Publications

differential effects of mitochondrial complex i inhibitors on production of reactive oxygen species.	we have investigated the production of reactive oxygen species (ros) by complex i in isolated open bovine heart submitochondrial membrane fragments during forward electron transfer in presence of nadh, by means of the probe 2',7'-dichlorodihydrofluorescein diacetate. ros production by complex i is strictly related to its inhibited state. our results indicate that different complex i inhibitors can be grouped into two classes: class a inhibitors (rotenone, piericidin a and rolliniastatin 1 and 2) ...	2009	19059197
differential effects of mitochondrial complex i inhibitors on production of reactive oxygen species.	we have investigated the production of reactive oxygen species (ros) by complex i in isolated open bovine heart submitochondrial membrane fragments during forward electron transfer in presence of nadh, by means of the probe 2',7'-dichlorodihydrofluorescein diacetate. ros production by complex i is strictly related to its inhibited state. our results indicate that different complex i inhibitors can be grouped into two classes: class a inhibitors (rotenone, piericidin a and rolliniastatin 1 and 2) ...	2009	19059197
superoxide dismutase from the eukaryotic thermophile alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.	prokaryotic thermophiles supply stable human protein homologs for structural biology; yet, eukaryotic thermophiles would provide more similar macromolecules plus those missing in microbes. alvinella pompejana is a deep-sea hydrothermal-vent worm that has been found in temperatures averaging as high as 68 degrees c, with spikes up to 84 degrees c. here, we used cu,zn superoxide dismutase (sod) to test if this eukaryotic thermophile can provide insights into macromolecular mechanisms and stability ...	2009	19063897
superoxide dismutase from the eukaryotic thermophile alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.	prokaryotic thermophiles supply stable human protein homologs for structural biology; yet, eukaryotic thermophiles would provide more similar macromolecules plus those missing in microbes. alvinella pompejana is a deep-sea hydrothermal-vent worm that has been found in temperatures averaging as high as 68 degrees c, with spikes up to 84 degrees c. here, we used cu,zn superoxide dismutase (sod) to test if this eukaryotic thermophile can provide insights into macromolecular mechanisms and stability ...	2009	19063897
identification of a new endogenous metabolite and the characterization of its protein interactions through an immobilization approach.	the emerging field of global mass-based metabolomics provides a platform for discovering unknown metabolites and their specific biochemical pathways. we report the identification of a new endogenous metabolite, n(4)-(n-acetylaminopropyl)spermidine and the use of a novel proteomics based method for the investigation of its protein interaction using metabolite immobilization on agarose beads. the metabolite was isolated from the organism pyrococcus furiosus, and structurally characterized through ...	2009	19055353
structure and non-essential function of glycerol kinase in plasmodium falciparum blood stages.	malaria pathology is caused by multiplication of asexual parasites within erythrocytes, whereas mosquito transmission of malaria is mediated by sexual precursor cells (gametocytes). microarray analysis identified glycerol kinase (gk) as the second most highly upregulated gene in plasmodium falciparum gametocytes with no expression detectable in asexual blood stage parasites. phosphorylation of glycerol by gk is the rate-limiting step in glycerol utilization. deletion of this gene from p. falcipa ...	2009	19040641
structure of sure protein from aquifex aeolicus vf5 at 1.5 a resolution.	sure is a stationary-phase survival protein found in bacteria, eukaryotes and archaea that exhibits a divalent-metal-ion-dependent phosphatase activity and acts as a nucleotidase and polyphosphate phosphohydrolase. the structure of the sure protein from the hyperthermophile aquifex aeolicus has been solved at 1.5 a resolution using molecular replacement with one dimer in the asymmetric unit and refined to an r factor of 15.6%. the crystal packing reveals that two dimers assemble to form a tetram ...	2009	20054112
structure of putative 4-amino-4-deoxychorismate lyase from thermus thermophilus hb8.	the pyridoxal 5'-phosphate-dependent enzyme 4-amino-4-deoxychorismate lyase converts 4-amino-4-deoxychorismate to p-aminobenzoate and pyruvate in one of the crucial steps in the folate-biosynthesis pathway. the primary structure of the hypothetical protein ttha0621 from thermus thermophilus hb8 suggests that ttha0621 is a putative 4-amino-4-deoxychorismate lyase. here, the crystal structure of ttha0621 is reported at 1.93 a resolution. the asymmetric unit contained four ncs molecules related by ...	2009	20054118
the mycobacterium tuberculosis mep (2c-methyl-d-erythritol 4-phosphate) pathway as a new drug target.	tuberculosis (tb) is still a major public health problem, compounded by the human immunodeficiency virus (hiv)-tb co-infection and recent emergence of multidrug-resistant (mdr) and extensively drug resistant (xdr)-tb. novel anti-tb drugs are urgently required. in this context, the 2c-methyl-d-erythritol 4-phosphate (mep) pathway of mycobacterium tuberculosis has drawn attention; it is one of several pathways vital for m. tuberculosis viability and the human host lacks homologous enzymes. thus, t ...	2009	18793870
the mycobacterium tuberculosis mep (2c-methyl-d-erythritol 4-phosphate) pathway as a new drug target.	tuberculosis (tb) is still a major public health problem, compounded by the human immunodeficiency virus (hiv)-tb co-infection and recent emergence of multidrug-resistant (mdr) and extensively drug resistant (xdr)-tb. novel anti-tb drugs are urgently required. in this context, the 2c-methyl-d-erythritol 4-phosphate (mep) pathway of mycobacterium tuberculosis has drawn attention; it is one of several pathways vital for m. tuberculosis viability and the human host lacks homologous enzymes. thus, t ...	2009	18793870
transcription inactivation through local refolding of the rna polymerase structure.	structural studies of antibiotics not only provide a shortcut to medicine allowing for rational structure-based drug design, but may also capture snapshots of dynamic intermediates that become 'frozen' after inhibitor binding. myxopyronin inhibits bacterial rna polymerase (rnap) by an unknown mechanism. here we report the structure of dmyx--a desmethyl derivative of myxopyronin b--complexed with a thermus thermophilus rnap holoenzyme. the antibiotic binds to a pocket deep inside the rnap clamp h ...	2009	18946472
unfolding thermodynamics of the delta-domain in the prohead i subunit of phage hk97: determination by factor analysis of raman spectra.	an early step in the morphogenesis of the double-stranded dna (dsdna) bacteriophage hk97 is the assembly of a precursor shell (prohead i) from 420 copies of a 384-residue subunit (gp5). although formation of prohead i requires direct participation of gp5 residues 2-103 (delta-domain), this domain is eliminated by viral protease prior to subsequent shell maturation and dna packaging. the prohead i delta-domain is thought to resemble a phage scaffolding protein, by virtue of its highly alpha-helic ...	2009	18983851
