Publications

xylose reductase from pichia stipitis with altered coenzyme preference improves ethanolic xylose fermentation by recombinant saccharomyces cerevisiae.	xylose reductase (xr) and xylitol dehydrogenase (xdh) from pichia stipitis are the two enzymes most commonly used in recombinant saccharomyces cerevisiae strains engineered for xylose utilization. the availability of nad+ for xdh is limited during anaerobic xylose fermentation because of the preference of xr for nadph. this in turn results in xylitol formation and reduced ethanol yield. the coenzyme preference of p. stipitis xr was changed by site-directed mutagenesis with the aim to engineer it ...	2009	19416504
atomic structure of a folate/fad-dependent trna t54 methyltransferase.	trnas from all 3 phylogenetic domains have a 5-methyluridine at position 54 (t54) in the t-loop. the methyl group is transferred from s-adenosylmethionine by trma methyltransferase in most gram-negative bacteria and some archaea and eukaryotes, whereas it is transferred from 5,10-methylenetetrahydrofolate (mthf) by trmfo, a folate/fad-dependent methyltransferase, in most gram-positive bacteria and some gram-negative bacteria. however, the catalytic mechanism remains unclear, because the crystal ...	2009	19416846
mechanism of sequence-specific pausing of bacterial rna polymerase.	sequence-specific pausing of multisubunit rna polymerases (rnaps) represents a rate-limiting step during transcription elongation. pausing occurs on average every 100 bases of dna. several models have been proposed to explain pausing, including backtracking of the ternary elongation complex, delay of translocation of the enzyme along dna, or a conformational change in the active site preventing formation of the phosphodiester bond. here, we performed biochemical characterization of previously-re ...	2009	19416863
contribution of ribosomal residues to p-site trna binding.	structural studies have revealed multiple contacts between the ribosomal p site and trna, but how these contacts contribute to p-trna binding remains unclear. in this study, the effects of ribosomal mutations on the dissociation rate (k(off)) of various trnas from the p site were measured. mutation of the 30s p site destabilized trnas to various degrees, depending on the mutation and the species of trna. these data support the idea that ribosome-trna interactions are idiosyncratically tuned to e ...	2009	19417061
structural insights into erf3 and stop codon recognition by erf1.	eukaryotic translation termination is mediated by two interacting release factors, erf1 and erf3, which act cooperatively to ensure efficient stop codon recognition and fast polypeptide release. the crystal structures of human and schizosaccharomyces pombe full-length erf1 in complex with erf3 lacking the gtpase domain revealed details of the interaction between these two factors and marked conformational changes in erf1 that occur upon binding to erf3, leading erf1 to resemble a trna molecule. ...	2009	19417105
yeast mitochondrial gln-trna(gln) is generated by a gatfab-mediated transamidation pathway involving arc1p-controlled subcellular sorting of cytosolic glurs.	it is impossible to predict which pathway, direct glutaminylation of trna(gln) or trna-dependent transamidation of glutamyl-trna(gln), generates mitochondrial glutaminyl-trna(gln) for protein synthesis in a given species. the report that yeast mitochondria import both cytosolic glutaminyl-trna synthetase and trna(gln) has challenged the widespread use of the transamidation pathway in organelles. here we demonstrate that yeast mitochondrial glutaminyl-trna(gln) is in fact generated by a transamid ...	2009	19417106
identification of genes contributing to the virulence of francisella tularensis schu s4 in a mouse intradermal infection model.	francisella tularensis is a highly virulent human pathogen. the most virulent strains belong to subspecies tularensis and these strains cause a sometimes fatal disease. despite an intense recent research effort, there is very limited information available that explains the unique features of subspecies tularensis strains that distinguish them from other f. tularensis strains and that explain their high virulence. here we report the use of targeted mutagenesis to investigate the roles of various ...	2009	19424499
roles of rel(spn) in stringent response, global regulation and virulence of serotype 2 streptococcus pneumoniae d39.	rela/spot homologue (rsh) proteins have (p)ppgpp synthetase and hydrolase activities that mediate major global responses to nutrient limitation and other stresses. rsh proteins are conserved in most bacteria and play diverse roles in bacterial pathogenesis. we report here that the rsh protein of streptococcus pneumoniae, rel(spn), can be deleted and is the primary source of (p)ppgpp synthesis in virulent strain d39 under some conditions. a d39 deltarel(spn) mutant grew well in complex medium, bu ...	2009	19426208
structure, stability, and flexibility of ribosomal protein l14e from sulfolobus solfataricus.	ribosomal protein l14e is a component of the large ribosomal subunit in both archaea and eukaryotes. we report here a high-resolution nmr solution structure of recombinant l14e and show that the n-terminal 57 residues adopt a classic sh3 fold. the protein contains a tight turn between strands 1 and 2 instead of the typical sh3 rt-loop, indicating that it is unlikely to interact with neighboring ribosomal proteins using the common sh3 site for proline-rich sequences. the remainder of the protein ...	2009	19432457
a spectroscopic investigation of a tridentate cu-complex mimicking the tyrosine-histidine cross-link of cytochrome c oxidase.	heme-copper oxidases have a crucial role in the energy transduction mechanism, catalyzing the reduction of dioxygen to water. the reduction of dioxygen takes place at the binuclear center, which contains heme a3 and cub. the x-ray crystal structures have revealed that the c6' of tyrosine 244 (bovine heart numbering) is cross-linked to a nitrogen of histidine 240, a ligand to cub. the role of the cross-linked tyrosine at the active site still remains unclear. in order to provide insight into the ...	2009	19438285
solution conformation of wild-type e. coli hsp70 (dnak) chaperone complexed with adp and substrate.	dnak is the canonical hsp70 molecular chaperone protein from escherichia coli. like other hsp70s, dnak comprises two main domains: a 44-kda n-terminal nucleotide-binding domain (nbd) that contains atpase activity, and a 25-kda substrate-binding domain (sbd) that harbors the substrate-binding site. here, we report an experimental structure for wild-type, full-length dnak, complexed with the peptide nrllltg and with adp. it was obtained in aqueous solution by using nmr residual dipolar coupling an ...	2009	19439666
plasmodial aspartyl-trna synthetases and peculiarities in plasmodium falciparum.	distinctive features of aspartyl-transfer rna (trna) synthetases (asprs) from the protozoan plasmodium genus are described. these apicomplexan asprss contain 29-31 amino acid insertions in their anticodon binding domains, a remarkably long n-terminal appendix that varies in size from 110 to 165 amino acids and two potential initiation codons. this article focuses on the atypical functional and structural properties of plasmodium falciparum cytosolic asprs, the causative parasite of human malaria ...	2009	19443655
