Publications

the [fefe] hydrogenase of nyctotherus ovalis has a chimeric origin.	the hydrogenosomes of the anaerobic ciliate nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. the hydrogenase permits direct reoxidation of nadh because it consists of a [fefe] hydrogenase module that is fused to two modules, which are homologous to the 24 kda and the 51 kda subunits of a mitochondrial complex i.	2007	18021395
assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data.	comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. this is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving.	2007	18047665
separating the effects of mutation and selection in producing dna skew in bacterial chromosomes.	many bacterial chromosomes display nucleotide asymmetry, or skew, between the leading and lagging strands of replication. mutational differences between these strands result in an overall pattern of skew that is centered about the origin of replication. such a pattern could also arise from selection coupled with a bias for genes coded on the leading strand. the relative contributions of selection and mutation in producing compositional skew are largely unknown.	2007	17935620
transcriptional regulatory network discovery via multiple method integration: application to e. coli k12.	transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ...	2007	17397539
phylogenetic distribution of translational gtpases in bacteria.	translational gtpases are a family of proteins in which gtpase activity is stimulated by the large ribosomal subunit. conserved sequence features allow members of this family to be identified.	2007	17214893
pseudouridylation of helix 69 of 23s rrna is necessary for an effective translation termination.	escherichia coli strains with inactivated rlud genes were previously found to lack the conserved pseudouridines in helix 69 of 23s ribosomal rna and to grow slowly. a suppressor mutant was isolated with a near normal growth rate that had changed the conserved glu-172 codon to a lys codon in prfb, encoding translation termination factor rf2. when nonsense suppression in strains with all combinations of prfb(+)/prfb(e172k) and rlud(+)/rlud::cat was analyzed, misreading of all three stop codons as ...	2007	18032607
scaffolding as an organizing principle in trans-translation. the roles of small protein b and ribosomal protein s1.	a eubacterial ribosome stalled on a defective mrna can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer-messenger rna, small protein b, and ribosome protein s1. by means of cryo-electron microscopy, we obtained a map of the complex composed of a stalled ribosome and small protein b, which appears near the decoding center. this result suggests that, when lacking a codon, the a-site on the small subunit ...	2007	17179154
scaffolding as an organizing principle in trans-translation. the roles of small protein b and ribosomal protein s1.	a eubacterial ribosome stalled on a defective mrna can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer-messenger rna, small protein b, and ribosome protein s1. by means of cryo-electron microscopy, we obtained a map of the complex composed of a stalled ribosome and small protein b, which appears near the decoding center. this result suggests that, when lacking a codon, the a-site on the small subunit ...	2007	17179154
functional organization of the rpb5 subunit shared by the three yeast rna polymerases.	rpb5, a subunit shared by the three yeast rna polymerases, combines a eukaryotic n-terminal module with a globular c-end conserved in all non-bacterial enzymes. conditional and lethal mutants of the moderately conserved eukaryotic module showed that its large n-terminal helix and a short motif at the end of the module are critical in vivo. lethal or conditional mutants of the c-terminal globe altered the binding of rpb5 to rpb1-beta25/26 (prolonging the bridge helix) and rpb1-alpha44/47 (ahead o ...	2007	17179178
functional organization of the rpb5 subunit shared by the three yeast rna polymerases.	rpb5, a subunit shared by the three yeast rna polymerases, combines a eukaryotic n-terminal module with a globular c-end conserved in all non-bacterial enzymes. conditional and lethal mutants of the moderately conserved eukaryotic module showed that its large n-terminal helix and a short motif at the end of the module are critical in vivo. lethal or conditional mutants of the c-terminal globe altered the binding of rpb5 to rpb1-beta25/26 (prolonging the bridge helix) and rpb1-alpha44/47 (ahead o ...	2007	17179178
crystallization and preliminary crystallographic analysis of molybdenum-cofactor biosynthesis protein c from thermus thermophilus.	the gram-negative aerobic eubacterium thermus thermophilus is an extremely important thermophilic microorganism that was originally isolated from a thermal vent environment in japan. the molybdenum cofactor in this organism is considered to be an essential component required by enzymes that catalyze diverse key reactions in the global metabolism of carbon, nitrogen and sulfur. the molybdenum-cofactor biosynthesis protein c derived from t. thermophilus was crystallized in two different space grou ...	2007	17183168
crystallization and preliminary x-ray diffraction analysis of an escherichia coli trna(gly) acceptor-stem microhelix.	the trna(gly) and glycyl-trna synthetase (glyrs) system is an evolutionary special case within the class ii aminoacyl-trna synthetases because two divergent types of glyrs exist: an archaebacterial/human type and an eubacterial type. the trna identity elements which determine the correct aminoacylation process are located in the aminoacyl domain of trna(gly). to obtain further insight concerning structural investigation of the identity elements, the escherichia coli seven-base-pair trna(gly) acc ...	2007	17183173
crystallization and preliminary x-ray diffraction analysis of an escherichia coli trna(gly) acceptor-stem microhelix.	the trna(gly) and glycyl-trna synthetase (glyrs) system is an evolutionary special case within the class ii aminoacyl-trna synthetases because two divergent types of glyrs exist: an archaebacterial/human type and an eubacterial type. the trna identity elements which determine the correct aminoacylation process are located in the aminoacyl domain of trna(gly). to obtain further insight concerning structural investigation of the identity elements, the escherichia coli seven-base-pair trna(gly) acc ...	2007	17183173
the structure of mycobacteria 2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase, an essential enzyme, provides a platform for drug discovery.	the prevalence of tuberculosis, the prolonged and expensive treatment that this disease requires and an increase in drug resistance indicate an urgent need for new treatments. the 1-deoxy-d-xylulose 5-phosphate pathway of isoprenoid precursor biosynthesis is an attractive chemotherapeutic target because it occurs in many pathogens, including mycobacterium tuberculosis, and is absent from humans. to underpin future drug development it is important to assess which enzymes in this biosynthetic path ...	2007	17956607