unfolding thermodynamics of the delta-domain in the prohead i subunit of phage hk97: determination by factor analysis of raman spectra.	an early step in the morphogenesis of the double-stranded dna (dsdna) bacteriophage hk97 is the assembly of a precursor shell (prohead i) from 420 copies of a 384-residue subunit (gp5). although formation of prohead i requires direct participation of gp5 residues 2-103 (delta-domain), this domain is eliminated by viral protease prior to subsequent shell maturation and dna packaging. the prohead i delta-domain is thought to resemble a phage scaffolding protein, by virtue of its highly alpha-helic ...	2009	18983851
escherichia coli tmrna lacking pseudoknot 1 tags truncated proteins in vivo and in vitro.	transfer-messenger rna (tmrna) and protein smpb facilitate trans-translation, a quality-control process that tags truncated proteins with short peptides recognized by a number of proteases and recycles ribosomes stalled at the 3' end of mrna templates lacking stop codons. the tmrna molecule is a hybrid of trna- and mrna-like domains that are usually connected by four pseudoknots (pk1-pk4). replacement of pk1 with a single-stranded rna yields pk1l, a mutant tmrna that tags truncated proteins very ...	2009	19001120
contributions of the two accessory subunits, rnaseh2b and rnaseh2c, to the activity and properties of the human rnase h2 complex.	eukaryotic rnase h2 is a heterotrimeric enzyme. here, we show that the biochemical composition and stoichiometry of the human rnase h2 complex is consistent with the properties previously deduced from genetic studies. the catalytic subunit of eukaryotic rnase h2, rnaseh2a, is well conserved and similar to the monomeric prokaryotic rnase hii. in contrast, the rnaseh2b and rnaseh2c subunits from human and saccharomyces cerevisiae share very little homology, although they both form soluble b/c comp ...	2009	19015152
contributions of the two accessory subunits, rnaseh2b and rnaseh2c, to the activity and properties of the human rnase h2 complex.	eukaryotic rnase h2 is a heterotrimeric enzyme. here, we show that the biochemical composition and stoichiometry of the human rnase h2 complex is consistent with the properties previously deduced from genetic studies. the catalytic subunit of eukaryotic rnase h2, rnaseh2a, is well conserved and similar to the monomeric prokaryotic rnase hii. in contrast, the rnaseh2b and rnaseh2c subunits from human and saccharomyces cerevisiae share very little homology, although they both form soluble b/c comp ...	2009	19015152
structural and biochemical studies of tigar (tp53-induced glycolysis and apoptosis regulator).	activation of the p53 tumor suppressor by cellular stress leads to variable responses ranging from growth inhibition to apoptosis. tigar is a novel p53-inducible gene that inhibits glycolysis by reducing cellular levels of fructose-2,6-bisphosphate, an activator of glycolysis and inhibitor of gluconeogenesis. here we describe structural and biochemical studies of tigar from danio rerio. the overall structure forms a histidine phosphatase fold with a phosphate molecule coordinated to the catalyti ...	2009	19015259
biosynthesis of undecaprenyl phosphate-galactosamine and undecaprenyl phosphate-glucose in francisella novicida.	lipid a of francisella tularensis subsp. novicida contains a galactosamine (galn) residue linked to its 1-phosphate group. as shown in the preceding paper, this galn unit is transferred to lipid a from the precursor undecaprenyl phosphate-beta-d-galn. a small portion of the free lipid a of francisella novicida is further modified with a glucose residue at position-6'. we now demonstrate that the two f. novicida homologues of escherichia coli arnc, designated flmf1 and flmf2, are essential for li ...	2009	19166326
characterization of oxidized guanosine 5'-triphosphate as a viable inhibitor of soluble guanylyl cyclase.	the guanine base is prone to oxidation by free radicals regardless of the cellular moiety it is bound to. however, under conditions of oxidative stress, 8-oxoguanosine triphosphate (oxo(8)gtp) formation has been shown to occur without oxidation of the guanine base in dna. in vitro studies have suggested that oxo(8)gtp could impact g-protein signaling and rna synthesis. whether increased levels of oxo(8)gtp translate into cellular malfunction is unknown. data presented herein show that oxo(8)gtp ...	2009	19167482
allosteric control of escherichia coli rrna promoter complexes by dksa.	the escherichia coli dksa protein inserts into the rna polymerase (rnap) secondary channel, modifying the transcription initiation complex so that promoters with specific kinetic characteristics are regulated by changes in the concentrations of ppgpp and ntps. we used footprinting assays to determine the specific kinetic intermediate, rp(i), on which dksa acts. genetic approaches identified substitutions in the rnap switch regions, bridge helix, and trigger loop that mimicked, reduced, or enhanc ...	2009	19171784
ribosomal translocation: one step closer to the molecular mechanism.	protein synthesis occurs in ribosomes, the targets of numerous antibiotics. how these large and complex machines read and move along mrna have proven to be challenging questions. in this review, we focus on translocation, the last step of the elongation cycle in which movement of trna and mrna is catalyzed by elongation factor g. translocation entails large-scale movements of the trnas and conformational changes in the ribosome that require numerous tertiary contacts to be disrupted and reformed ...	2009	19173642
molecular modeling and site-directed mutagenesis reveal essential residues for catalysis in a prokaryote-type aspartate aminotransferase.	we recently reported that aspartate (asp) biosynthesis in plant chloroplasts is catalyzed by two different asp aminotransferases (aat): a previously characterized eukaryote type and a prokaryote type (pt-aat) similar to bacterial and archaebacterial enzymes. the available molecular and kinetic data suggest that the eukaryote-type aat is involved in the shuttling of reducing equivalents through the plastidic membrane, whereas the pt-aat could be involved in the biosynthesis of the asp-derived ami ...	2009	19176717
a green fluorescent protein screen for identification of well-expressed membrane proteins from a cohort of extremophilic organisms.	green fluorescent protein (gfp) fusion proteins provide a potentially facile tool for identification of well expressed, properly behaved membrane proteins for biochemical and structural study. here, we present a gfp-expression survey of >300 membrane proteins from 18 bacterial and archaeal extremophiles, organisms expected to be rich sources of membrane proteins having robust biophysical properties. we find that gfp-fusion fluorescence intensity is an excellent indicator of over-expression poten ...	2009	19177357
a green fluorescent protein screen for identification of well-expressed membrane proteins from a cohort of extremophilic organisms.	green fluorescent protein (gfp) fusion proteins provide a potentially facile tool for identification of well expressed, properly behaved membrane proteins for biochemical and structural study. here, we present a gfp-expression survey of >300 membrane proteins from 18 bacterial and archaeal extremophiles, organisms expected to be rich sources of membrane proteins having robust biophysical properties. we find that gfp-fusion fluorescence intensity is an excellent indicator of over-expression poten ...	2009	19177357
constant c10 ring stoichiometry in the escherichia coli atp synthase analyzed by cross-linking.	the subunit c stoichiometry of escherichia coli atp synthase was studied by intermolecular cross-linking via oxidation of bi-cysteine-substituted subunit c (ca21c/cm65c). independent of the carbon source used for growth and independent of the presence of other fof1 subunits, an equal pattern of cross-link formation stopping at the formation of decamers was obtained.	2009	19181809