electrostatics of the fes clusters in respiratory complex i.	respiratory complex i couples the transfer of electrons from nadh to ubiquinone and the translocation of protons across the mitochondrial membrane. a detailed understanding of the midpoint reduction potentials (e(m)) of each redox center and the factors which influence those potentials are critical in the elucidation of the mechanism of electron transfer in this enzyme. we present accurate electrostatic interaction energies for the iron-sulfur (fes) clusters of complex i to facilitate the develo ...	2009	19445896
regulation of translation by the redox state of elongation factor g in the cyanobacterium synechocystis sp. pcc 6803.	elongation factor g (ef-g), a key protein in translational elongation, was identified as a primary target of inactivation by reactive oxygen species within the translational machinery of the cyanobacterium synechocystis sp. pcc 6803 (kojima, k., oshita, m., nanjo, y., kasai, k., tozawa, y., hayashi, h., and nishiyama, y. (2007) mol. microbiol. 65, 936-947). in the present study, we found that inactivation of ef-g (slr1463) by h(2)o(2) was attributable to the oxidation of two specific cysteine re ...	2009	19447882
transcription activity of individual rrn operons in bacillus subtilis mutants deficient in (p)ppgpp synthetase genes, rela, yjbm, and ywac.	in bacillus subtilis a null mutation of the rela gene, whose gene product is involved in the synthesis and/or hydrolysis of (p)ppgpp, causes a growth defect that can be suppressed by mutation(s) of yjbm and/or ywac coding for small (p)ppgpp synthetases. all 35 suppressor mutations newly isolated were classified into two groups, either yjbm or ywac, by mapping and sequencing their mutations, suggesting that there are no (p)ppgpp synthetases other than rela, yjbm, and ywac in b. subtilis. in order ...	2009	19447912
substrate specificity of a mannose-6-phosphate isomerase from bacillus subtilis and its application in the production of l-ribose.	the uncharacterized gene previously proposed as a mannose-6-phosphate isomerase from bacillus subtilis was cloned and expressed in escherichia coli. the maximal activity of the recombinant enzyme was observed at ph 7.5 and 40 degrees c in the presence of 0.5 mm co(2+). the isomerization activity was specific for aldose substrates possessing hydroxyl groups oriented in the same direction at the c-2 and c-3 positions, such as the d and l forms of ribose, lyxose, talose, mannose, and allose. the en ...	2009	19447949
sequential processing of the toxoplasma apicoplast membrane protein ftsh1 in topologically distinct domains during intracellular trafficking.	ftsh proteins are hexameric transmembrane proteases found in chloroplasts, mitochondria and bacteria. in the protozoan toxoplasma gondii, ftsh1 is localized to membranes of the apicoplast, a relict chloroplast present in many apicomplexan parasites. we have shown that although t. gondii ftsh1 lacks the typical bipartite targeting presequence seen on apicoplast luminal proteins, it is targeted to the apicoplast via the endoplasmic reticulum. in this report, we show that ftsh1 undergoes processing ...	2009	19450729
translocation of proteins through the sec61 and secyeg channels.	the sec61 and secyeg translocation channels mediate the selective transport of proteins across the endoplasmic reticulum and bacterial inner membrane, respectively. these channels are also responsible for the integration of membrane proteins. to accomplish these two critical events in protein expression, the transport channels undergo conformational changes to permit the export of lumenal domains and the integration of transmembrane spans. novel insight into how these channels open during protei ...	2009	19450960
understanding the sequence specificity of trna binding to elongation factor tu using trna mutagenesis.	measuring the binding affinities of 42 single-base-pair mutants in the acceptor and t psi c stems of saccharomyces cerevisiae trna phe to thermus thermophilus elongation factor tu (ef-tu) revealed that much of the specificity for trna occurs at the 49-65, 50-64, and 51-63 base pairs. introducing the same mutations at the three positions into escherichia coli trna cag leu resulted in similar changes in binding affinity. swapping the three pairs from several e. coli trnas into yeast trna phe resul ...	2009	19452597
structural basis for adp-mediated transcriptional regulation by p1 and p7 para.	the accurate segregation of dna is essential for the faithful inheritance of genetic information. segregation of the prototypical p1 plasmid par system requires two proteins, para and parb, and a centromere. when bound to atp, para mediates segregation by interacting with centromere-bound parb, but when bound to adp, para fulfils a different function: dna-binding transcription autoregulation. the structure of para is unknown as is how distinct nucleotides arbitrate its different functions. to ad ...	2009	19461582
comprehensive analysis of phosphorylated proteins of escherichia coli ribosomes.	phosphorylation of bacterial ribosomal proteins has been known for decades; however, there is still very limited information available on specific locations of the phosphorylation sites in ribosomal proteins and the role they might play in protein synthesis. in this study, we have mapped the specific phosphorylation sites in 24 escherichia coli ribosomal proteins by tandem mass spectrometry. detection of phosphorylation was achieved by either phosphorylation specific visualization techniques, pr ...	2009	19469554
compressing the free energy range of substructure stabilities in iso-1-cytochrome c.	evolutionary conservation of substructure architecture between yeast iso-1-cytochrome c and the well-characterized horse cytochrome c is studied with limited proteolysis, the alkaline conformational transition and global unfolding with guanidine-hcl. mass spectral analysis of limited proteolysis cleavage products for iso-1-cytochrome c show that its least stable substructure is the same as horse cytochrome c. the limited proteolysis data yield a free energy of 3.8 +/- 0.4 kcal mol(-1) to unfold ...	2009	19472325
the genome sequence of geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to geobacter sulfurreducens.	the genome sequence of geobacter metallireducens is the second to be completed from the metal-respiring genus geobacter, and is compared in this report to that of geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences.	2009	19473543
analysis of proteins with the 'hot dog' fold: prediction of function and identification of catalytic residues of hypothetical proteins.	the hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. the fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme a-binding enzymes with a variety of substrates located at their active sites.	2009	19473548
isolation, crystallization and preliminary x-ray analysis of the transamidosome, a ribonucleoprotein involved in asparagine formation.	thermus thermophilus deprived of asparagine synthetase synthesizes asn on trna(asn) via a trna-dependent pathway involving a nondiscriminating aspartyl-trna synthetase that charges asp onto trna(asn) prior to conversion of the asp to asn by gatcab, a trna-dependent amidotransferase. this pathway also constitutes the route of asn-trna(asn) formation by bacteria and archaea deprived of asparaginyl-trna synthetase. the partners involved in trna-dependent asn formation in t. thermophilus assemble in ...	2009	19478435
crystallization of mycobacterium smegmatis methionyl-trna synthetase in the presence of methionine and adenosine.	methionyl-trna synthetase (metrs) from mycobacterium smegmatis was recombinantly expressed in escherichia coli and purified using ni(2+)-affinity and size-exclusion chromatography. crystals formed readily in the presence of the ligands methionine and adenosine. these two ligands are components of an intermediate in the two-step catalytic mechanism of metrs. the crystals were produced using the vapour-diffusion method and a full data set to 2.1 a resolution was collected from a single crystal. th ...	2009	19478446
