement and interpretation of 15n-1h residual dipolar couplings in larger proteins. | a decade ago, dr. l.e. kay and co-workers described an ingenious hnco-based triple-resonance experiment from which several protein backbone rdcs can be measured simultaneously (yang et al. (1999) [1]). they implemented a j-scaling technique in the (15)n dimension of the 3d experiment to obtain the nh rdcs. we have used this idea to carry out j-scaling in a 2d (15)n-(1)h-trosy experiment and have found it to be an excellent method to obtain nh rdcs for larger proteins upto 70 kda, far superior to ... | 2010 | 20018538 |
| measurement and interpretation of 15n-1h residual dipolar couplings in larger proteins. | a decade ago, dr. l.e. kay and co-workers described an ingenious hnco-based triple-resonance experiment from which several protein backbone rdcs can be measured simultaneously (yang et al. (1999) [1]). they implemented a j-scaling technique in the (15)n dimension of the 3d experiment to obtain the nh rdcs. we have used this idea to carry out j-scaling in a 2d (15)n-(1)h-trosy experiment and have found it to be an excellent method to obtain nh rdcs for larger proteins upto 70 kda, far superior to ... | 2010 | 20018538 |
| modifications of protein environment of the [2fe-2s] cluster of the bc1 complex: effects on the biophysical properties of the rieske iron-sulfur protein and on the kinetics of the complex. | the rate-determining step in the overall turnover of the bc(1) complex is electron transfer from ubiquinol to the rieske iron-sulfur protein (isp) at the q(o)-site. structures of the isp from rhodobacter sphaeroides show that serine 154 and tyrosine 156 form h-bonds to s-1 of the [2fe-2s] cluster and to the sulfur atom of the cysteine liganding fe-1 of the cluster, respectively. these are responsible in part for the high potential (e(m)(,7) approximately 300 mv) and low pk(a) (7.6) of the isp, w ... | 2010 | 20023300 |
| modifications of protein environment of the [2fe-2s] cluster of the bc1 complex: effects on the biophysical properties of the rieske iron-sulfur protein and on the kinetics of the complex. | the rate-determining step in the overall turnover of the bc(1) complex is electron transfer from ubiquinol to the rieske iron-sulfur protein (isp) at the q(o)-site. structures of the isp from rhodobacter sphaeroides show that serine 154 and tyrosine 156 form h-bonds to s-1 of the [2fe-2s] cluster and to the sulfur atom of the cysteine liganding fe-1 of the cluster, respectively. these are responsible in part for the high potential (e(m)(,7) approximately 300 mv) and low pk(a) (7.6) of the isp, w ... | 2010 | 20023300 |
| mapping of the signal peptide-binding domain of escherichia coli seca using förster resonance energy transfer. | identification of the signal peptide-binding domain within seca atpase is an important goal for understanding the molecular basis of seca preprotein recognition as well as elucidating the chemo-mechanical cycle of this nanomotor during protein translocation. in this study, forster resonance energy transfer methodology was employed to map the location of the seca signal peptide-binding domain using a collection of functional monocysteine seca mutants and alkaline phosphatase signal peptides label ... | 2010 | 20025247 |
| dissecting the role of critical residues and substrate preference of a fatty acyl-coa synthetase (fadd13) of mycobacterium tuberculosis. | newly emerging multi-drug resistant strains of mycobacterium tuberculosis (m.tb) severely limit the treatment options for tuberculosis (tb); hence, new antitubercular drugs are urgently needed. the myma operon is essential for the virulence and intracellular survival of m.tb and thus represents an attractive target for the development of new antitubercular drugs. this study is focused on the structure-function relationship of fatty acyl-coa synthetase (fadd13, rv3089) belonging to the myma opero ... | 2009 | 20027301 |
| the pseudomonas aeruginosa magnesium transporter mgte inhibits transcription of the type iii secretion system. | pseudomonas aeruginosa is an opportunistic pathogen that causes life-long pneumonia in individuals with cystic fibrosis (cf). these long-term infections are maintained by bacterial biofilm formation in the cf lung. we have recently developed a model of p. aeruginosa biofilm formation on cultured cf airway epithelial cells. using this model, we discovered that mutation of a putative magnesium transporter gene, called mgte, led to increased cytotoxicity of p. aeruginosa toward epithelial cells. th ... | 2010 | 20028803 |