interaction of smpb with ribosome from directed hydroxyl radical probing.	to add a tag-peptide for degradation to the nascent polypeptide in a stalled ribosome, an unusual translation called trans-translation is facilitated by transfer-messenger rna (tmrna) having an upper half of the trna structure and the sequence encoding the tag-peptide except the first alanine. during this event, tmrna enters the vacant a-site of the stalled ribosome without a codon-anticodon interaction, but with a protein factor smpb. here, we studied the sites and modes of binding of smpb to t ...	2007	17959652
domain i of ribosomal protein l1 is sufficient for specific rna binding.	ribosomal protein l1 has a dual function as a ribosomal protein binding 23s rrna and as a translational repressor binding its mrna. l1 is a two-domain protein with n- and c-termini located in domain i. earlier it was shown that l1 interacts with the same targets on both rrna and mrna mainly through domain i. we have suggested that domain i is necessary and sufficient for specific rna-binding by l1. to test this hypothesis, a truncation mutant of l1 from thermus thermophilus, representing domain ...	2007	17962298
mutational analysis of s12 protein and implications for the accuracy of decoding by the ribosome.	the fidelity of aminoacyl-trna selection by the ribosome depends on a conformational switch in the decoding center of the small ribosomal subunit induced by cognate but not by near-cognate aminoacyl-trna. the aminoglycosides paromomycin and streptomycin bind to the decoding center and induce related structural rearrangements that explain their observed effects on miscoding. structural and biochemical studies have identified ribosomal protein s12 (as well as specific nucleotides in 16s ribosomal ...	2007	17967466
novel hexamerization motif is discovered in a conserved cytoplasmic protein from salmonella typhimurium.	the cytoplasmic protein stm3548 of unknown function obtained from a strain of salmonella typhimurium was determined by x-ray crystallography at a resolution of 2.25 a. the asymmetric unit contains a hexamer of structurally identical monomers. the monomer is a globular domain with a long beta-hairpin protrusion that distinguishes this structure. this beta-hairpin occupies a central position in the hexamer, and its residues participate in the majority of interactions between subunits of the hexame ...	2007	17968677
translation initiation region sequence preferences in escherichia coli.	the mrna translation initiation region (tir) comprises the initiator codon, shine-dalgarno (sd) sequence and translational enhancers. probably the most abundant class of enhancers contains a/u-rich sequences. we have tested the influence of sd sequence length and the presence of enhancers on the efficiency of translation initiation.	2007	17973990
zinc is the metal cofactor of borrelia burgdorferi peptide deformylase.	peptide deformylase (pdf, e.c. 3.5.1.88) catalyzes the removal of n-terminal formyl groups from nascent ribosome-synthesized polypeptides. pdf contains a catalytically essential divalent metal ion, which is tetrahedrally coordinated by three protein ligands (his, his, and cys) and a water molecule. previous studies revealed that the metal cofactor is a fe2+ ion in escherichia coli and many other bacterial pdfs. in this work, we found that pdfs from two iron-deficient bacteria, borrelia burgdorfe ...	2007	17977509
the role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn rna.	the role of 2'-hydroxyl groups in stabilizing the tightly kinked geometry of the kink-turn (k-turn) has been investigated. individual 2'-oh groups have been removed by chemical synthesis, and the kinking of the rna has been studied by gel electrophoresis and fluorescence resonance energy transfer. the results have been analyzed by reference to a database of 11 different crystallographic structures of k-turns. the potential hydrogen bonds fall into several classes. the most important are those in ...	2007	17158708
infantile encephalopathy and defective mitochondrial dna translation in patients with mutations of mitochondrial elongation factors efg1 and eftu.	mitochondrial protein translation is a complex process performed within mitochondria by an apparatus composed of mitochondrial dna (mtdna)-encoded rnas and nuclear dna-encoded proteins. although the latter by far outnumber the former, the vast majority of mitochondrial translation defects in humans have been associated with mutations in rna-encoding mtdna genes, whereas mutations in protein-encoding nuclear genes have been identified in a handful of cases. genetic investigation involving patient ...	2007	17160893
infantile encephalopathy and defective mitochondrial dna translation in patients with mutations of mitochondrial elongation factors efg1 and eftu.	mitochondrial protein translation is a complex process performed within mitochondria by an apparatus composed of mitochondrial dna (mtdna)-encoded rnas and nuclear dna-encoded proteins. although the latter by far outnumber the former, the vast majority of mitochondrial translation defects in humans have been associated with mutations in rna-encoding mtdna genes, whereas mutations in protein-encoding nuclear genes have been identified in a handful of cases. genetic investigation involving patient ...	2007	17160893
a thin-layer electrophoretic assay for asp-trnaasn/glu-trnagln amidotransferase.		2007	17113030
a thin-layer electrophoretic assay for asp-trnaasn/glu-trnagln amidotransferase.		2007	17113030
interpretation of electron density with stereographic roadmap projections.	the program rivem (radial interpretation of viral electron density maps) was developed to project density radially onto a sphere that is then presented as a stereographic diagram. this permits features resulting from an asymmetric reconstruction to be projected and positioned onto an icosahedral virus surface. the features that constitute the viral surface can also be simultaneously represented in terms of atoms, amino acid residues, potential charge distribution, and surface topology. the proce ...	2007	17116403
interpretation of electron density with stereographic roadmap projections.	the program rivem (radial interpretation of viral electron density maps) was developed to project density radially onto a sphere that is then presented as a stereographic diagram. this permits features resulting from an asymmetric reconstruction to be projected and positioned onto an icosahedral virus surface. the features that constitute the viral surface can also be simultaneously represented in terms of atoms, amino acid residues, potential charge distribution, and surface topology. the proce ...	2007	17116403
mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent dna polymerase.	numerous template-dependent dna polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end dna. such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. here, we employed pre-steady state kinetics and x-ray crystallography to establish a mechanism for blunt-end additions catalyzed by sulfolobus solfataricus dpo4. our kinetic studies indicated that the first blunt-end dat ...	2007	17095011
mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent dna polymerase.	numerous template-dependent dna polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end dna. such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. here, we employed pre-steady state kinetics and x-ray crystallography to establish a mechanism for blunt-end additions catalyzed by sulfolobus solfataricus dpo4. our kinetic studies indicated that the first blunt-end dat ...	2007	17095011