mechanistic and functional insights into fatty acid activation in mycobacterium tuberculosis.	the recent discovery of fatty acyl-amp ligases (faals) in mycobacterium tuberculosis (mtb) provided a new perspective of fatty acid activation. these proteins convert fatty acids to the corresponding adenylates, which are intermediates of acyl-coa-synthesizing fatty acyl-coa ligases (facls). presently, it is not evident how obligate pathogens such as mtb have evolved such new themes of functional versatility and whether the activation of fatty acids to acyladenylates could indeed be a general me ...	2009	19182784
x-ray crystal structure of garr-tartronate semialdehyde reductase from salmonella typhimurium.	tartronate semialdehyde reductases (tsrs), also known as 2-hydroxy-3-oxopropionate reductases, catalyze the reduction of tartronate semialdehyde using nad as cofactor in the final stage of d-glycerate biosynthesis. these enzymes belong to family of structurally and mechanically related beta-hydroxyacid dehydrogenases which differ in substrate specificity and catalyze reactions in specific metabolic pathways. here, we present the crystal structure of garr a tsr from salmonella typhimurium determi ...	2009	19184529
mechanism of inhibition of the v-type molecular motor by tributyltin chloride.	tributyltin chloride (tbt-cl) is an endocrine disruptor found in many animal species, and it is also known to be an inhibitor for the v-atpases that are emerging as potential targets in the treatment of diseases such as osteoporosis and cancer. we demonstrated by using biochemical and single-molecular imaging techniques that tbt-cl arrests an elementary step for rotary catalysis of the v(1) motor domain. in the presence of tbt-cl, the consecutive rotation of v(1) paused for a long duration ( app ...	2009	19186155
accommodation of two diatomic molecules in cytochrome bo: insights into no reductase activity in terminal oxidases.	bacterial heme-copper terminal oxidases react quickly with no to form a heme-nitrosyl complex, which, in some of these enzymes, can further react with a second no molecule to produce n(2)o. previously, we characterized the heme a(3)-no complex formed in cytochrome ba(3) from thermus thermophilus and the product of its low-temperature illumination. we showed that the photolyzed no group binds to cu(b)(i) to form an end-on no-cu(b) or a side-on copper-nitrosyl complex, which is likely to represent ...	2009	19187032
enhancement of the seed-target recognition step in rna silencing by a piwi/mid domain protein.	target recognition in rna silencing is governed by the "seed sequence" of a guide rna strand associated with the piwi/mid domain of an argonaute protein in risc. using a reconstituted in vitro target recognition system, we show that a model piwi/mid domain protein confers position-dependent tightening and loosening of guide-strand-target interactions. over the seed sequence, the interaction affinity is enhanced up to approximately 300-fold. enhancement is achieved through a reduced entropy penal ...	2009	19187762
an unexpected type of ribosomes induced by kasugamycin: a look into ancestral times of protein synthesis?	translation of leaderless mrnas, lacking ribosomal recruitment signals other than the 5'-terminal aug-initiating codon, occurs in all three domains of life. contemporary leaderless mrnas may therefore be viewed as molecular fossils resembling ancestral mrnas. here, we analyzed the phenomenon of sustained translation of a leaderless mrna in the presence of the antibiotic kasugamycin. unexpected from the known in vitro effects of the drug, kasugamycin induced the formation of stable approximately ...	2009	19187763
evolutionary basis for the coupled-domain motions in thermus thermophilus leucyl-trna synthetase.	aminoacyl-trna synthetases are multidomain proteins that catalyze the covalent attachment of amino acids to their cognate transfer rna. various domains of an aminoacyl-trna synthetase perform their specific functions in a highly coordinated manner to maintain high accuracy in protein synthesis in cells. the coordination of their function, therefore, requires communication between domains. in this study we explored the relevance of enzyme motion in domain-domain communications. specifically, we a ...	2009	19188368
critical roles of subunit nuoh (nd1) in the assembly of peripheral subunits with the membrane domain of escherichia coli ndh-1.	the bacterial proton-translocating nadh:quinone oxidoreductase (ndh-1) consists of two domains, a peripheral arm and a membrane arm. nuoh is a counterpart of nd1, which is one of seven mitochondrially encoded hydrophobic subunits, and is considered to be involved in quinone/inhibitor binding. sequence comparison in a wide range of species showed that nuoh is comprehensively conserved, particularly with charged residues in the cytoplasmic side loops. we have constructed 40 mutants of 27 conserved ...	2009	19189973
a minimized rrna-binding site for ribosomal protein s4 and its implications for 30s assembly.	primary ribosomal protein s4 is essential for 30s ribosome biogenesis in eubacteria, because it nucleates subunit assembly and helps coordinate assembly with the synthesis of its rrna and protein components. s4 binds a five-helix junction (5wj) that bridges the 5' and 3' ends of the 16s 5' domain. to delineate which nucleotides contribute to s4 recognition, sequential deletions of the 16s 5' domain were tested in competitive s4-binding assays based on electrophoretic mobility shifts. s4 binds th ...	2009	19190093
delineation of alternative conformational states in escherichia coli peptide deformylase via thermodynamic studies for the binding of actinonin.	we investigated the binding of a naturally occurring antibiotic, actinonin, to the ni(2+)-reconstituted recombinant form of escherichia coli peptide deformylase (pdf(ec)) via isothermal titration microcalorimetry. the binding data conformed to both exothermic and endothermic phases with magnitudes of deltag degrees , deltah degrees , and tdeltas degrees being equal to -12, -2.7, and 9.3 kcal/mol and -8.7, 3.9, and 12.6 kcal/mol, respectively. evidently, although both phases are dominated by favo ...	2009	19191548
hgf and bmp-7 ameliorate high glucose-induced epithelial-to-mesenchymal transition of peritoneal mesothelium.	over time, peritoneal dialysis results in functional and structural alterations of the peritoneal membrane, but the underlying mechanisms and whether these changes are reversible are not completely understood. here, we studied the effects of high levels of glucose, which are found in the dialysate, on human peritoneal mesothelial cells (hpmcs). we found that high concentrations of glucose induced epithelial-to-mesenchymal transition (emt) of hpmc, suggested by decreased expression of e-cadherin ...	2009	19193779
crystallization and x-ray analysis of human cytoplasmic phenylalanyl-trna synthetase.	human cytosolic phenylalanyl-trna synthetase (hcphers) is responsible for the covalent attachment of phenylalanine to its cognate trna(phe). significant differences between the amino-acid sequences of eukaryotic and prokaryotic pherss indicate that the domain composition of hcphers differs from that of the thermus thermophilus analogue. as a consequence of the absence of the anticodon-recognizing b8 domain, the binding mode of trna(phe) to hcphers is expected to differ from that in prokaryotes. ...	2009	19193993