| the pseudomonas aeruginosa magnesium transporter mgte inhibits transcription of the type iii secretion system. | pseudomonas aeruginosa is an opportunistic pathogen that causes life-long pneumonia in individuals with cystic fibrosis (cf). these long-term infections are maintained by bacterial biofilm formation in the cf lung. we have recently developed a model of p. aeruginosa biofilm formation on cultured cf airway epithelial cells. using this model, we discovered that mutation of a putative magnesium transporter gene, called mgte, led to increased cytotoxicity of p. aeruginosa toward epithelial cells. th ... | 2010 | 20028803 |
| the oxidative dna glycosylases of mycobacterium tuberculosis exhibit different substrate preferences from their escherichia coli counterparts. | the dna glycosylases that remove oxidized dna bases fall into two general families: the fpg/nei family and the nth superfamily. based on protein sequence alignments, we identified four putative fpg/nei family members, as well as a putative nth protein in mycobacterium tuberculosis h37rv. all four fpg/nei proteins were successfully overexpressed using a bicistronic vector created in our laboratory. the mtunth protein was also overexpressed in soluble form. the substrate specificities of the purif ... | 2010 | 20031487 |
| the oxidative dna glycosylases of mycobacterium tuberculosis exhibit different substrate preferences from their escherichia coli counterparts. | the dna glycosylases that remove oxidized dna bases fall into two general families: the fpg/nei family and the nth superfamily. based on protein sequence alignments, we identified four putative fpg/nei family members, as well as a putative nth protein in mycobacterium tuberculosis h37rv. all four fpg/nei proteins were successfully overexpressed using a bicistronic vector created in our laboratory. the mtunth protein was also overexpressed in soluble form. the substrate specificities of the purif ... | 2010 | 20031487 |
| polymorphisms associated with resistance and cross-resistance to aminoglycosides and capreomycin in mycobacterium tuberculosis isolates from south korean patients with drug-resistant tuberculosis. | the aminoglycosides streptomycin, amikacin, and kanamycin and the cyclic polypeptide capreomycin are all widely used in second-line therapy for patients who develop multidrug-resistant tuberculosis. we have characterized a set of 106 clinical isolates of mycobacterium tuberculosis using phenotypic drug susceptibility testing (dst) to determine the extent of resistance to each agent and cross-resistance between agents. these results were compared with polymorphisms in the dna sequences of ribosom ... | 2010 | 20032248 |
| polymorphisms associated with resistance and cross-resistance to aminoglycosides and capreomycin in mycobacterium tuberculosis isolates from south korean patients with drug-resistant tuberculosis. | the aminoglycosides streptomycin, amikacin, and kanamycin and the cyclic polypeptide capreomycin are all widely used in second-line therapy for patients who develop multidrug-resistant tuberculosis. we have characterized a set of 106 clinical isolates of mycobacterium tuberculosis using phenotypic drug susceptibility testing (dst) to determine the extent of resistance to each agent and cross-resistance between agents. these results were compared with polymorphisms in the dna sequences of ribosom ... | 2010 | 20032248 |
| structural motifs of the bacterial ribosomal proteins s20, s18 and s16 that contact rrna present in the eukaryotic ribosomal proteins s25, s26 and s27a, respectively. | the majority of constitutive proteins in the bacterial 30s ribosomal subunit have orthologues in eukarya and archaea. the eukaryotic counterparts for the remainder (s6, s16, s18 and s20) have not been identified. we assumed that amino acid residues in the ribosomal proteins that contact rrna are to be constrained in evolution and that the most highly conserved of them are those residues that are involved in forming the secondary protein structure. we aligned the sequences of the bacterial riboso ... | 2010 | 20034956 |
| accommodation of tmrna-smpb into stalled ribosomes: a cryo-em study. | in eubacteria, translation of defective messenger rnas (mrnas) produces truncated polypeptides that stall on the ribosome. a quality control mechanism referred to as trans-translation is performed by transfer-messenger rna (tmrna), a specialized rna acting as both a trna and an mrna, associated with small protein b (smpb). so far, a clear view of the structural movements of both the protein and rna necessary to perform accommodation is still lacking. by using a construct containing the trna-like ... | 2010 | 20038631 |