cloning and analysis of a bifunctional methyltransferase/restriction endonuclease tspgwi, the prototype of a thermus sp. enzyme family.	restriction-modification systems are a diverse class of enzymes. they are classified into four major types: i, ii, iii and iv. we have previously proposed the existence of a thermus sp. enzyme family, which belongs to type ii restriction endonucleases (reases), however, it features also some characteristics of types i and iii. members include related thermophilic endonucleases: tspgwi, taqii, tspdti, and tth111ii.	2009	19480701
asymmetric amino acid activation by class ii histidyl-trna synthetase from escherichia coli.	aminoacyl-trna synthetases (arss) join amino acids to their cognate trnas to initiate protein synthesis. class ii ars possess a unique catalytic domain fold, possess active site signature sequences, and are dimers or tetramers. the dimeric class i enzymes, notably tyrrs, exhibit half-of-sites reactivity, but its mechanistic basis is unclear. in class ii histidyl-trna synthetase (hisrs), amino acid activation occurs at different rates in the two active sites when trna is absent, but half-of-sites ...	2009	19487703
aquifex aeolicus trna (n2,n2-guanine)-dimethyltransferase (trm1) catalyzes transfer of methyl groups not only to guanine 26 but also to guanine 27 in trna.	transfer rna (n2,n2-guanine)-dimethyltransferase (trm1) catalyzes n2,n2-dimethylguanine formation at position 26 (m(2)(2)g26) in trna. in the reaction, n2-guanine at position 26 (m(2)g26) is generated as an intermediate. the trm1 genes are found only in archaea and eukaryotes, although it has been reported that aquifex aeolicus, a hyper-thermophilic eubacterium, has a putative trm1 gene. to confirm whether a. aeolicus trm1 has trna methyltransferase activity, we purified recombinant trm1 protein ...	2009	19491098
characterization of three beta-galactoside phosphorylases from clostridium phytofermentans: discovery of d-galactosyl-beta1->4-l-rhamnose phosphorylase.	we characterized three d-galactosyl-beta1-->3-n-acetyl-d-hexosamine phosphorylase (ec 2.4.1.211) homologs from clostridium phytofermentans (cphy0577, cphy1920, and cphy3030 proteins). cphy0577 and cphy3030 proteins exhibited similar activity on galacto-n-biose (gnb; d-gal-beta1-->3-d-galnac) and lacto-n-biose i (lnb; d-gal-beta1-->3-d-glcnac), thus indicating that they are d-galactosyl-beta1-->3-n-acetyl-d-hexosamine phosphorylases, subclassified as gnb/lnb phosphorylase. in contrast, cphy1920 p ...	2009	19491100
vibriobactin antibodies: a vaccine strategy.	a new target strategy in the development of bacterial vaccines, the induction of antibodies to microbial outer membrane ferrisiderophore complexes, is explored. a vibriobactin (vib) analogue, with a thiol tether, 1-(2,3-dihydroxybenzoyl)-5,9-bis[[(4s,5r)-2-(2,3-dihydroxyphenyl)-4,5-dihydro-5-methyl-4-oxazolyl]carbonyl]-14-(3-mercaptopropanoyl)-1,5,9,14-tetraazatetradecane, was synthesized and linked to ovalbumin (ova) and bovine serum albumin (bsa). the antigenicity of the vib microbial iron che ...	2009	19492834
two structurally independent domains of e. coli nusg create regulatory plasticity via distinct interactions with rna polymerase and regulators.	nusg is a conserved regulatory protein that interacts with elongation complexes (ecs) of rna polymerase, dna, and rna to modulate transcription in multiple and sometimes opposite ways. in escherichia coli, nusg suppresses pausing and increases elongation rate, enhances termination by e. coli rho and phage hk022 nun protein, and promotes antitermination by lambdan and in ribosomal rna operons. we report nmr studies that suggest that e. coli nusg consists of two largely independent n- and c-termin ...	2009	19500594
the folding trajectory of rnase h is dominated by its topology and not local stability: a protein engineering study of variants that fold via two-state and three-state mechanisms.	proteins can sample a variety of partially folded conformations during the transition between the unfolded and native states. some proteins never significantly populate these high-energy states and fold by an apparently two-state process. however, many proteins populate detectable, partially folded forms during the folding process. the role of such intermediates is a matter of considerable debate. a single amino acid change can convert escherichia coli ribonuclease h from a three-state folder th ...	2009	19501596
toward the catalytic mechanism of a cysteine ligase (mshc) from mycobacterium smegmatis: an enzyme involved in the biosynthetic pathway of mycothiol.	mycobacterium tuberculosis and other members of the actinomycete family produce mycothiol (msh or acetylcysteine-glucosamine-inositol, accys-glcn-ins) to protect the organism against oxidative and antibiotic stress. the biosynthesis of msh proceeds via a five-step process that involves four unique enzymes, msha-d, which represent specific targets for inhibitor design. recombinant mycobacterium smegmatis mshc catalyzes the atp-dependent condensation of glucosamine-inositol (glcn-ins) and cysteine ...	2009	19505149
the 5' terminal uracil of let-7a is critical for the recruitment of mrna to argonaute2.	small rnas modulate gene expression by forming a ribonucleoprotein complex with argonaute proteins and directing them to specific complementary sites in target nucleic acids. however, the interactions required for the recruitment of the target nucleic acid to the ribonucleoprotein complex are poorly understood. in the present manuscript we have investigated this question by using let-7a, argonaute2 and a fully complementary mrna target. importantly, we have found that recombinant argonaute2 is s ...	2009	19508234
hsp70 structure, function, regulation and influence on yeast prions.	heat shock proteins protect cells from various conditions of stress. hsp70, the most ubiquitous and highly conserved hsp, helps proteins adopt native conformation or regain function after misfolding. various co-chaperones specify hsp70 function and broaden its substrate range. we discuss hsp70 structure and function, regulation by co-factors and influence on propagation of yeast prions.	2009	19519514
hsp104 and prion propagation.	high-ordered aggregates (amyloids) may disrupt cell functions, cause toxicity at certain conditions and provide a basis for self-perpetuated, protein-based infectious heritable agents (prions). heat shock proteins acting as molecular chaperones counteract protein aggregation and influence amyloid propagation. the yeast hsp104/hsp70/hsp40 chaperone complex plays a crucial role in interactions with both ordered and unordered aggregates. the main focus of this review will be on the hsp104 chaperone ...	2009	19519517
insights into trna-dependent amidotransferase evolution and catalysis from the structure of the aquifex aeolicus enzyme.	many bacteria form gln-trna(gln) and asn-trna(asn) by conversion of the misacylated glu-trna(gln) and asp-trna(asn) species catalyzed by the gatcab amidotransferase in the presence of atp and an amide donor (glutamine or asparagine). here, we report the crystal structures of gatcab from the hyperthermophilic bacterium aquifex aeolicus, complexed with glutamine, asparagine, aspartate, adp, or atp. in contrast to the staphylococcus aureus gatcab, the a. aeolicus enzyme formed acyl-enzyme intermedi ...	2009	19520089