mutagenesis of rat acyl-coa synthetase 4 indicates amino acids that contribute to fatty acid binding.	although each of the five mammalian long-chain acyl-coa synthetases (acsl) can bind saturated and unsaturated fatty acids ranging from 12 to 22 carbons, acsl4 prefers longer chain polyunsaturated fatty acids. in order to gain a better understanding of acsl4 fatty acid binding, we based a mutagenesis approach on sequence alignments related to ttlc-facs crystallized from thermus thermophilus hb8. four residues selected for mutagenesis corresponded to residues in ttlc-facs that comprise the fatty a ...	2007	17110164
loss of a universal trna feature.	trna(his) has thus far always been found with one of the most distinctive of trna features, an extra 5' nucleotide that is usually a guanylate. trna(his) genes in a disjoint alphaproteobacterial group comprising the rhizobiales, rhodobacterales, caulobacterales, parvularculales, and pelagibacter generally fail to encode this extra guanylate, unlike those of other alphaproteobacteria and bacteria in general. rather than adding an extra 5' guanylate posttranscriptionally as eukaryotes do, evidence ...	2007	17172343
loss of a universal trna feature.	trna(his) has thus far always been found with one of the most distinctive of trna features, an extra 5' nucleotide that is usually a guanylate. trna(his) genes in a disjoint alphaproteobacterial group comprising the rhizobiales, rhodobacterales, caulobacterales, parvularculales, and pelagibacter generally fail to encode this extra guanylate, unlike those of other alphaproteobacteria and bacteria in general. rather than adding an extra 5' guanylate posttranscriptionally as eukaryotes do, evidence ...	2007	17172343
x-ray crystal structure of mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase ii (mtkasb).	mycolic acids are long chain alpha-alkyl branched, beta-hydroxy fatty acids that represent a characteristic component of the mycobacterium tuberculosis cell wall. through their covalent attachment to peptidoglycan via an arabinogalactan polysaccharide, they provide the basis for an essential outer envelope membrane. mycobacteria possess two fatty acid synthases (fas); fas-i carries out de novo synthesis of fatty acids while fas-ii is considered to elongate medium chain length fatty acyl primers ...	2007	17174327
x-ray crystal structure of mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase ii (mtkasb).	mycolic acids are long chain alpha-alkyl branched, beta-hydroxy fatty acids that represent a characteristic component of the mycobacterium tuberculosis cell wall. through their covalent attachment to peptidoglycan via an arabinogalactan polysaccharide, they provide the basis for an essential outer envelope membrane. mycobacteria possess two fatty acid synthases (fas); fas-i carries out de novo synthesis of fatty acids while fas-ii is considered to elongate medium chain length fatty acyl primers ...	2007	17174327
cloning, expression, purification, crystallization and preliminary x-ray diffraction analysis of universal stress protein f (ynaf) from salmonella typhimurium.	the universal stress protein uspf (ynaf) is a small cytoplasmic bacterial protein. the expression of stress proteins is enhanced when cells are exposed to heat shock, nutrition starvation and certain other stress-inducing agents. ynaf promotes cell survival during prolonged exposure to stress and may activate a general mechanism for stress endurance. this manuscript reports preliminary crystallographic studies on ynaf from salmonella typhimurium. the gene coding for ynaf was cloned and overexpre ...	2007	18007050
crystallization and preliminary x-ray diffraction studies of tetrameric malate dehydrogenase from the novel antarctic psychrophile flavobacterium frigidimaris kuc-1.	flavobacterium frigidimaris kuc-1 is a novel psychrotolerant bacterium isolated from antarctic seawater. malate dehydrogenase (mdh) is an essential metabolic enzyme in the citric acid cycle and has been cloned, overexpressed and purified from f. frigidimaris kuc-1. in contrast to the already known dimeric form of mdh from the psychrophile aquaspirillium arcticum, f. frigidimaris mdh exists as a tetramer. it was crystallized at 288 k by the hanging-drop vapour-diffusion method using ammonium sulf ...	2007	18007057
structural basis of j cochaperone binding and regulation of hsp70.	the many protein processing reactions of the atp-hydrolyzing hsp70s are regulated by j cochaperones, which contain j domains that stimulate hsp70 atpase activity and accessory domains that present protein substrates to hsp70s. we report the structure of a j domain complexed with a j responsive portion of a mammalian hsp70. the j domain activates atpase activity by directing the linker that connects the hsp70 nucleotide binding domain (nbd) and substrate binding domain (sbd) toward a hydrophobic ...	2007	17996706
structural aspects of rbfa action during small ribosomal subunit assembly.	ribosome binding factor a (rbfa) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16s ribosomal rna (rrna) during assembly of the small (30s) ribosomal subunit. here we present a crystal structure of thermus thermophilus (tth) rbfa and a three-dimensional cryo-electron microscopic (em) map of the tth 30s*rbfa complex. rbfa binds to the 30s subunit in a position overlapping the binding sites of the a and p site trnas, and rbfa's functionally im ...	2007	17996707
two distinct components of release factor function uncovered by nucleophile partitioning analysis.	during translation termination, release factor (rf) protein catalyzes a hydrolytic reaction in the large subunit peptidyl transferase center to release the finished polypeptide chain. while the mechanism of catalysis of peptide release remains obscure, important contributing factors have been identified, including conserved active-site nucleotides and a ggq tripeptide motif in the rf. here we describe pre-steady-state kinetic and nucleophile competition experiments to examine rf contributions to ...	2007	17996709
fourier transform infrared characterization of a cub-nitrosyl complex in cytochrome ba3 from thermus thermophilus: relevance to no reductase activity in heme-copper terminal oxidases.	the two heme-copper terminal oxidases of thermus thermophilus have been shown to catalyze the two-electron reduction of nitric oxide (no) to nitrous oxide (n2o) [giuffre, a.; stubauer, g.; sarti, p.; brunori, m.; zumft, w. g.; buse, g.; soulimane, t. proc. natl. acad. sci. u.s.a. 1999, 96, 14718-14723]. while it is well-established that no binds to the reduced heme a3 to form a low-spin heme {feno}7 species, the role cub plays in the binding of the second no remains unclear. here we present low- ...	2007	17997553
reversible dissociation of flavin mononucleotide from the mammalian membrane-bound nadh: ubiquinone oxidoreductase (complex i).	conditions for the reversible dissociation of flavin mononucleotide (fmn) from the membrane-bound mitochondrial nadh:ubiquinone oxidoreductase (complex i) are described. the catalytic activities of the enzyme, i.e. rotenone-insensitive nadh:hexaammineruthenium iii reductase and rotenone-sensitive nadh:quinone reductase decline when bovine heart submitochondrial particles are incubated with nadh in the presence of rotenone or cyanide at alkaline ph. fmn protects and fully restores the nadh-induce ...	2007	18037377