| the adenosine wedge: a new structural motif in ribosomal rna. | here, we present a new recurrent rna arrangement, the so-called adenosine wedge (a-wedge), which is found in three places of the ribosomal rna in both ribosomal subunits. the arrangement has a hierarchical structure, consisting of elements previously described as recurrent motifs, namely, the along-groove packing motif, the a-minor and the hook-turn. within the a-wedge, these elements are involved in different types of cause-effect relationships, providing together for the particular tertiary st ... | 2010 | 20038632 |
| discovery of 3-formyl-tyrosine metabolites from pseudoalteromonas tunicata through heterologous expression. | genome mining and identification of natural product gene clusters typically relies on the presence of canonical nonribosomal polypeptide synthetase (nrps) or polyketide synthase (pks) domains. recently, other condensation enzymes, such as the atp-grasp ligases, have been recognized as important players in natural product biosynthesis. in this study, sequence based searching for homologues of ddaf, the atp-grasp amide ligase from dapdiamide biosynthesis, led to the identification of a previously ... | 2010 | 20041686 |
| discovery of 3-formyl-tyrosine metabolites from pseudoalteromonas tunicata through heterologous expression. | genome mining and identification of natural product gene clusters typically relies on the presence of canonical nonribosomal polypeptide synthetase (nrps) or polyketide synthase (pks) domains. recently, other condensation enzymes, such as the atp-grasp ligases, have been recognized as important players in natural product biosynthesis. in this study, sequence based searching for homologues of ddaf, the atp-grasp amide ligase from dapdiamide biosynthesis, led to the identification of a previously ... | 2010 | 20041686 |
| the chlamydial functional homolog of ksga confers kasugamycin sensitivity to chlamydia trachomatis and impacts bacterial fitness. | rrna adenine dimethyltransferases, represented by the escherichia coli ksga protein, are highly conserved phylogenetically and are generally not essential for growth. they are responsible for the post-transcriptional transfer of two methyl groups to two universally conserved adenosines located near the 3'end of the small subunit rrna and participate in ribosome maturation. all sequenced genomes of chlamydia reveal a ksga homolog in each species, including c. trachomatis. yet absence of a s-adeno ... | 2009 | 20043826 |
| flexible recognition of the trna g18 methylation target site by trmh methyltransferase through first binding and induced fit processes. | transfer rna (gm18) methyltransferase (trmh) catalyzes methyl transfer from s-adenosyl-l-methionine to a conserved g18 in trna. we investigated the recognition mechanism of thermus thermophilus trmh for its guanosine target. thirteen yeast trna(phe) mutant transcripts were prepared in which the modification site and/or other nucleotides in the d-loop were substituted by dg, inosine, or other nucleotides. we then conducted methyl transfer kinetic studies, gel shift assays, and inhibition experime ... | 2010 | 20053984 |
| structure of sure protein from aquifex aeolicus vf5 at 1.5 a resolution. | sure is a stationary-phase survival protein found in bacteria, eukaryotes and archaea that exhibits a divalent-metal-ion-dependent phosphatase activity and acts as a nucleotidase and polyphosphate phosphohydrolase. the structure of the sure protein from the hyperthermophile aquifex aeolicus has been solved at 1.5 a resolution using molecular replacement with one dimer in the asymmetric unit and refined to an r factor of 15.6%. the crystal packing reveals that two dimers assemble to form a tetram ... | 2009 | 20054112 |
| structure of putative 4-amino-4-deoxychorismate lyase from thermus thermophilus hb8. | the pyridoxal 5'-phosphate-dependent enzyme 4-amino-4-deoxychorismate lyase converts 4-amino-4-deoxychorismate to p-aminobenzoate and pyruvate in one of the crucial steps in the folate-biosynthesis pathway. the primary structure of the hypothetical protein ttha0621 from thermus thermophilus hb8 suggests that ttha0621 is a putative 4-amino-4-deoxychorismate lyase. here, the crystal structure of ttha0621 is reported at 1.93 a resolution. the asymmetric unit contained four ncs molecules related by ... | 2009 | 20054118 |