insights into the role of val45 and gln182 of escherichia coli muty in dna substrate binding and specificity.	escherichia coli muty (ecmuty) reduces mutagenesis by removing adenines paired with guanines or 7,8-dihydro-8-oxo-guanines (8-oxog). v45 and q182 of ecmuty are considered to be the key determinants of adenine specificity. both residues are spatially close to each other in the active site and are conserved in muty family proteins but not in methanobacterium thermoautotrophicum mig.mthi t/g mismatch dna glycosylase (a50 and l187 at the corresponding respective positions).	2009	19523222
a link between hinge-bending domain motions and the temperature dependence of catalysis in 3-isopropylmalate dehydrogenase.	enzyme function depends on specific conformational motions. we show that the temperature dependence of enzyme kinetic parameters can provide insight into these functionally relevant motions. while investigating the catalytic properties of ipmdh from escherichia coli, we found that its catalytic efficiency (k(cat)/k(m,ipm)) for the substrate ipm has an unusual temperature dependence, showing a local minimum at approximately 35 degrees c. in search of an explanation, we measured the individual con ...	2009	19527660
classification and energetics of the base-phosphate interactions in rna.	structured rna molecules form complex 3d architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. a significant percentage of the bases in structured rna molecules in the protein data bank (pdb) hydrogen-bond with phosphates of other nucleotides. by extracting and superimposing base-phosphate (bph) interactions from a reduced-redundancy subset of 3d structures from the pdb, we identified recurrent phosphate-binding sites on the rna bases. qua ...	2009	19528080
towards the immunoproteome of neisseria meningitidis.	despite the introduction of conjugated polysaccharide vaccines for many of the neisseria meningitidis serogroups, neisserial infections continue to cause septicaemia and meningitis across the world. this is in part due to the difficulties in developing a, cross-protective vaccine that is effective against all serogroups, including serogroup b meningococci. although convalescent n. meningitidis patients develop a natural long-lasting cross-protective immunity, the antigens that mediate this respo ...	2009	19529772
site-directed mutagenesis as a probe of the acid-base catalytic mechanism of homoisocitrate dehydrogenase from saccharomyces cerevisiae.	homoisocitrate dehydrogenase (hicdh) catalyzes the mg2+- and k+-dependent oxidative decarboxylation of homoisocitrate to alpha-ketoadipate using nad as the oxidant. a recent consideration of the structures of enzymes in the same family as hicdh, including isopropylmalate and isocitrate dehydrogenases, suggests all of the family members utilize a lys-tyr pair to catalyze the acid-base chemistry of the reaction [aktas, d. f., and cook, p. f. (2009) biochemistry 48, 3565-3577]. multiple-sequence al ...	2009	19530703
identification of candidate structured rnas in the marine organism 'candidatus pelagibacter ubique'.	metagenomic sequence data are proving to be a vast resource for the discovery of biological components. yet analysis of this data to identify functional rnas lags behind efforts to characterize protein diversity. the genome of 'candidatus pelagibacter ubique' htcc 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. it is also small, contains little non-coding dna, and has strikingly low gc content.	2009	19531245
mechanism for the hydrolysis of a sulfur-sulfur bond based on the crystal structure of the thiosulfohydrolase soxb.	soxb is an essential component of the bacterial sox sulfur oxidation pathway. soxb contains a di-manganese(ii) site and is proposed to catalyze the release of sulfate from a protein-bound cysteine s-thiosulfonate. a direct assay for soxb activity is described. the structure of recombinant thermus thermophilus soxb was determined by x-ray crystallography to a resolution of 1.5 a. structures were also determined for soxb in complex with the substrate analogue thiosulfate and in complex with the pr ...	2009	19535341
conformational changes in switch i of ef-g drive its directional cycling on and off the ribosome.	we have trapped elongation factor g (ef-g) from escherichia coli in six, functionally defined states, representing intermediates in its unidirectional catalytic cycle, which couples gtp hydrolysis to trna-mrna translocation in the ribosome. by probing ef-g with trypsin in each state, we identified a substantial conformational change involving its conserved switch i (sw1) element, which contacts the gtp substrate. by attaching febabe (a hydroxyl radical generating probe) to sw1, we could monitor ...	2009	19536129
a newly discovered protein export machine in malaria parasites.	several hundred malaria parasite proteins are exported beyond an encasing vacuole and into the cytosol of the host erythrocyte, a process that is central to the virulence and viability of the causative plasmodium species. the trafficking machinery responsible for this export is unknown. here we identify in plasmodium falciparum a translocon of exported proteins (ptex), which is located in the vacuole membrane. the ptex complex is atp-powered, and comprises heat shock protein 101 (hsp101; a clpa/ ...	2009	19536257
gain-of-function mutations identify amino acids within transmembrane domains of the yeast vacuolar transporter zrc1 that determine metal specificity.	cation diffusion facilitator transporters are found in all three kingdoms of life and are involved in transporting transition metals out of the cytosol. the metals they transport include zn2+, co2+, fe2+, cd2+, ni2+ and mn2+; however, no single transporter transports all metals. previously we showed that a single amino acid mutation in the yeast vacuolar zinc transporter zrc1 changed its substrate specificity from zn2+ to fe2+ and mn2+ [lin, kumanovics, nelson, warner, ward and kaplan (2008) j. ...	2009	19538181
smpb contributes to reading frame selection in the translation of transfer-messenger rna.	transfer-messenger rna (tmrna) acts first as a trna and then as an mrna template to rescue stalled ribosomes in eubacteria. together with its protein partner, smpb (small protein b), tmrna enters stalled ribosomes and transfers an ala residue to the growing polypeptide chain. a remarkable step then occurs: the ribosome leaves the stalled mrna and resumes translation using tmrna as a template, adding a short peptide tag that destines the aborted protein for destruction. exactly how the ribosome s ...	2009	19540849
anaerobic respiration of elemental sulfur and thiosulfate by shewanella oneidensis mr-1 requires psra, a homolog of the phsa gene of salmonella enterica serovar typhimurium lt2.	shewanella oneidensis mr-1, a facultatively anaerobic gammaproteobacterium, respires a variety of anaerobic terminal electron acceptors, including the inorganic sulfur compounds sulfite (so3(2-)), thiosulfate (s2o3(2-)), tetrathionate (s4o6(2-)), and elemental sulfur (s(0)). the molecular mechanism of anaerobic respiration of inorganic sulfur compounds by s. oneidensis, however, is poorly understood. in the present study, we identified a three-gene cluster in the s. oneidensis genome whose trans ...	2009	19542325