dodecamer rotor ring defines h+/atp ratio for atp synthesis of prokaryotic v-atpase from thermus thermophilus.	atp synthesis by v-atpase from the thermophilic bacterium thermus thermophilus driven by the acid-base transition was investigated. the rate of atp synthesis increased in parallel with the increase in proton motive force (pmf) >110 mv, which is composed of a difference in proton concentration (deltaph) and the electrical potential differences (deltapsi) across membranes. the optimum rate of synthesis reached 85 s(-1), and the h(+)/atp ratio of 4.0 +/- 0.1 was obtained. atp was synthesized at a c ...	2007	18077374
soj (para) dna binding is mediated by conserved arginines and is essential for plasmid segregation.	soj is a member of the para family of atpases involved in plasmid and chromosomal segregation. it binds nonspecifically and cooperatively to dna although the function of this binding is unknown. here, we show that mutation of conserved arginine residues that map to the surface of bacillus subtilis soj caused only minimal effects on nucleotide-dependent dimerization but had dramatic effects on dna binding. using a model plasmid partitioning system in escherichia coli, we find that soj dna-binding ...	2007	18077387
structure of the minimized alpha/beta-hydrolase fold protein from thermus thermophilus hb8.	the gene encoding ttha1544 is a singleton found in the thermus thermophilus hb8 genome and encodes a 131-amino-acid protein. the crystal structure of ttha1544 has been determined at 2.0 a resolution by the single-wavelength anomalous dispersion method in order to elucidate its function. there are two molecules in the asymmetric unit. each molecule consists of four alpha-helices and six beta-strands, with the beta-strands composing a central beta-sheet. a structural homology search revealed that ...	2007	18084077
structure of bacillus subtilis superoxide dismutase.	the soda gene of bacillus subtilis was expressed in escherichia coli, purified and crystallized. the crystal structure of mnsod was solved by molecular replacement with four dimers per asymmetric unit and refined to an r factor of 21.1% at 1.8 a resolution. the dimer structure is very similar to that of the related enzyme from b. anthracis. larger structural differences were observed with the human mnsod, which has one less helix in the helical domain and a longer loop between two beta-strands a ...	2007	18084079
an unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from thermus thermophilus.	past work has shown that it is feasible to mutate surface residues of soluble proteins and to a lesser extent membrane proteins in order to improve their crystallization behavior. described here is a successful application of this approach to the integral membrane protein thermus thermophilus cytochrome ba(3) oxidase. two mutant forms of this enzyme (i-k258r and i-k258r/ii-e4q) were created in which symmetrical crystal contacts within crystals of wild-type enzyme were modified. these mutant prot ...	2007	18084085
the hsp70 chaperone system maintains high concentrations of active proteins and suppresses atp consumption during heat shock.	hsp70 chaperones assist protein folding by cycling between the atp-bound t state with low affinity for substrates and the adp-bound r state with high affinity for substrates. the transition from the t to r state is catalyzed by the synergistic action of the substrate and dnaj cochaperones. the reverse transition from the r state to the t state is accelerated by the nucleotide exchange factor grpe. these two processes, t-to-r and r-to-t conversion, are affected differently by temperature change. ...	2007	19003436
a systematic evaluation of the function of the protein-remodeling factor hsp104 in [psi+] prion propagation in s. cerevisiae by comprehensive chromosomal mutations.	the yeast prion [psi(+)] represents an aggregated state of the translational release factor sup35 (erf3) and deprives termination complexes of functional sup35, resulting in nonsense codon suppression. protein-remodeling factor hsp104 is involved in thermotolerance and [psi(+)] propagation, however the structure-and-function relationship of hsp104 for [psi(+)] remains unclear. in this study, we engineered 58 chromosomal hsp104 mutants that affect residues considered structurally or functionally ...	2007	19164920
use of a dominant rpsl allele conferring streptomycin dependence for positive and negative selection in thermus thermophilus.	a spontaneous rpsl mutant of thermus thermophilus was isolated in a search for new selection markers for this organism. this new allele, named rpsl1, encodes a k47r/k57e double mutant s12 ribosomal protein that confers a streptomycin-dependent (sd) phenotype to t. thermophilus. models built on the available three-dimensional structures of the 30s ribosomal subunit revealed that the k47r mutation directly affects the streptomycin binding site on s12, whereas the k57e does not apparently affect th ...	2007	17601820
mechanistic studies of the long chain acyl-coa synthetase faa1p from saccharomyces cerevisiae.	long chain acyl-coa synthetase (acsl; fatty acid coa ligase: amp forming; ec 6.2.1.3) catalyzes the formation of acyl-coa through a process, which requires fatty acid, atp and coenzymea as substrates. in the yeast saccharomyces cerevisiae the principal acsl is faa1p (encoded by the faa1 gene). the preferred substrates for this enzyme are cis-monounsaturated long chain fatty acids. our previous work has shown faa1p is a principal component of a fatty acid transport/activation complex that also in ...	2007	17604220
thermostability of proteins: role of metal binding and ph on the stability of the dinuclear cua site of thermus thermophilus.	the dinuclear copper center (ttcua) forming the electron entry site in the subunit ii of the cytochrome c oxidase in thermus thermophilus shows high stability toward thermal as well as denaturant-induced unfolding of the protein at ambient ph. we have studied the effect of ph on the stability of the holo-protein as well as of the apo-protein by uv-visible absorption, far-uv, and visible circular dichroism spectroscopy. the results show that the holo-protein both in the native mixed-valence state ...	2007	17604317
structural characterization of the ribosome maturation protein, rimm.	the rimm protein has been implicated in the maturation of the 30s ribosomal subunit. it binds to ribosomal protein s19, located in the head domain of the 30s subunit. multiple sequence alignments predicted that rimm possesses two domains in its n- and c-terminal regions. in the present study, we have produced thermus thermophilus rimm in both the full-length form (162 residues) and its n-terminal fragment, spanning residues 1 to 85, as soluble proteins in escherichia coli and have performed stru ...	2007	17616598
use of an escherichia coli recombinant producing thermostable polyphosphate kinase as an atp regenerator to produce fructose 1,6-diphosphate.	heat-treated escherichia coli producing thermus polyphosphate kinase regenerated atp by using exogenous polyphosphate. this recombinant could be used as a platform to produce valuable compounds in combination with thermostable phosphorylating or energy-requiring enzymes. in this work, we demonstrated the production of fructose 1,6-diphosphate from fructose and polyphosphate.	2007	17616610