escherichia coli trna(arg) acceptor-stem isoacceptors: comparative crystallization and preliminary x-ray diffraction analysis.	the aminoacylation of trna is a crucial step in cellular protein biosynthesis. recognition of the cognate trna by the correct aminoacyl-trna synthetase is ensured by trna identity elements. in trna(arg), the identity elements consist of the anticodon, parts of the d-loop and the discriminator base. the minor groove of the aminoacyl stem interacts with the arginyl-trna synthetase. as a consequence of the redundancy of the genetic code, six trna(arg) isoacceptors exist. in the present work, three ...	2009	19193994
crystallization, data collection and data processing of maltose-binding protein (male) from the phytopathogen xanthomonas axonopodis pv. citri.	maltose-binding protein is the periplasmic component of the abc transporter responsible for the uptake of maltose/maltodextrins. the xanthomonas axonopodis pv. citri maltose-binding protein male has been crystallized at 293 k using the hanging-drop vapour-diffusion method. the crystal belonged to the primitive hexagonal space group p6(1)22, with unit-cell parameters a = 123.59, b = 123.59, c = 304.20 a, and contained two molecules in the asymetric unit. it diffracted to 2.24 a resolution.	2009	19193996
preliminary x-ray crystallographic analysis of ornithine acetyltransferase (rv1653) from mycobacterium tuberculosis.	the gene product of open reading frame rv1653 from mycobacterium tuberculosis is annotated as encoding a probable ornithine acetyltransferase (oatase; ec 2.3.1.35), an enzyme that catalyzes two steps in the arginine-biosynthesis pathway. it transfers an acetyl group from n-acetylornithine to l-glutamate to produce n-acetylglutamate and l-ornithine. rv1653 was crystallized using the sitting-drop vapour-diffusion method. the native crystals diffracted to a resolution of 1.7 a and belonged to space ...	2009	19194014
three genomes from the phylum acidobacteria provide insight into the lifestyles of these microorganisms in soils.	the complete genomes of three strains from the phylum acidobacteria were compared. phylogenetic analysis placed them as a unique phylum. they share genomic traits with members of the proteobacteria, the cyanobacteria, and the fungi. the three strains appear to be versatile heterotrophs. genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. the genomes encode low-specificity major facilitator ...	2009	19201974
three-dimensional structure of a1a0 atp synthase from the hyperthermophilic archaeon pyrococcus furiosus by electron microscopy.	the archaeal atp synthase is a multisubunit complex that consists of a catalytic a(1) part and a transmembrane, ion translocation domain a(0). the a(1)a(0) complex from the hyperthermophile pyrococcus furiosus was isolated. mass analysis of the complex by laser-induced liquid bead ion desorption (lilbid) indicated a size of 730 +/- 10 kda. a three-dimensional map was generated by electron microscopy from negatively stained images. the map at a resolution of 2.3 nm shows the a(1) and a(0) domain, ...	2009	19203996
characterization of dna polymerase x from thermus thermophilus hb8 reveals the polxc and php domains are both required for 3'-5' exonuclease activity.	the x-family dna polymerases (polxs) comprise a highly conserved dna polymerase family found in all kingdoms. mammalian polxs are known to be involved in several dna-processing pathways including repair, but the cellular functions of bacterial polxs are less known. many bacterial polxs have a polymerase and histidinol phosphatase (php) domain at their c-termini in addition to a polx core (polxc) domain, and possess 3'-5' exonuclease activity. although both domains are highly conserved in bacteri ...	2009	19211662
functional expression of a bacterial xylose isomerase in saccharomyces cerevisiae.	in industrial fermentation processes, the yeast saccharomyces cerevisiae is commonly used for ethanol production. however, it lacks the ability to ferment pentose sugars like d-xylose and l-arabinose. heterologous expression of a xylose isomerase (xi) would enable yeast cells to metabolize xylose. however, many attempts to express a prokaryotic xi with high activity in s. cerevisiae have failed so far. we have screened nucleic acid databases for sequences encoding putative xis and finally were a ...	2009	19218403
characterization of a mimivirus rna cap guanine-n2 methyltransferase.	a 2,2,7-trimethylguanosine (tmg) cap is a signature feature of eukaryal snrnas, telomerase rnas, and trans-spliced nematode mrnas. tmg and 2,7-dimethylguanosine (dmg) caps are also present on mrnas of two species of alphaviruses (positive strand rna viruses of the togaviridae family). it is presently not known how viral mrnas might acquire a hypermethylated cap. mimivirus, a giant dna virus that infects amoeba, encodes many putative enzymes and proteins implicated in rna transactions, including ...	2009	19218551
reduction of hydrophilic ubiquinones by the flavin in mitochondrial nadh:ubiquinone oxidoreductase (complex i) and production of reactive oxygen species.	nadh:ubiquinone oxidoreductase (complex i) from bovine heart mitochondria is a complicated, energy-transducing, membrane-bound enzyme that contains 45 different subunits, a non-covalently bound flavin mononucleotide, and eight iron-sulfur clusters. the mechanisms of nadh oxidation and intramolecular electron transfer by complex i are gradually being defined, but the mechanism linking ubiquinone reduction to proton translocation remains unknown. studies of ubiquinone reduction by isolated complex ...	2009	19220002
a genetic screen for components of the mammalian rna interference pathway in bloom-deficient mouse embryonic stem cells.	genetic screens performed in model organisms have helped identify key components of the rna interference (rnai) pathway. recessive genetic screens have recently become feasible through the use of mouse embryonic stem (es) cells that are bloom's syndrome protein (blm) deficient. here, we developed and performed a recessive genetic screen to identify components of the mammalian rnai pathway in blm-deficient es cells. genome-wide mutagenesis using a retroviral gene trap strategy resulted in the iso ...	2009	19223321
dodecin is the key player in flavin homeostasis of archaea.	flavins are employed to transform physical input into biological output signals. in this function, flavins catalyze a variety of light-induced reactions and redox processes. however, nature also provides flavoproteins with the ability to uncouple the mediation of signals. such proteins are the riboflavin-binding proteins (rfbps) with their function to store riboflavin for fast delivery of fmn and fad. here we present in vitro and in vivo data showing that the recently discovered archaeal dodecin ...	2009	19224924
idiosyncratic helix-turn-helix motif in methanosarcina barkeri seryl-trna synthetase has a critical architectural role.	all seryl-trna synthetases (serrss) are functional homodimers with a c-terminal active site domain typical for class ii aminoacyl-trna synthetases and an n-terminal domain involved in trna binding. the recently solved three-dimensional structure of methanosarcina barkeri serrs revealed the idiosyncratic features of methanogenic-type serrss; that is, an active site zinc ion, a unique trna binding domain, and an insertion of approximately 30 residues in the catalytic domain, which adopt a helix-tu ...	2009	19228694