avoiding dangerous missense: thermophiles display especially low mutation rates.	rates of spontaneous mutation have been estimated under optimal growth conditions for a variety of dna-based microbes, including viruses, bacteria, and eukaryotes. when expressed as genomic mutation rates, most of the values were in the vicinity of 0.003-0.004 with a range of less than two-fold. because the genome sizes varied by roughly 10(4)-fold, the mutation rates per average base pair varied inversely by a similar factor. even though the commonality of the observed genomic rates remains une ...	2009	19543367
the 2.1 a crystal structure of an acyl-coa synthetase from methanosarcina acetivorans reveals an alternate acyl-binding pocket for small branched acyl substrates.	the acyl-amp forming family of adenylating enzymes catalyze two-step reactions to activate a carboxylate with the chemical energy derived from atp hydrolysis. x-ray crystal structures have been determined for multiple members of this family and, together with biochemical studies, provide insights into the active site and catalytic mechanisms used by these enzymes. these studies have shown that the enzymes use a domain rotation of 140 degrees to reconfigure a single active site to catalyze the tw ...	2009	19544569
amino acid changes in elongation factor tu of mycoplasma pneumoniae and mycoplasma genitalium influence fibronectin binding.	mycoplasma pneumoniae and mycoplasma genitalium are closely related organisms that cause distinct clinical manifestations and possess different tissue predilections despite their high degree of genome homology. we reported earlier that surface-localized m. pneumoniae elongation factor tu (ef-tu(mp)) mediates binding to the extracellular matrix component fibronectin (fn) through the carboxyl region of ef-tu. in this study, we demonstrate that surface-associated m. genitalium ef-tu (ef-tu(mg)), in ...	2009	19546194
comparative analysis of activator-esigma54 complexes formed with nucleotide-metal fluoride analogues.	bacterial rna polymerase (rnap) containing the major variant sigma(54) factor forms open promoter complexes in a reaction in which specialized activator proteins hydrolyse atp. here we probe binding interactions between sigma(54)-rnap (esigma(54)) and the atpases associated with various cellular activities (aaa+) domain of the escherichia coli activator protein, pspf, using nucleotide-metal fluoride (bef and alf) analogues representing ground and transition states of atp, which allow complexes ( ...	2009	19553192
fluorescently labeled ribosomes as a tool for analyzing antibiotic binding.	measuring the binding of antibiotics and other small-molecular-weight ligands to the 2.5 mda ribosome often presents formidable challenges. here, we describe a general method for studying binding of ligands to ribosomes that carry a site-specific fluorescent label covalently attached to one of the ribosomal proteins. as a proof of principle, an environment-sensitive fluorescent group was placed at several specific sites within the ribosomal protein s12. small ribosomal subunits were reconstitute ...	2009	19553343
the obge/cgta gtpase influences the stringent response to amino acid starvation in escherichia coli.	the stringent response is important for bacterial survival under stressful conditions, such as amino acid starvation, and is characterized by the accumulation of ppgpp and pppgpp. obge (cgta, yhbz) is an essential conserved gtpase in escherichia coli and several observations have implicated the protein in the control of the stringent response. however, consequences of the protein on specific responses to amino acid starvation have not been noted. we show that obge binds to ppgpp with biologicall ...	2009	19555460
genome analysis and genome-wide proteomics of thermococcus gammatolerans, the most radioresistant organism known amongst the archaea.	thermococcus gammatolerans was isolated from samples collected from hydrothermal chimneys. it is one of the most radioresistant organisms known amongst the archaea. we report the determination and annotation of its complete genome sequence, its comparison with other thermococcales genomes, and a proteomic analysis.	2009	19558674
millisecond dynamics in the allosteric enzyme imidazole glycerol phosphate synthase (igps) from thermotoga maritima.	igps is a 51 kda heterodimeric enzyme comprised of two proteins, hish and hisf, that catalyze the hydrolysis of glutamine to produce nh(3) in the hish active site and the cyclization of ammonia with n'-[(5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide (prfar) in hisf to produce imidazole glycerol phosphate (igp) and 5-aminoimidazole-4-carboxamide ribotide (aicar). binding of prfar and igp stimulates glutaminase activity in the hish enzyme over 5,000 and 100-fold, res ...	2009	19565337
properties of arg481 mutants of the aa3-type cytochrome c oxidase from rhodobacter sphaeroides suggest that neither r481 nor the nearby d-propionate of heme a3 is likely to be the proton loading site of the proton pump.	cytochrome c oxidase utilizes the energy from electron transfer and reduction of oxygen to water and pumps protons across the membrane, generating a proton motive force. a large body of biochemical work has shown that all the pumped protons enter the enzyme through the d-channel, which is apparent in x-ray structures as a chain of water molecules connecting d132 at the cytoplasmic surface of the enzyme to e286, near the enzyme active site. the exit pathway utilized by pumped protons beyond this ...	2009	19575527
conservation of structure and activity in plasmodium purine nucleoside phosphorylases.	purine nucleoside phosphorylase (pnp) is central to purine salvage mechanisms in plasmodium parasites, the causative agents of malaria. most human malaria results from infection either by plasmodium falciparum (pf), the deadliest form of the parasite, or by the widespread plasmodium vivax (pv). whereas the pnp enzyme from pf has previously been studied in detail, despite the prevalence of pv little is known about many of the key metabolic enzymes from this parasite, including pvpnp.	2009	19575810
domain features of the peripheral stalk subunit h of the methanogenic a1ao atp synthase and the nmr solution structure of h(1-47).	a series of truncated forms of subunit h were generated to establish the domain features of that protein. circular dichroism analysis demonstrated that h is divided at least into a c-terminal coiled-coil domain within residues 54-104, and an n-terminal domain formed by adjacent alpha-helices. with a cysteine at the c-terminus of each of the truncated proteins (h(1-47), h(1-54), h(1-59), h(1-61), h(1-67), h(1-69), h(1-71), h(1-78), h(1-80), h(1-91), and h(47-105)), the residues involved in format ...	2009	19580766
inactivation and unfolding of the hyperthermophilic inorganic pyrophosphatase from thermus thermophilus by sodium dodecyl sulfate.	inorganic pyrophosphatase (ppase, ec 3.6.1.1) is an essential constitutive enzyme for energy metabolism and clearance of excess pyrophosphate. in this research, we investigated the sodium dodecyl sulfate (sds)-induced inactivation and unfolding of ppase from thermus thermophilus (t-ppase), a hyperthermophilic enzyme. the results indicated that like many other mesophilic enzymes, t-ppase could be fully inactivated at a low sds concentration of 2 mm. using an enzyme activity assay, sds was shown t ...	2009	19582233
the closest relatives of icosahedral viruses of thermophilic bacteria are among viruses and plasmids of the halophilic archaea.	we have sequenced the genome and identified the structural proteins and lipids of the novel membrane-containing, icosahedral virus p23-77 of thermus thermophilus. p23-77 has an approximately 17-kb circular double-stranded dna genome, which was annotated to contain 37 putative genes. virions were subjected to dissociation analysis, and five protein species were shown to associate with the internal viral membrane, while three were constituents of the protein capsid. analysis of the bacteriophage g ...	2009	19587059