crystallization and preliminary x-ray analysis of the oxygenase component (hpab) of 4-hydroxyphenylacetate 3-monooxygenase from thermus thermophilus hb8.	the 4-hydroxyphenylacetate (4hpa) 3-monooxygenase enzyme catalyzes the hydroxylation of 4hpa to 3,4-dihydroxyphenylacetate in the initial step of the degradation pathway of 4hpa. this enzyme consists of two components: an oxygenase (hpab) and a reductase (hpac). hpab hydroxylates 4hpa using an oxygen molecule and a reduced flavin, which is supplied by hpac. hpab from thermus thermophilus hb8 was overexpressed in escherichia coli and crystallized. crystals of hpab were grown in 0.4 m 1,6-hexanedi ...	2007	17620709
crystallization and preliminary x-ray crystallographic study of a putative aspartyl-trna synthetase from the crenarchaeon sulfolobus tokodaii strain 7.	genome analysis suggests that the aspartyl-trna synthetase of the crenarchaeon sulfolobus tokodaii strain 7 belongs to the nondiscriminating type that is believed to catalyze aspartylation of trna(asp) and trna(asn). this protein has been overexpressed in escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method from 100 mm sodium hepes buffer ph 7.5 containing 100 mm nacl and 1.6 m (nh4)2so4 as the crystallizing reagent. diffraction data were collected to 2.3 a ...	2007	17620724
human endonuclease viii-like (neil) proteins in the giant dna mimivirus.	endonuclease viii (nei), which recognizes and repairs oxidized pyrimidines in the base excision repair (ber) pathway, is sparsely distributed among both the prokaryotes and eukaryotes. recently, we and others identified three homologs of escherichia coli endonuclease viii-like (neil) proteins in humans. here, we report identification of human neil homologs in mimivirus, a giant dna virus that infects acanthamoeba. characterization of the two mimiviral homologs, mvnei1 and mvnei2, showed that the ...	2007	17627905
molecular breeding of polymerases for amplification of ancient dna.	in the absence of repair, lesions accumulate in dna. thus, dna persisting in specimens of paleontological, archaeological or forensic interest is inevitably damaged. we describe a strategy for the recovery of genetic information from damaged dna. by molecular breeding of polymerase genes from the genus thermus (taq (thermus aquaticus), tth (thermus thermophilus) and tfl (thermus flavus)) and compartmentalized self-replication selection, we have evolved polymerases that can extend single, double ...	2007	17632524
effects of the deletion of the escherichia coli frataxin homologue cyay on the respiratory nadh:ubiquinone oxidoreductase.	frataxin is discussed as involved in the biogenesis of iron-sulfur clusters. recently it was discovered that a frataxin homologue is a structural component of the respiratory nadh:ubiquinone oxidoreductase (complex i) in thermus thermophilus. it was not clear whether frataxin is in general a component of complex i from bacteria. the escherichia coli homologue of frataxin is coined cyay.	2007	17650323
changes in the conformation of 5s rrna cause alterations in principal functions of the ribosomal nanomachine.	5s rrna is an integral component of the large ribosomal subunit in virtually all living organisms. polyamine binding to 5s rrna was investigated by cross-linking of n1-azidobenzamidino (aba)-spermine to naked 5s rrna or 50s ribosomal subunits and whole ribosomes from escherichia coli cells. aba-spermine cross-linking sites were kinetically measured and their positions in 5s rrna were localized by primer extension analysis. helices iii and v, and loops a, c, d and e in naked 5s rrna were found to ...	2007	17652323
a comparative analysis of the triloops in all high-resolution rna structures reveals sequence structure relationships.	despite an increasing number of experimentally determined rna structures, the gap between the number of structures and that of rna families is still growing. to overcome this limitation, efficient and reliable rna modeling methodologies must be developed. in order to reach this goal, here, we show how triloop sequence-structure relationships have been inferred through a systematic analysis of all triloops found in available high-resolution structures. the structural annotation of all triloops al ...	2007	17652406
biosynthesis of isoprenoids in plants: structure of the 2c-methyl-d-erithrytol 2,4-cyclodiphosphate synthase from arabidopsis thaliana. comparison with the bacterial enzymes.	the x-ray crystal structure of the 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase (mcs) from arabidopsis thaliana has been solved at 2.3 a resolution in complex with a cytidine-5-monophosphate (cmp) molecule. this is the first structure determined of an mcs enzyme from a plant. major differences between the a. thaliana and bacterial mcs structures are found in the large molecular cavity that forms between subunits and involve residues that are highly conserved among plants. in some bacteri ...	2007	17660251
tertiary structure and function of an rna motif required for plant vascular entry to initiate systemic trafficking.	vascular entry is a decisive step for the initiation of long-distance movement of infectious and endogenous rnas, silencing signals and developmental/defense signals in plants. however, the mechanisms remain poorly understood. we used potato spindle tuber viroid (pstvd) as a model to investigate the direct role of the rna itself in vascular entry. we report here the identification of an rna motif that is required for pstvd to traffic from nonvascular into the vascular tissue phloem to initiate s ...	2007	17660743
negamycin binds to the wall of the nascent chain exit tunnel of the 50s ribosomal subunit.	negamycin, a small-molecule inhibitor of protein synthesis, binds the haloarcula marismortui 50s ribosomal subunit at a single site formed by highly conserved rna nucleotides near the cytosolic end of the nascent chain exit tunnel. the mechanism of antibiotic action and the function of this unexplored tunnel region remain intriguingly elusive.	2007	17664317
crystallization and preliminary x-ray diffraction analysis of a soluble domain of the putative zinc transporter czrb from thermus thermophilus.	czrb is a putative zinc transporter from thermus thermophilus. the protein is proposed to consist of a hexahelical transmembrane domain with a cytosolic extramembranal c-terminus. the latter 92-residue fragment may be expressed free and may function independently of the full-length integral membrane protein. a 6xhis-tagged form of the water-soluble fragment has been overexpressed in escherichia coli and diffraction-quality crystals of the tagged and tag-free variants have been grown. preliminary ...	2007	17671365
crystallization and preliminary x-ray diffraction analysis of the cytosolic domain of the mg2+ transporter mgte.	the mgte family of mg(2+) transporters is ubiquitously conserved in all domains of life. the cytosolic domains of the mgte mg(2+) transporters include a cystathionine-beta-synthase (cbs) domain which is known to play a regulatory function in transporter proteins. the cytosolic domain of mgte from thermus thermophilus was overexpressed, purified and crystallized in the presence and absence of mg(2+). the crystals formed in the presence of mg(2+) diffracted x-rays to 2.3 a resolution using synchro ...	2007	17671366