gtpase activation of elongation factor ef-tu by the ribosome during decoding.	we have used single-particle reconstruction in cryo-electron microscopy to determine a structure of the thermus thermophilus ribosome in which the ternary complex of elongation factor tu (ef-tu), trna and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. this represents the state in the decoding process just after codon recognition by trna and the resulting gtp hydrolysis by ef-tu, but before the release of ef-tu from the ribosome. progress in sample purificati ...	2009	19229291
a molybdopterin oxidoreductase is involved in h2 oxidation in desulfovibrio desulfuricans g20.	three mutants deficient in hydrogen/formate uptake were obtained through screening of a transposon mutant library containing 5,760 mutants of desulfovibrio desulfuricans g20. mutations were in the genes encoding the type i tetraheme cytochrome c(3) (cyca), fe hydrogenase (hydb), and molybdopterin oxidoreductase (mopb). mutations did not decrease the ability of cells to produce h(2) or formate during growth. complementation of the cyca and mopb mutants with a plasmid carrying the intact cyca and/ ...	2009	19233927
stimulation of expression of a silica-induced protein (sip) in thermus thermophilus by supersaturated silicic acid.	the effects of silicic acid on the growth of thermus thermophilus tmy, an extreme thermophile isolated from a siliceous deposit formed from geothermal water at a geothermal power plant in japan, were examined at 75 degrees c. at concentrations higher than the solubility of amorphous silica (400 to 700 ppm sio(2)), a silica-induced protein (sip) was isolated from the cell envelope fraction of log-phase tmy cells grown in the presence of supersaturated silicic acid. two-dimensional sodium dodecyl ...	2009	19233950
domain architecture of the stator complex of the a1a0-atp synthase from thermoplasma acidophilum.	a key structural element in the ion translocating f-, a-, and v-atpases is the peripheral stalk, an assembly of two polypeptides that provides a structural link between the atpase and ion channel domains. previously, we have characterized the peripheral stalk forming subunits e and h of the a-atpase from thermoplasma acidophilum and demonstrated that the two polypeptides interact to form a stable heterodimer with 1:1 stoichiometry (kish-trier, e., briere, l. k., dunn, s. d., and wilkens, s. (200 ...	2009	19234304
improving the functional expression of a bacillus licheniformis laccase by random and site-directed mutagenesis.	laccases have huge potential for biotechnological applications due to their broad substrate spectrum and wide range of reactions they are able to catalyze. these include, for example, the formation and degradation of dimers, oligomers, polymers, and ring cleavage as well as oxidation of aromatic compounds. potential applications of laccases include detoxification of industrial effluents, decolorization of textile dyes and the synthesis of natural products by, for instance, dimerization of phenol ...	2009	19236694
structures of alternatively spliced isoforms of human ketohexokinase.	a molecular understanding of the unique aspects of dietary fructose metabolism may be the key to understanding and controlling the current epidemic of fructose-related obesity, diabetes and related adverse metabolic states in western populations. fructose catabolism is initiated by its phosphorylation to fructose 1-phosphate, which is performed by ketohexokinase (khk). here, the crystal structures of the two alternatively spliced isoforms of human ketohexokinase, hepatic khk-c and the peripheral ...	2009	19237742
dna uracil repair initiated by the archaeal exoiii homologue mth212 via direct strand incision.	no genes for any of the known uracil dna glycosylases of the udg superfamily are present in the genome of methanothermobacter thermautotrophicus deltah, making it difficult to imagine how dna-u repair might be initiated in this organism. recently, mth212, the exoiii homologue of m. thermautotrophicus deltah has been characterized as a dna uridine endonuclease, which suggested the possibility of a novel endonucleolytic entry mechanism for dna uracil repair. with no system of genetic experimentati ...	2009	19240141
involvement of a carboxylated lysine in uv damage endonuclease.	uv damage endonuclease is a dna repair enzyme that can both recognize damage such as uv lesions and introduce a nick directly 5' to them. recently, the crystal structure of the enzyme from thermus thermophilus was solved. in the electron density map of this structure, unexplained density near the active site was observed at the tip of lys229. based on this finding, it was proposed that lys229 is post-translationally modified. in this article, we give evidence that this modification is a carboxyl ...	2009	19241382
allopatric speciation in ticks: genetic and reproductive divergence between geographic strains of rhipicephalus (boophilus) microplus.	the cattle tick, rhipicephalus (boophilus) microplus, economically impact cattle industry in tropical and subtropical regions of the world. the morphological and genetic differences among r. microplus strains have been documented in the literature, suggesting that biogeographical and ecological separation may have resulted in boophilid ticks from america/africa and those from australia being different species. to test the hypothesis of the presence of different boophilid species, herein we perfo ...	2009	19243585
identification of neisserial dna binding components.	neisseria meningitidis, a causative agent of meningitis and septicaemia, expresses type iv pili, a feature correlating with the uptake of exogenous dna from the environment by natural transformation. the outer membrane complex pilq, through which pili are extruded and retracted, has previously been shown to bind dna in its pore region. in order to further elucidate how dna is transported across the membranes, we searched for dna binding proteins within the meningococcal inner membrane. inner mem ...	2009	19246756
the family x dna polymerase from deinococcus radiodurans adopts a non-standard extended conformation.	deinococcus radiodurans is an extraordinarily radioresistant bacterium that is able to repair hundreds of radiation-induced double-stranded dna breaks. one of the players in this pathway is an x family dna polymerase (polx(dr)). deletion of polx(dr) has been shown to decrease the rate of repair of double-stranded dna breaks and increase cell sensitivity to gamma-rays. a 3'-->5' exonuclease activity that stops cutting close to dna loops has also been demonstrated. the present crystal structure of ...	2009	19251692
crystallization and preliminary characterization of the thermus thermophilus rna helicase hera c-terminal domain.	heat-resistant rna-dependent atpase (hera) from thermus thermophilus is a dead-box rna helicase. two constructs encompassing the second reca-like domain and the c-terminal domain of hera were overproduced in escherichia coli and purified to homogeneity. single crystals of both hera constructs were obtained in three crystal forms. a tetragonal crystal form belonged to space group p4(1)2(1)2, with unit-cell parameters a = 65.5, c = 153.0 a, and contained one molecule per asymmetric unit. two ortho ...	2009	19255475
defects in transient trna translocation bypass trna synthetase quality control mechanisms.	quality control mechanisms during protein synthesis are essential to fidelity and cell survival. leucyl-trna synthetase (leurs) misactivates non-leucine amino acids including isoleucine, methionine, and norvaline. to prevent translational errors, mischarged trna products are translocated 30a from the canonical aminoacylation core to a hydrolytic editing-active site within a completely separate domain. because it is transient, the trna translocation mechanism has been difficult to isolate. we hav ...	2009	19258309
contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis.	superoxide dismutase (sod) enzymes are critical in controlling levels of reactive oxygen species (ros) that are linked to aging, cancer, and neurodegenerative disease. superoxide (o(2)(*-)) produced during respiration is removed by the product of the sod2 gene, the homotetrameric manganese superoxide dismutase (mnsod). here, we examine the structural and catalytic roles of the highly conserved active-site residue tyr34, based upon structure-function studies of mnsod enzymes with mutations at thi ...	2009	19265433
a novel endo-hydrogenase activity recycles hydrogen produced by nitrogen fixation.	nitrogen (n(2)) fixation also yields hydrogen (h(2)) at 1:1 stoichiometric amounts. in aerobic diazotrophic (able to grow on n(2) as sole n-source) bacteria, orthodox respiratory hupsl-encoded hydrogenase activity, associated with the cell membrane but facing the periplasm (exo-hydrogenase), has nevertheless been presumed responsible for recycling such endogenous hydrogen.	2009	19277114
a recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center.	the ribosome is an ancient macromolecular machine responsible for the synthesis of all proteins in all living organisms. here we demonstrate that the ribosomal peptidyl transferase center (ptc) is supported by a framework of magnesium microclusters (mg(2+)-muc's). common features of mg(2+)-muc's include two paired mg(2+) ions that are chelated by a common bridging phosphate group in the form mg((a))(2+)-(o1p-p-o2p)-mg((b))(2+). this bridging phosphate is part of a 10-membered chelation ring in t ...	2009	19279186
an archaeal rad54 protein remodels dna and stimulates dna strand exchange by rada.	rad54 protein is a key member of the rad52 epistasis group required for homologous recombination in eukaryotes. rad54 is a duplex dna translocase that remodels both dna and protein-dna complexes, and functions at multiple steps in the recombination process. here we use biochemical criteria to demonstrate the existence of this important protein in a prokaryotic organism. the sulfolobus solfataricus rad54 (ssorad54) protein is a double-strand dna-dependent atpase that can alter the topology of dup ...	2009	19282450
the complete genome and proteome of laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.	laribacter hongkongensis is a newly discovered gram-negative bacillus of the neisseriaceae family associated with freshwater fish-borne gastroenteritis and traveler's diarrhea. the complete genome sequence of l. hongkongensis hlhk9, recovered from an immunocompetent patient with severe gastroenteritis, consists of a 3,169-kb chromosome with g+c content of 62.35%. genome analysis reveals different mechanisms potentially important for its adaptation to diverse habitats of human and freshwater fish ...	2009	19283063
the genome of bacillus subtilis bacteriophage spo1.	we report the genome sequence of bacillus subtilis phage spo1. the unique genome sequence is 132,562 bp long, and dna packaged in the virion (the chromosome) has a 13,185-bp terminal redundancy, giving a total of 145,747 bp. we predict 204 protein-coding genes and 5 trna genes, and we correlate these findings with the extensive body of investigations of spo1, including studies of the functions of the 61 previously defined genes and studies of the virion structure. sixty-nine percent of the encod ...	2009	19285085
structural rearrangements in the active site of the thermus thermophilus 16s rrna methyltransferase ksga in a binary complex with 5'-methylthioadenosine.	posttranscriptional modification of ribosomal rna (rrna) occurs in all kingdoms of life. the s-adenosyl-l-methionine-dependent methyltransferase ksga introduces the most highly conserved rrna modification, the dimethylation of a1518 and a1519 of 16s rrna. loss of this dimethylation confers resistance to the antibiotic kasugamycin. here, we report biochemical studies and high-resolution crystal structures of ksga from thermus thermophilus. methylation of 30s ribosomal subunits by t. thermophilus ...	2009	19285505
resampling and editing of mischarged trna prior to translation elongation.	faithful translation of the genetic code depends on the gtpase ef-tu delivering correctly charged aminoacyl-trnas to the ribosome for pairing with cognate codons. the accurate coupling of cognate amino acids and trnas by the aminoacyl-trna synthetases is achieved through a combination of substrate specificity and product editing. once released by aminoacyl-trna synthetases, both cognate and near-cognate aminoacyl-trnas were considered to be committed to ribosomal protein synthesis through their ...	2009	19285947
structure and function of a campylobacter jejuni thioesterase cj0915, a hexameric hot dog fold enzyme.	acyl-coenzyme a (coa) thioesterases are a large family of enzymes that hydrolyze acyl-coa esters to the free fatty acid and coa and thereby regulate essential cellular functions such as lipid metabolism, membrane synthesis, signal transduction, and gene transcription. to better understand the virulence mechanisms of campylobacter jejuni, and its possible link to membrane lipid biosynthesis, we have investigated c. jejuni thioesterases, annotated as putative proteins. while little is known about ...	2009	19303060
mutational analysis of mycobacterium uvrd1 identifies functional groups required for atp hydrolysis, dna unwinding, and chemomechanical coupling.	mycobacterial uvrd1 is a dna-dependent atpase and a ku-dependent 3' to 5' dna helicase. the uvrd1 motor domain resembles that of the prototypal superfamily i helicases uvrd and pcra. here we performed a mutational analysis of uvrd1 guided by the crystal structure of a dna-bound escherichia coli uvrd-adp-mgf(3) transition state mimetic. alanine scanning and conservative substitutions identified amino acids essential for both atp hydrolysis and duplex unwinding, including those implicated in phosp ...	2009	19317511
maintenance of rna-dna hybrid length in bacterial rna polymerases.	during transcription elongation the nascent rna remains base-paired to the template strand of the dna before it is displaced and the two strands of the dna reanneal, resulting in the formation of a transcription "bubble" of approximately 10 bp. to examine how the length of the rna-dna hybrid is maintained, we assembled transcription elongation complexes on synthetic nucleic acid scaffolds that mimic the situation in which transcript displacement is compromised and the polymerase synthesizes an e ...	2009	19321439
connection between stop codon reassignment and frequent use of shifty stop frameshifting.	ciliated protozoa of the genus euplotes have undergone genetic code reassignment, redefining the termination codon uga to encode cysteine. in addition, euplotes spp. genes very frequently employ shifty stop frameshifting. both of these phenomena involve noncanonical events at a termination codon, suggesting they might have a common cause. we recently demonstrated that euplotes octocarinatus peptide release factor erf1 ignores uga termination codons while continuing to recognize uaa and uag. here ...	2009	19329535
parb deficiency in pseudomonas aeruginosa destabilizes the partner protein para and affects a variety of physiological parameters.	deletions leading to complete or partial removal of parb were introduced into the pseudomonas aeruginosa chromosome. fluorescence microscopy of fixed cells showed that parb mutants lacking the c-terminal domain or hth motif formed multiple, less intense foci scattered irregularly, in contrast to the one to four parb foci per cell symmetrically distributed in wild-type p. aeruginosa. all parb mutations affected both bacterial growth and swarming and swimming motilities, and increased the producti ...	2009	19332810