a structural view on the mechanism of the ribosome-catalyzed peptide bond formation.	the ribosome is a large ribonucleoprotein particle that translates genetic information encoded in mrna into specific proteins. its highly conserved active site, the peptidyl-transferase center (ptc), is located on the large (50s) ribosomal subunit and is comprised solely of rrna, which makes the ribosome the only natural ribozyme with polymerase activity. the last decade witnessed a rapid accumulation of atomic-resolution structural data on both ribosomal subunits as well as on the entire riboso ...	2009	19595805
card is an essential regulator of rrna transcription required for mycobacterium tuberculosis persistence.	mycobacterium tuberculosis is arguably the world's most successful infectious agent because of its ability to control its own cell growth within the host. bacterial growth rate is closely coupled to rrna transcription, which in e. coli is regulated through dksa and (p)ppgpp. the mechanisms of rrna transcriptional control in mycobacteria, which lack dksa, are undefined. here we identify card as an essential mycobacterial protein that controls rrna transcription. loss of card is lethal for mycobac ...	2009	19596241
probing the relationship between gram-negative and gram-positive s1 proteins by sequence analysis.	escherichia coli ribosomal protein s1 is required for the translation initiation of messenger rnas, in particular when their shine-dalgarno sequence is degenerated. closely related forms of the protein, composed of the same number of domains (six), are found in all gram-negative bacteria. more distant proteins, generally formed of fewer domains, have been identified, by sequence similarities, in gram-positive bacteria and are also termed 's1 proteins'. however in the absence of functional inform ...	2009	19605565
functional role for the conformationally mobile phenylalanine 223 in the reaction of methylenetetrahydrofolate reductase from escherichia coli.	the flavoprotein methylenetetrahydrofolate reductase from escherichia coli catalyzes the reduction of 5,10-methylenetetrahydrofolate (ch(2)-h(4)folate) by nadh via a ping-pong reaction mechanism. structures of the reduced enzyme in complex with nadh and of the oxidized glu28gln enzyme in complex with ch(3)-h(4)folate [pejchal, r., sargeant, r., and ludwig, m. l. (2005) biochemistry 44, 11447-11457] have revealed phe223 as a conformationally mobile active site residue. in the nadh complex, the na ...	2009	19610625
purification and biochemical characterization of a specific beta-glucosidase from the digestive fluid of larvae of the palm weevil, rhynchophorus palmarum.	a beta-glucosidase was purified from the digestive fluid of the palm weevil rhynchophorus palmarum l. (coleoptera: curculionidae) by chromatography on anion-exchange, gel filtration, and hydrophobic interaction columns. the preparation was shown to be homogeneous on polyacrylamide gels, beta-glucosidase is a monomeric protein with a molecular weight of 58 kda based on its mobility in sds-page and 60 kda based on gel filtration. maximal beta-glucosidase activity occurred at 55 degrees c and ph 5. ...	2009	19611239
global stabilization of rrna structure by ribosomal proteins s4, s17, and s20.	ribosomal proteins stabilize the folded structure of the ribosomal rna and enable the recruitment of further proteins to the complex. quantitative hydroxyl radical footprinting was used to measure the extent to which three different primary assembly proteins, s4, s17, and s20, stabilize the three-dimensional structure of the escherichia coli 16s 5' domain. the stability of the complexes was perturbed by varying the concentration of mgcl(2). each protein influences the stability of the ribosomal ...	2009	19616559
an examination of the relationship between active site loop size and thermodynamic activation parameters for orotidine 5'-monophosphate decarboxylase from mesophilic and thermophilic organisms.	closure of the active site phosphate gripper loop of orotidine 5'-monophosphate decarboxylase from saccharomyces cerevisiae (scompdc) over the bound substrate orotidine 5'-monophosphate (omp) activates the bound substrate for decarboxylation by at least 10(4)-fold [amyes, t. l., richard, j. p., and tait, j. j. (2005) j. am. chem. soc. 127, 15708-15709]. the 19-residue phosphate gripper loop of the mesophilic scompdc is much larger than the nine-residue loop at the ortholog from the thermophile m ...	2009	19618917
structural and functional studies of the thermus thermophilus 16s rrna methyltransferase rsmg.	the rsmg methyltransferase is responsible for n(7) methylation of g527 of 16s rrna in bacteria. here, we report the identification of the thermus thermophilus rsmg gene, the isolation of rsmg mutants, and the solution of rsmg x-ray crystal structures at up to 1.5 a resolution. like their counterparts in other species, t. thermophilus rsmg mutants are weakly resistant to the aminoglycoside antibiotic streptomycin. growth competition experiments indicate a physiological cost to loss of rsmg activi ...	2009	19622680
binding and cleavage specificities of human argonaute2.	the endonuclease argonaute2 (ago2) mediates the degradation of the target mrna within the rna-induced silencing complex. we determined the binding and cleavage properties of recombinant human ago2. human ago2 was unable to cleave preformed rna duplexes and exhibited weaker binding affinity for rna duplexes compared with the single strand rna. the enzyme exhibited greater rnase h activity in the presence of mn2+ compared with mg2+. human ago2 exhibited weaker binding affinities and reduced cleava ...	2009	19625255
structural characterization of a viral neil1 ortholog unliganded and bound to abasic site-containing dna.	endonuclease viii (nei) is a dna glycosylase of the base excision repair pathway that recognizes and excises oxidized pyrimidines. we determined the crystal structures of a neil1 ortholog from the giant mimivirus (mvnei1) unliganded and bound to dna containing tetrahydrofuran (thf), which is the first structure of any nei with an abasic site analog. the mvnei1 structures exhibit the same overall architecture as other enzymes of the fpg/nei family, which consists of two globular domains joined by ...	2009	19625256
structural basis for the mechanism of respiratory complex i.	complex i plays a central role in cellular energy production, coupling electron transfer between nadh and quinone to proton translocation. the mechanism of this highly efficient enzyme is currently unknown. mitochondrial complex i is a major source of reactive oxygen species, which may be one of the causes of aging. dysfunction of complex i is implicated in many human neurodegenerative diseases. we have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex ...	2009	19635800
acyl-coa dehydrogenases: dynamic history of protein family evolution.	the acyl-coa dehydrogenases (acads) are enzymes that catalyze the alpha,beta-dehydrogenation of acyl-coa esters in fatty acid and amino acid catabolism. eleven acads are now recognized in the sequenced human genome, and several homologs have been reported from bacteria, fungi, plants, and nematodes. we performed a systematic comparative genomic study, integrating homology searches with methods of phylogenetic reconstruction, to investigate the evolutionary history of this family. sequence analys ...	2009	19639238