crystallization and preliminary x-ray diffraction analysis of the full-length mg2+ transporter mgte.	the mgte family of mg(2+) transporters are ubiquitously conserved in all three domains. the genes encoding full-length mgte from seven different species were cloned. three of the seven mgte transporters were overexpressed and purified for use in crystallization trials. only thermus thermophilus mgte was successfully crystallized using the sitting-drop vapour-diffusion method. selenomethionine-substituted (semet) crystals were obtained by cross-microseeding using the native microcrystals. the sem ...	2007	17671367
crystallization and preliminary crystallographic analysis of hygromycin b phosphotransferase from escherichia coli.	aminoglycoside antibiotics, such as hygromycin, kanamycin, neomycin, spectinomycin and streptomycin, inhibit protein synthesis by acting on bacterial and eukaryotic ribosomes. hygromycin b phosphotransferase (hph; ec 2.7.1.119) converts hygromycin b to 7''-o-phosphohygromycin using a phosphate moiety from atp, resulting in the loss of its cell-killing activity. the hph protein has been crystallized for the first time using a thermostable mutant and the hanging-drop vapour-diffusion method. the c ...	2007	17671368
complete genomic sequence and mass spectrometric analysis of highly diverse, atypical bacillus thuringiensis phage 0305phi8-36.	to investigate the apparent genomic complexity of long-genome bacteriophages, we have sequenced the 218,948-bp genome (6479-bp terminal repeat), and identified the virion proteins (55), of bacillus thuringiensis bacteriophage 0305phi8-36. phage 0305phi8-36 is an atypical myovirus with three large curly tail fibers. an accurate mode of dna pyrosequencing was used to sequence the genome and mass spectrometry was used to accomplish the comprehensive virion protein survey. advanced informatic techni ...	2007	17673272
the archaeon methanosarcina acetivorans contains a protein disulfide reductase with an iron-sulfur cluster.	methanosarcina acetivorans, a strictly anaerobic methane-producing species belonging to the domain archaea, contains a gene cluster annotated with homologs encoding oxidative stress proteins. one of the genes (ma3736) is annotated as a gene encoding an uncharacterized carboxymuconolactone decarboxylase, an enzyme required for aerobic growth with aromatic compounds by species in the domain bacteria. methane-producing species are not known to utilize aromatic compounds, suggesting that ma3736 is i ...	2007	17675382
crystal structure of the escherichia coli regulator of sigma70, rsd, in complex with sigma70 domain 4.	the escherichia coli rsd protein binds tightly and specifically to the rna polymerase (rnap) sigma(70) factor. rsd plays a role in alternative sigma factor-dependent transcription by biasing the competition between sigma(70) and alternative sigma factors for the available core rnap. here, we determined the 2.6 a-resolution x-ray crystal structure of rsd bound to sigma(70) domain 4 (sigma(70)(4)), the primary determinant for rsd binding within sigma(70). the structure reveals that rsd binding int ...	2007	17681541
discovery of novel dna gyrase inhibitors by high-throughput virtual screening.	the bacterial type ii topoisomerases dna gyrase and topoisomerase iv are validated targets for clinically useful quinolone antimicrobial drugs. a significant limitation to widely utilized quinolone inhibitors is the emergence of drug-resistant bacteria due to an altered dna gyrase. to address this problem, we have used structure-based molecular docking to identify novel drug-like small molecules that target sites distinct from those targeted by quinolone inhibitors. a chemical ligand database co ...	2007	17682095
analysis of a nuclease activity of catalytic domain of thermus thermophilus muts2 by high-accuracy mass spectrometry.	electrospray ionization with fourier-transform ion cyclotron resonance mass spectrometry (esi-ft icr ms) is a powerful tool for analyzing the precise structural features of biopolymers, including oligonucleotides. here, we described the detailed characterization of a newly discovered nuclease activity of the c-terminal domain of thermus thermophilus muts2 (ttmuts2). using this method, the length, nucleotide content and nature of the 5'- and 3'-termini of the product oligonucleotides were accurat ...	2007	17686785
hitting bacteria at the heart of the central dogma: sequence-specific inhibition.	abstract: an important objective in developing new drugs is the achievement of high specificity to maximize curing effect and minimize side-effects, and high specificity is an integral part of the antisense approach. the antisense techniques have been extensively developed from the application of simple long, regular antisense rna (asrna) molecules to highly modified versions conferring resistance to nucleases, stability of hybrid formation and other beneficial characteristics, though still pres ...	2007	17692125
identification of indole derivatives as self-growth inhibitors of symbiobacterium thermophilum, a unique bacterium whose growth depends on coculture with a bacillus sp.	symbiobacterium thermophilum is a syntrophic bacterium whose growth depends on coculture with a bacillus sp. recently, we discovered that co(2) generated by bacillus is the major inducer for the growth of s. thermophilum; however, the evidence suggested that an additional element is required for its full growth. here, we studied the self-growth-inhibitory substances produced by s. thermophilum. we succeeded in purifying two substances from an ether extract of the culture supernatant of s. thermo ...	2007	17693561
type i and type ii fatty acid biosynthesis in eimeria tenella: enoyl reductase activity and structure.	apicomplexan parasites of the genus eimeria are the major causative agent of avian coccidiosis, leading to high economic losses in the poultry industry. recent results show that eimeria tenella harbours an apicoplast organelle, and that a key biosynthetic enzyme, enoyl reductase, is located in this organelle. in related parasites, enoyl reductase is one component of a type ii fatty acid synthase (fas) and has proven to be an attractive target for antimicrobial compounds. we cloned and expressed ...	2007	17697396
a functional interaction of smpb with tmrna for determination of the resuming point of trans-translation.	in trans-translation, transfer-messenger rna (tmrna), possessing a dual function as a trna and an mrna, relieves a stalled translation on the ribosome with the help of smpb. here, we established an in vitro system using escherichia coli translation and trans-translation factors to evaluate two steps of trans-translation, peptidyl transfer from peptidyl-trna to alanyl-tmrna and translation of the resume codon on tmrna. using this system, the effects of several mutations upstream of the tag-encodi ...	2007	17698641
conformations of flanking bases in hiv-1 rna dis kissing complexes studied by molecular dynamics.	explicit solvent molecular dynamics simulations (in total almost 800 ns including locally enhanced sampling runs) were applied with different ion conditions and with two force fields (amber and charmm) to characterize typical geometries adopted by the flanking bases in the rna kissing-loop complexes. we focus on flanking base positions in multiple x-ray and nmr structures of hiv-1 dis kissing complexes and kissing complex from the large ribosomal subunit of haloarcula marismortui. an initial x-r ...	2007	17704156