structural insight into the inhibition of human kynurenine aminotransferase i/glutamine transaminase k.	human kynurenine aminotransferase i (hkat i) catalyzes the formation of kynurenic acid, a neuroactive compound. here, we report three high-resolution crystal structures (1.50-1.55 a) of hkat i that are in complex with glycerol and each of two inhibitors of hkat i: indole-3-acetic acid (iac) and tris. because tris is able to occupy the substrate binding position, we speculate that this may be the basis for hkat i inhibition. furthermore, the hkat/iac complex structure reveals that the binding moi ...	2009	19338303
degradation of ppgpp by nudix pyrophosphatase modulates the transition of growth phase in the bacterium thermus thermophilus.	a major bacterial alarmone, guanosine 3',5'-bispyrophosphate (ppgpp), controls cellular growth under conditions of nutritional starvation. for most bacteria, intracellular ppgpp levels are tightly controlled by the synthesis/degradation cycle of rela and spot activities. this study shows a novel ppgpp regulatory protein governing the cellular growth of thermus thermophilus, ndx8, a member of the nudix pyrophosphatase family that degrades ppgpp to yield guanosine 3',5'-bisphosphate. the ndx8-null ...	2009	19346251
three-dimensional structure and enzymatic function of proapoptotic human p53-inducible quinone oxidoreductase pig3.	tumor suppressor p53 regulates the expression of p53-induced genes (pig) that trigger apoptosis. pig3 or tp53i3 is the only known member of the medium chain dehydrogenase/reductase superfamily induced by p53 and is used as a proapoptotic marker. although the participation of pig3 in the apoptotic pathway is proven, the protein and its mechanism of action were never characterized. we analyzed human pig3 enzymatic function and found nadph-dependent reductase activity with ortho-quinones, which is ...	2009	19349281
mitochondrial respiratory complex i: structure, function and implication in human diseases.	mitochondria are ubiquitous organelles in eukaryotic cells whose primary function is to generate energy supplies in the form of atp through oxidative phosphorylation. as the entry point for most electrons into the respiratory chain, nadh:ubiquinone oxidoreductase, or complex i, is the largest and least understood component of the mitochondrial oxidative phosphorylation system. substantial progress has been made in recent years in understanding its subunit composition, its assembly, the interacti ...	2009	19355884
deciphering peculiar protein-protein interacting modules in deinococcus radiodurans.	interactomes of proteins under positive selection from ionizing-radiation-resistant bacteria (irrb) might be a part of the answer to the question as to how irrb, particularly deinococcus radiodurans r1 (deira), resist ionizing radiation. here, using the database of interacting proteins (dip) and the protein structural interactome (psi)-base server for psi map, we have predicted novel interactions of orthologs of the 58 proteins under positive selection in deira and other irrb, but which are abse ...	2009	19356244
bioinformatics analysis suggests base modifications of trnas and mirnas in arabidopsis thaliana.	modifications of rna bases have been found in some mrnas and non-coding rnas including rrnas, trnas, and snrnas, where modified bases are important for rna function. little is known about rna base modifications in arabidopsis thaliana.	2009	19358740
allostery in hsp70 chaperones is transduced by subdomain rotations.	hsp70s (heat shock protein 70 kda) are central to protein folding, refolding, and trafficking in organisms ranging from archaea to homo sapiens under both normal and stressed cellular conditions. hsp70s are comprised of a nucleotide-binding domain (nbd) and a substrate-binding domain (sbd). the nucleotide binding site in the nbd and the substrate binding site in the sbd are allosterically linked: adp binding promotes substrate binding, while atp binding promotes substrate release. hsp70s have be ...	2009	19361428
molecular dynamism of fe-s cluster biosynthesis implicated by the structure of the sufc(2)-sufd(2) complex.	maturation of iron-sulfur (fe-s) proteins is achieved by the suf machinery in a wide number of eubacteria and archaea, as well as eukaryotic chloroplasts. this machinery is encoded in escherichia coli by the sufabcdse operon, where three suf components, sufb, sufc, and sufd, form a complex and appear to provide an intermediary site for the fe-s cluster assembly. here, we report the quaternary structure of the sufc(2)-sufd(2) complex in which sufc is bound to the c-terminal domain of sufd. compar ...	2009	19361433
structural and motional contributions of the bacillus subtilis clpc n-domain to adaptor protein interactions.	the aaa(+) (atpases associated with a variety of cellular activities) superfamily protein clpc is a key regulator of cell development in bacillus subtilis. as part of a large oligomeric complex, clpc controls an array of cellular processes by recognizing, unfolding, and providing misfolded and aggregated proteins as substrates for the clpp peptidase. clpc is unique compared to other hsp100/clp proteins, as it requires an adaptor protein for all fundamental activities. the nmr solution structure ...	2009	19361434
the lateral gate of secyeg opens during protein translocation.	the secyeg translocon of escherichia coli mediates the translocation of preproteins across the cytoplasmic membrane. here, we have examined the role of the proposed lateral gate of the translocon in translocation. a dual cysteine cross-linking approach allowed the introduction of cross-linker arms of various lengths between adjoining aminoacyl positions of transmembrane segments 2b and 7 of the lateral gate. oxidation and short spacer linkers that fix the gate in the closed state abolished prepr ...	2009	19366685
alliance of proteomics and genomics to unravel the specificities of sahara bacterium deinococcus deserti.	to better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, deinococcus deserti vcd115, isolated from sahara surface sand. its genome consists of a 2.8-mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. from the large corpus of ms/ms spectra recorded, 1,348 proteins w ...	2009	19370165
functional characterization of excision repair and reca-dependent recombinational dna repair in campylobacter jejuni.	the presence and functionality of dna repair mechanisms in campylobacter jejuni are largely unknown. in silico analysis of the complete translated genome of c. jejuni nctc 11168 suggests the presence of genes involved in methyl-directed mismatch repair (mmr), nucleotide excision repair, base excision repair (ber), and recombinational repair. to assess the functionality of these putative repair mechanisms in c. jejuni, muts, uvrb, ung, and reca knockout mutants were constructed and analyzed for t ...	2009	19376866
from a consortium sequence to a unified sequence: the bacillus subtilis 168 reference genome a decade later.	comparative genomics is the cornerstone of identification of gene functions. the immense number of living organisms precludes experimental identification of functions except in a handful of model organisms. the bacterial domain is split into large branches, among which the firmicutes occupy a considerable space. bacillus subtilis has been the model of firmicutes for decades and its genome has been a reference for more than 10 years. sequencing the genome involved more than 30 laboratories, with ...	2009	19383706