selection of peptides that target the aminoacyl-trna site of bacterial 16s ribosomal rna.	for almost five decades, antibiotics have been used successfully to control infectious diseases caused by bacterial pathogens. more recently, however, two-thirds of bacterial pathogens exhibit resistance and are continually evolving new resistance mechanisms against almost every clinically used antibiotic. novel efforts are required for the development of new drugs or drug leads to combat these infectious diseases. a number of antibiotics target the bacterial aminoacyl-trna site (a site) of 16s ...	2009	19645415
evolved beta-galactosidases from geobacillus stearothermophilus with improved transgalactosylation yield for galacto-oligosaccharide production.	a mutagenesis approach was applied to the beta-galactosidase bgab from geobacillus stearothermophilus kve39 in order to improve its enzymatic transglycosylation of lactose into oligosaccharides. a simple screening strategy, which was based on the reduction of the hydrolysis of a potential transglycosylation product (lactosucrose), provided mutant enzymes possessing improved synthetic properties for the autocondensation product from nitrophenyl-galactoside and galacto-oligosaccharides (gos) from ...	2009	19666723
subcomplex ilambda specifically controls integrated mitochondrial functions in caenorhabditis elegans.	complex i dysfunction is a common, heterogeneous cause of human mitochondrial disease having poorly understood pathogenesis. the extensive conservation of complex i composition between humans and caenorhabditis elegans permits analysis of individual subunit contribution to mitochondrial functions at both the whole animal and mitochondrial levels. we provide the first experimentally-verified compilation of complex i composition in c. elegans, demonstrating 84% conservation with human complex i. i ...	2009	19672299
the uracil dna glycosylase udgb of mycobacterium smegmatis protects the organism from the mutagenic effects of cytosine and adenine deamination.	spontaneous hydrolytic deamination of dna bases represents a considerable mutagenic threat to all organisms, particularly those living in extreme habitats. cytosine is readily deaminated to uracil, which base pairs with adenine during replication, and most organisms encode at least one uracil dna glycosylase (udg) that removes this aberrant base from dna with high efficiency. adenine deaminates to hypoxanthine approximately 10-fold less efficiently, and its removal from dna in vivo has to date b ...	2009	19684133
crystal structure of human selenocysteine trna.	selenocysteine (sec) is the 21st amino acid in translation. sec trna (trna(sec)) has an anticodon complementary to the uga codon. we solved the crystal structure of human trna(sec). trna(sec) has a 9-bp acceptor stem and a 4-bp t stem, in contrast with the 7-bp acceptor stem and the 5-bp t stem in the canonical trnas. the acceptor stem is kinked between the u6:u67 and g7:c66 base pairs, leading to a bent acceptor-t stem helix. trna(sec) has a 6-bp d stem and a 4-nt d loop. the long d stem includ ...	2009	19692584
small molecule dnak modulators targeting the beta-domain.	the molecular chaperone dnak is essential for the survival of bacterial pathogens in the hostile environment of the host. hence, it is in principle a promising target for drug design but for which no current inhibitors are available apart from certain antimicrobial peptides. to this end, we have screened libraries of small molecules for their ability to interact with the substrate-binding domain of dnak. the most promising hit from the screen was synthesized and along with its analogs subjected ...	2009	19694756
immunoproteomic analysis of outer membrane proteins and extracellular proteins of actinobacillus pleuropneumoniae jl03 serotype 3.	actinobacillus pleuropneumoniae is the causative agent of porcine contagious pleuropneumonia, a highly contagious respiratory infection in pigs, and all the 15 serotypes are able to cause disease. current vaccines including subunit vaccines could not provide satisfactory protection against a. pleuropneumoniae. in this study, the immunoproteomic approach was applied to the analysis of extracellular and outer membrane proteins of a. pleuropneumoniae jl03 serotype 3 for the identification of novel ...	2009	19695095
formation of the first peptide bond: the structure of ef-p bound to the 70s ribosome.	elongation factor p (ef-p) is an essential protein that stimulates the formation of the first peptide bond in protein synthesis. here we report the crystal structure of ef-p bound to the thermus thermophilus 70s ribosome along with the initiator transfer rna n-formyl-methionyl-trna(i) (fmet-trna(i)(fmet)) and a short piece of messenger rna (mrna) at a resolution of 3.5 angstroms. ef-p binds to a site located between the binding site for the peptidyl trna (p site) and the exiting trna (e site). i ...	2009	19696344
genetic incorporation of a small, environmentally sensitive, fluorescent probe into proteins in saccharomyces cerevisiae.	here, we report that the fluorescent amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (anap), can be genetically incorporated into proteins in yeast with excellent selectivity and efficiency by means of an orthogonal trna/aminoacyl-trna synthetase pair. this small, environmentally sensitive fluorophore was site-specifically incorporated into escherichia coli glutamine binding protein and used to directly probe local structural changes caused by ligand binding. the small size of ...	2009	19702307
a paradigm shift for the amino acid editing mechanism of human cytoplasmic leucyl-trna synthetase.	leucyl-trna synthetase (leurs) has been identified as a target for a novel class of boron-containing small molecules that bind to its editing active site. when the 3' end of trna(leu) binds to the editing active site, the boron cross-links to the cis-diols of its terminal ribose. the cross-linked rna-protein complex blocks the overall aminoacylation activity of the enzyme. similar to those of other leurss, the human cytoplasmic enzyme (hscleurs) editing active site resides in a discrete domain c ...	2009	19702327
phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis.	mitochondria, the powerhouse of eukaryotic cells, have their own translation machinery that is solely responsible for synthesis of 13 mitochondrially encoded protein subunits of oxidative phosphorylation complexes. phosphorylation is a well-known post-translational modification in regulation of many processes in mammalian mitochondria including oxidative phosphorylation. however, there is still very limited knowledge on phosphorylation of mitochondrial ribosomal proteins and their role(s) in rib ...	2009	19702336
a rubisco mutant that confers growth under a normally "inhibitory" oxygen concentration.	ribulose-1,5-bisphosphate (rubp) carboxylase/oxygenase (rubisco) is a globally significant biocatalyst that facilitates the removal and sequestration of co2 from the biosphere. rubisco-catalyzed co2 reduction thus provides virtually all of the organic carbon utilized by living organisms. despite catalyzing the rate-limiting step of photosynthetic and chemoautotrophic co2 assimilation, rubisco is markedly inefficient as the competition between o2 and co2 for the same substrate limits the ability ...	2009	19705820
prokaryotic homologs of argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements.	in eukaryotes, rna interference (rnai) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mrnas. the rnai systems recognize the target rna molecules via small guide rnas that are completely or partially complementary to a region of the target. key components of the rnai systems are proteins of the argonaute-piwi family some of which function as slicers, the nucleases that cleave the target rna that is base-paired to a guide r ...	2009	19706170