enzymes involved in dna ligation and end-healing in the radioresistant bacterium deinococcus radiodurans.	enzymes involved in dna metabolic events of the highly radioresistant bacterium deinococcus radiodurans are currently examined to understand the mechanisms that protect and repair the deinococcus radiodurans genome after extremely high doses of gamma-irradiation. although several deinococcus radiodurans dna repair enzymes have been characterised, no biochemical data is available for dna ligation and dna endhealing enzymes of deinococcus radiodurans so far. dna ligases are necessary to seal broke ...	2007	17705817
allosteric control of the rna polymerase by the elongation factor rfah.	efficient transcription of long polycistronic operons in bacteria frequently relies on accessory proteins but their molecular mechanisms remain obscure. rfah is a cellular elongation factor that acts as a polarity suppressor by increasing rna polymerase (rnap) processivity. in this work, we provide evidence that rfah acts by reducing transcriptional pausing at certain positions rather than by accelerating rnap at all sites. we show that 'fast' rnap variants are characterized by pause-free rna ch ...	2007	17711918
messenger rna conformations in the ribosomal e site revealed by x-ray crystallography.	a comparison of messenger rna in x-ray crystal structures of 70s ribosomal complexes in the initiation, post-initiation and elongation states of translation shows distinct conformational differences in the exit (e) codon. here, we present structural evidence indicating that, after the initiation event, the e codon nucleotides relax and form a classical a-helical conformation. this conformation is similar to that of the p and a codons, and is favourable for establishing watson-crick interactions ...	2007	17721443
human tryptophanyl-trna synthetase is switched to a trna-dependent mode for tryptophan activation by mutations at v85 and i311.	for most aminoacyl-trna synthetases (aars), their cognate trna is not obligatory to catalyze amino acid activation, with the exception of four class i (aars): arginyl-trna synthetase, glutamyl-trna synthetase, glutaminyl-trna synthetase and class i lysyl-trna synthetase. furthermore, for arginyl-, glutamyl- and glutaminyl-trna synthetase, the integrated 3' end of the trna is necessary to activate the atp-ppi exchange reaction. tryptophanyl-trna synthetase is a class i aars that catalyzes tryptop ...	2007	17726052
anticodon recognition and discrimination by the alpha-helix cage domain of class i lysyl-trna synthetase.	aminoacyl-trna synthetases are normally found in one of two mutually exclusive structural classes, the only known exception being lysyl-trna synthetase which exists in both classes i (lysrs1) and ii (lysrs2). differences in trna acceptor stem recognition between lysrs1 and lysrs2 do not drastically impact cellular aminoacylation levels, focusing attention on the mechanism of trna anticodon recognition by lysrs1. on the basis of structure-based sequence alignments, seven trnalys anticodon variant ...	2007	17760422
redox-dependent change of nucleotide affinity to the active site of the mammalian complex i.	a very potent and specific inhibitor of mitochondrial nadh:ubiquinone oxidoreductase (complex i), a derivative of nadh (nadh-oh) has recently been discovered (kotlyar, a. b., karliner, j. s., and cecchini, g. (2005) febs lett. 579, 4861-4866). here we present a quantitative analysis of the interaction of nadh-oh and other nucleotides with oxidized and reduced complex i in tightly coupled submitochondrial particles. both the rate of the nadh-oh binding and its affinity to complex i are strongly d ...	2007	17760425
structure-based design of robust glucose biosensors using a thermotoga maritima periplasmic glucose-binding protein.	we report the design and engineering of a robust, reagentless fluorescent glucose biosensor based on the periplasmic glucose-binding protein obtained from thermotoga maritima (tmgbp). the gene for this protein was cloned from genomic dna and overexpressed in escherichia coli, the identity of its cognate sugar was confirmed, ligand binding was studied, and the structure of its glucose complex was solved to 1.7 angstrom resolution by x-ray crystallography. tmgbp is specific for glucose and exhibit ...	2007	17766373
analysis of promoter targets for escherichia coli transcription elongation factor grea in vivo and in vitro.	transcription elongation factor grea induces nucleolytic activity of bacterial rna polymerase (rnap). in vitro, transcript cleavage by grea contributes to transcription efficiency by (i) suppressing pauses and arrests, (ii) stimulating rnap promoter escape, and (iii) enhancing transcription fidelity. however, it is unclear which of these functions is (are) most relevant in vivo. by comparing global gene expression profiles of escherichia coli strains lacking gre factors and strains expressing ei ...	2007	17766423
an aminoacyl-trna synthetase:elongation factor complex for substrate channeling in archaeal translation.	translation requires the specific attachment of amino acids to trnas by aminoacyl-trna synthetases (aarss) and the subsequent delivery of aminoacyl-trnas to the ribosome by elongation factor 1 alpha (ef-1alpha). interactions between ef-1alpha and various aarss have been described in eukaryotes, but the role of these complexes remains unclear. to investigate possible interactions between ef-1alpha and other cellular components, a yeast two-hybrid screen was performed for the archaeon methanotherm ...	2007	17766929
purification, crystallization and preliminary x-ray characterization of a human mitochondrial phenylalanyl-trna synthetase.	human monomeric mitochondrial phenylalanyl-trna synthetase (mitphers) is an enzyme that catalyzes the charging of trna with the cognate amino acid phenylalanine. human mitphers is a chimera of the bacterial alpha-subunit of phers and the b8 domain of its beta-subunit. together, the alpha-subunit and the 'rnp-domain' (b8 domain) at the c-terminus form the minimal structural set to construct an enzyme with phenylalanylation activity. the recombinant human mitphers was purified to homogeneity and c ...	2007	17768348
crystallization and preliminary x-ray crystallographic analysis of a 40 kda n-terminal fragment of the yeast prion-remodeling factor hsp104.	a 40 kda n-terminal fragment of saccharomyces cerevisiae hsp104 was crystallized in two different crystal forms. native 1 diffracted to 2.6 a resolution and belonged to space group p2(1)2(1)2(1), with unit-cell parameters a = 66.6, b = 75.8, c = 235.7 a. native 2 diffracted to 2.9 a resolution and belonged to space group p6(1)22 or p6(5)22, with unit-cell parameters a = 179.1, b = 179.1, c = 69.7 a. this is the first report of the crystallization of a eukaryotic member of the hsp100 family of mo ...	2007	17768355