the crystal structures of chikungunya and venezuelan equine encephalitis virus nsp3 macro domains define a conserved adenosine binding pocket.	macro domains (also called "x domains") constitute a protein module family present in all kingdoms of life, including viruses of the coronaviridae and togaviridae families. crystal structures of the macro domain from the chikungunya virus (an "old world" alphavirus) and the venezuelan equine encephalitis virus (a "new world" alphavirus) were determined at resolutions of 1.65 and 2.30 a, respectively. these domains are active as adenosine di-phosphoribose 1''-phosphate phosphatases. both the chik ...	2009	19386706
accuracy modulating mutations of the ribosomal protein s4-s5 interface do not necessarily destabilize the rps4-rps5 protein-protein interaction.	during the process of translation, an aminoacyl trna is selected in the a site of the decoding center of the small subunit based on the correct codon-anticodon base pairing. though selection is usually accurate, mutations in the ribosomal rna and proteins and the presence of some antibiotics like streptomycin alter translational accuracy. recent crystallographic structures of the ribosome suggest that cognate trnas induce a "closed conformation" of the small subunit that stabilizes the codon-ant ...	2009	19386726
resonance raman studies of the (his)(cys)3 2fe-2s cluster of mitoneet: comparison to the (cys)4 mutant and implications of the effects of ph on the labile metal center.	mitoneet is a 2fe-2s outer mitochondrial membrane protein that was initially identified as a target for anti-diabetic drugs. it exhibits a novel protein fold, and in contrast to other 2fe-2s proteins such as rieske proteins and ferredoxins, the metal clusters in the mitoneet homodimer are each coordinated by one histidine residue and three cysteine residues. the interaction of the ligating his87 residue with the 2fe-2s moiety is especially significant because previous studies have shown that rep ...	2009	19388667
molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of transport.	we have examined the network of connected internal cavities in cytochrome c oxidase along which water produced at the catalytic center is removed from the enzyme. using combination of structural analysis, molecular dynamics simulations, and free energy calculations we have identified two exit pathways that connect the mg2+ ion cavity to the outside of the enzyme. each pathway has a well-defined bottleneck, which determines the overall rate of water traffic along the exit pathway, and a specific ...	2009	19393218
redox-dependent conformational changes in cytochrome c oxidase suggest a gating mechanism for proton uptake.	a role for conformational change in the coupling mechanism of cytochrome c oxidase is the subject of controversy. relatively small conformational changes have been reported in comparisons of reduced and oxidized crystal structures of bovine oxidase but none in bacterial oxidases. comparing the x-ray crystal structures of the reduced (at 2.15 a resolution) and oxidized forms of cytochrome c oxidase from rhodobacter sphaeroides, we observe a displacement of heme a(3) involving both the porphyrin r ...	2009	19397279
structure of ttha1623, a novel metallo-beta-lactamase superfamily protein from thermus thermophilus hb8.	ttha1623 is a metallo-beta-lactamase superfamily protein from the extremely thermophilic bacterium thermus thermophilus hb8. homologues of ttha1623 exist in a wide range of bacteria and archaea and one eukaryote, giardia lamblia, but their function remains unknown. to analyze the structural properties of ttha1623, the crystal structures of its iron-bound and zinc-bound forms have been determined to 2.8 and 2.2 a resolution, respectively. ttha1623 possesses an alphabetabetaalpha-fold similar to t ...	2009	19407375
crystallization and preliminary x-ray crystallographic analysis of a novel histidinol-phosphate phosphatase from thermococcus onnurineus na1.	the ton_0887 gene product from thermococcus onnurineus na1 is a 240-residue protein that has histidinol-phosphate phosphatase (holpase) activity. according to analysis of its primary structure, the ton_0887 gene product is a monofunctional holpase that belongs to the dddd superfamily. this contrasts with the generally accepted classification that bifunctional holpases belong to the dddd superfamily. the ton_0887 gene product was purified and crystallized at 295 k. a 2.2 a resolution data set was ...	2009	19407379
cloning, expression, purification and crystallization as well as x-ray fluorescence and preliminary x-ray diffraction analyses of human adp-ribosylhydrolase 1.	human adp-ribosylhydrolase 1 (harh1, adprh) cleaves the glycosidic bond of adp-ribose attached to an arg residue of a protein. harh1 has been cloned, expressed heterologously in escherichia coli, purified and crystallized in complex with k(+) and adp. the orthorhombic crystals contained one monomer per asymmetric unit, exhibited a solvent content of 43% and diffracted x-rays to a resolution of 1.9 a. a prerequisite for obtaining well diffracting crystals was the performance of x-ray fluorescence ...	2009	19407395
structure, stability, and folding of ribonuclease h1 from the moderately thermophilic chlorobium tepidum: comparison with thermophilic and mesophilic homologues.	proteins from thermophilic organisms are able to function under conditions that render a typical mesophilic protein inactive. pairwise comparisons of homologous mesophilic and thermophilic proteins can help to identify the energetic features of a protein's energy landscape that lead to such thermostability. previous studies of bacterial ribonucleases h (rnases h) from the thermophile thermus thermophilus and the mesophile escherichia coli revealed that the thermostability arises in part from an ...	2009	19408959
versatile solidified nanofibrous cellulose-containing media for growth of extremophiles.	solidified media that employ a porous matrix of nanofibrous cellulose are described. the physicochemical stability of the porous structure allows the development of solidified media that can support the growth of extremophiles, such as acidophilic acidiphilium, alkaliphilic bacillus, thermophilic geobacillus and thermus, alkalithermophilic bacillus, and acidothermophilic sulfolobus microbes. the cellulose-supported media have several advantages over agar- and gellan gum-derived media, including ...	2009	19411423
diversity of 23s rrna genes within individual prokaryotic genomes.	the concept of ribosomal constraints on rrna genes is deduced primarily based on the comparison of consensus rrna sequences between closely related species, but recent advances in whole-genome sequencing allow evaluation of this concept within organisms with multiple rrna operons.	2009	19415112
allosteric regulation of the primase (dnag) activity by the clamp-loader (tau) in vitro.	during dna replication the helicase (dnab) recruits the primase (dnag) in the replisome to initiate the polymerization of new dna strands. dnab is attached to the tau subunit of the clamp-loader that loads the beta clamp and interconnects the core polymerases on the leading and lagging strands. the tau-dnab-dnag ternary complex is at the heart of the replisome and its function is likely to be modulated by a complex network of allosteric interactions. using a stable ternary complex comprising the ...	2009	19415803