mechanism of adp-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-adp-ribosylhydrolase drag.	adp-ribosylation is a ubiquitous regulatory posttranslational modification involved in numerous key processes such as dna repair, transcription, cell differentiation, apoptosis, and the pathogenic mechanism of certain bacterial toxins. despite the importance of this reversible process, very little is known about the structure and mechanism of the hydrolases that catalyze removal of the adp-ribose moiety. in the phototrophic bacterium rhodospirillum rubrum, dinitrogenase reductase-activating glyc ...	2009	19706507
nob1 binds the single-stranded cleavage site d at the 3'-end of 18s rrna with its pin domain.	ribosome assembly is a hierarchical process that involves pre-rrna folding, modification, and cleavage and assembly of ribosomal proteins. in eukaryotes, this process requires a macromolecular complex comprising over 200 proteins and rnas. whereas the rrna modification machinery is well-characterized, rrna cleavage to release mature rrnas is poorly understood, and in yeast, only 2 of 8 endonucleases have been identified. the essential and conserved ribosome assembly factor nob1 has been suggeste ...	2009	19706509
crystal structures and biochemical analyses suggest a unique mechanism and role for human glycyl-trna synthetase in ap4a homeostasis.	aminoacyl-trna synthetases catalyze the attachment of amino acids to their cognate trnas for protein synthesis. however, the aminoacylation reaction can be diverted to produce diadenosine tetraphosphate (ap4a), a universal pleiotropic signaling molecule needed for cell regulation pathways. the only known mechanism for ap4a production by a trna synthetase is through the aminoacylation reaction intermediate aminoacyl-amp, thus making ap4a synthesis amino acid-dependent. here, we demonstrate a new ...	2009	19710017
structure of escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.	three new structures of escherichia coli succinate-quinone oxidoreductase (sqr) have been solved. one with the specific quinone-binding site (q-site) inhibitor carboxin present has been solved at 2.4 a resolution and reveals how carboxin inhibits the q-site. the other new structures are with the q-site inhibitor pentachlorophenol and with an empty q-site. these structures reveal important details unresolved in earlier structures. comparison of the new sqr structures shows how subtle rearrangemen ...	2009	19710024
the thermus thermophilus dead box helicase hera contains a modified rna recognition motif domain loosely connected to the helicase core.	dead box family helicases consist of a helicase core that is formed by two flexibly linked reca-like domains. the helicase activity can be regulated by n- or c-terminal extensions flanking the core. thermus thermophilus heat resistant rna-dependent atpase (hera) is the first dead box helicase that forms a dimer using a unique dimerization domain. in addition to the dimerization domain, hera contains a c-terminal rna binding domain (rbd) that shares sequence homology only to uncharacterized prote ...	2009	19710183
the yeast iron regulatory proteins grx3/4 and fra2 form heterodimeric complexes containing a [2fe-2s] cluster with cysteinyl and histidyl ligation.	the transcription of iron uptake and storage genes in saccharomyces cerevisiae is primarily regulated by the transcription factor aft1. nucleocytoplasmic shuttling of aft1 is dependent upon mitochondrial fe-s cluster biosynthesis via a signaling pathway that includes the cytosolic monothiol glutaredoxins (grx3 and grx4) and the bola homologue fra2. however, the interactions between these proteins and the iron-dependent mechanism by which they control aft1 localization are unclear. to reconstitut ...	2009	19715344
identification of x-ding-cd4, a new member of human ding protein family that is secreted by hiv-1 resistant cd4(+) t cells and has anti-viral activity.	we reported previously the anti-viral activity named hrf (hiv-1 resistance factor) secreted by hiv-1 resistant cells. this work describes the identification of hrf from cell culture supernatant of hrf-producing cells (hrf(+) cells). employing the proteomics and cell based activity assay we recovered ten peptides sharing 80-93% sequence homology with other eukaryotic ding proteins; discrete amino acid characteristics found in our material suggested that hrf is a new member of ding proteins family ...	2009	19720052
interaction of the thermoplasma acidophilum a1a0-atp synthase peripheral stalk with the catalytic domain.	the peripheral stalk of the archaeal atp synthase (a1a0)-atp synthase is formed by the heterodimeric eh complex and is part of the stator domain, which counteracts the torque of rotational catalysis. here we used nuclear magnetic resonance spectroscopy to probe the interaction of the c-terminal domain of the eh heterodimer (e(ct1)h(ct)) with the n-terminal 23 residues of the b subunit (b(nt)). the data show a specific interaction of b(nt) peptide with 26 residues of the e(ct1)h(ct) domain, there ...	2009	19720061
characterization of two seryl-trna synthetases in albomycin-producing streptomyces sp. strain atcc 700974.	the trojan horse antibiotic albomycin, produced by streptomyces sp. strain atcc 700974, contains a thioribosyl nucleoside moiety linked to a hydroxamate siderophore through a serine residue. the seryl nucleoside structure (sb-217452) is a potent inhibitor of seryl-trna synthetase (serrs) in the pathogenic bacterium staphylococcus aureus, with a 50% inhibitory concentration (ic(50)) of approximately 8 nm. in the albomycin-producing streptomyces sp., a bacterial serrs homolog (alb10) was found to ...	2009	19721072
a non-canonical dna structure enables homologous recombination in various genetic systems.	homologous recombination, which is critical to genetic diversity, depends on homologous pairing (hp). hp is the switch from parental to recombinant base pairs, which requires expansion of inter-base pair spaces. this expansion unavoidably causes untwisting of the parental double-stranded dna. reca/rad51-catalyzed atp-dependent hp is extensively stimulated in vitro by negative supercoils, which compensates for untwisting. however, in vivo, double-stranded dna is relaxed by bound proteins and thus ...	2009	19729448
frameshifting rna pseudoknots: structure and mechanism.	programmed ribosomal frameshifting (prf) is one of the multiple translational recoding processes that fundamentally alters triplet decoding of the messenger rna by the elongating ribosome. the ability of the ribosome to change translational reading frames in the -1 direction (-1 prf) is employed by many positive strand rna viruses, including economically important plant viruses and many human pathogens, such as retroviruses, e.g., hiv-1, and coronaviruses, e.g., the causative agent of severe acu ...	2009	18621088
frameshifting rna pseudoknots: structure and mechanism.	programmed ribosomal frameshifting (prf) is one of the multiple translational recoding processes that fundamentally alters triplet decoding of the messenger rna by the elongating ribosome. the ability of the ribosome to change translational reading frames in the -1 direction (-1 prf) is employed by many positive strand rna viruses, including economically important plant viruses and many human pathogens, such as retroviruses, e.g., hiv-1, and coronaviruses, e.g., the causative agent of severe acu ...	2009	18621088