purification, crystallization and preliminary x-ray analysis of the fumarylacetoacetase family member ttha0809 from thermus thermophilus hb8.	fumarylacetoacetase catalyzes the final step of tyrosine and phenylalanine catabolism. a recombinant form of the fumarylacetoacetase family member ttha0809 from thermus thermophilus hb8 has been crystallized by the oil-microbatch method using sodium chloride as a precipitating agent. the crystals belong to the monoclinic space group p2(1), with unit-cell parameters a = 93.3, b = 73.4, c = 122.6 a, beta = 111.8 degrees. the crystals are most likely to contain two dimers in the asymmetric unit, wi ...	2007	17768357
ribosome biogenesis and the translation process in escherichia coli.	translation, the decoding of mrna into protein, is the third and final element of the central dogma. the ribosome, a nucleoprotein particle, is responsible and essential for this process. the bacterial ribosome consists of three rrna molecules and approximately 55 proteins, components that are put together in an intricate and tightly regulated way. when finally matured, the quality of the particle, as well as the amount of active ribosomes, must be checked. the focus of this review is ribosome b ...	2007	17804668
nmr analysis of [methyl-13c]methionine uvrb from bacillus caldotenax reveals uvrb-domain 4 heterodimer formation in solution.	uvrb is a central dna damage recognition protein involved in bacterial nucleotide excision repair. structural information has been limited by the apparent disorder of the c-terminal domain 4 in crystal structures of intact uvrb; in solution, the isolated domain 4 is found to form a helix-loop-helix dimer. in order to gain insight into the behavior of uvrb in solution, we have performed nmr studies on [methyl-13c]methionine-labeled uvrb from bacillus caldotenax (molecular mass=75 kda). the 13 met ...	2007	17822711
elongation factor 1a mediates the specificity of mitochondrial trna import in t. brucei.	mitochondrial trna import is widespread in eukaryotes. yet, the mechanism that determines its specificity is unknown. previous in vivo experiments using the trnas(met), trna(ile) and trna(lys) have suggested that the t-stem nucleotide pair 51:63 is the main localization determinant of trnas in trypanosoma brucei. in the cytosol-specific initiator trna(met), this nucleotide pair is identical to the main antideterminant that prevents interaction with cytosolic elongation factor (eef1a). here we sh ...	2007	17853889
structural and kinetic characterization of quinolinate phosphoribosyltransferase (hqprtase) from homo sapiens.	human quinolinate phosphoribosyltransferase (ec 2.4.2.19) (hqprtase) is a member of the type ii phosphoribosyltransferase family involved in the catabolism of quinolinic acid (qa). it catalyses the formation of nicotinic acid mononucleotide from quinolinic acid, which involves a phosphoribosyl transfer reaction followed by decarboxylation. hqprtase has been implicated in a number of neurological conditions and in order to study it further, we have carried out structural and kinetic studies on re ...	2007	17868694
substrate specificity and properties of the escherichia coli 16s rrna methyltransferase, rsme.	the small ribosome subunit of escherichia coli contains 10 base-methylated sites distributed in important functional regions. at present, seven enzymes responsible for methylation of eight bases are known, but most of them have not been well characterized. one of these enzymes, rsme, was recently identified and shown to specifically methylate u1498. here we describe the enzymatic properties and substrate specificity of rsme. the enzyme forms dimers in solution and is most active in the presence ...	2007	17872509
conformational energy and structure in canonical and noncanonical forms of trna determined by temperature analysis of the rate of s(4)u8-c13 photocrosslinking.	bacterial trnas frequently have 4-thiouridine (s(4)u) modification at position 8, which is adjacent to the c13-g22-m(7)g46 base triple in the elbow region of the trna tertiary structure. irradiation with light in the uva range induces an efficient photocrosslink between s(4)u8 and c13. the temperature dependence of the rate constants for photocrosslinking between the s(4)u8 and c13 has been used to investigate the trna conformational energy and structure in escherichia coli trna(val), trna(phe), ...	2007	17872510
phosphopantetheine adenylyltransferase from escherichia coli: investigation of the kinetic mechanism and role in regulation of coenzyme a biosynthesis.	phosphopantetheine adenylyltransferase (ppat) from escherichia coli is an essential hexameric enzyme that catalyzes the penultimate step in coenzyme a (coa) biosynthesis and is a target for antibacterial drug discovery. the enzyme utilizes mg-atp and phosphopantetheine (php) to generate dephospho-coa (dpcoa) and pyrophosphate. when overexpressed in e. coli, ppat copurifies with tightly bound coa, suggesting a feedback inhibitory role for this cofactor. using an enzyme-coupled assay for the forwa ...	2007	17873050
pathogenic mechanism of a human mitochondrial trnaphe mutation associated with myoclonic epilepsy with ragged red fibers syndrome.	human mitochondrial trna (hmt-trna) mutations are associated with a variety of diseases including mitochondrial myopathies, diabetes, encephalopathies, and deafness. because the current understanding of the precise molecular mechanisms of these mutations is limited, there is no efficient method to treat their associated mitochondrial diseases. here, we use a variety of known mutations in hmt-trna(phe) to investigate the mechanisms that lead to malfunctions. we tested the impact of hmt-trna(phe) ...	2007	17878308
human ribosomal protein s13 regulates expression of its own gene at the splicing step by a feedback mechanism.	the expression of ribosomal protein (rp) genes is regulated at multiple levels. in yeast, two genes are autoregulated by feedback effects of the protein on pre-mrna splicing. here, we have investigated whether similar mechanisms occur in eukaryotes with more complicated and highly regulated splicing patterns. comparisons of the sequences of ribosomal protein s13 gene (rps13) among mammals and birds revealed that intron 1 is more conserved than the other introns. transfection of hek 293 cells wit ...	2007	17881366
role of hsp104 in the propagation and inheritance of the [het-s] prion.	the chaperones of the clpb/hsp100 family play a central role in thermotolerance in bacteria, plants, and fungi by ensuring solubilization of heat-induced protein aggregates. in addition in yeast, hsp104 was found to be required for prion propagation. herein, we analyze the role of podospora anserina hsp104 (pahsp104) in the formation and propagation of the [het-s] prion. we show that deltapahsp104 strains propagate [het-s], making [het-s] the first native fungal prion to be propagated in the abs ...	2007	17881723
saturation mutagenesis of a +1 programmed frameshift-inducing mrna sequence derived from a yeast retrotransposon.	errors during the process of translating mrna information into protein products occur infrequently. frameshift errors occur less frequently than other types of errors, suggesting that the translational machinery has more robust mechanisms for precluding that kind of error. despite these mechanisms, mrna sequences have evolved that increase the frequency up to 10,000-fold. these sequences, termed programmed frameshift sites, usually consist of a heptameric nucleotide sequence, at which the change ...	2007	17881742