Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
|---|
| crystal structure of prephenate dehydrogenase from aquifex aeolicus. insights into the catalytic mechanism. | the enzyme prephenate dehydrogenase catalyzes the oxidative decarboxylation of prephenate to 4-hydroxyphenylpyruvate for the biosynthesis of tyrosine. prephenate dehydrogenases exist as either monofunctional or bifunctional enzymes. the bifunctional enzymes are diverse, since the prephenate dehydrogenase domain is associated with other enzymes, such as chorismate mutase and 3-phosphoskimate 1-carboxyvinyltransferase. we report the first crystal structure of a monofunctional prephenate dehydrogen ... | 2006 | 16513644 |
| crystallization and preliminary x-ray crystallographic study of the wild type and two mutants of the cp1 hydrolytic domain from aquifex aeolicus leucyl-trna synthetase. | the editing or hydrolytic cp1 domain of leucyl-trna synthetase (leurs) hydrolyses several misactivated amino acids. the cp1 domain of aquifex aeolicus leurs was expressed, purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. crystals belong to space group p2(1)2(1)2(1), with unit-cell parameters a = 38.8, b = 98.4, c = 116.7 a. crystals diffract to beyond 1.8 a resolution and contain two monomers in the asymmetric unit. two cp1 mutants in w ... | 2005 | 16511190 |
| structure of a class ii trmh trna-modifying enzyme from aquifex aeolicus. | biological rnas contain a variety of post-transcriptional modifications that facilitate their efficient function in the cellular environment. one of the two most common forms of modification is methylation of the 2'-hydroxyl group of the ribose sugar, which is performed by a number of s-adenosylmethionine (sam) dependent methyltransferases. in bacteria, many of these modifications in trna and rrna are carried out by the alpha/beta-knot superfamily of enzymes, whose sam-binding pocket is created ... | 2005 | 16511140 |
| interaction analysis between tmrna and smpb from thermus thermophilus. | small protein b, smpb, is a tmrna-specific binding protein essential for trans-translation. we examined the interaction between smpb and tmrna from thermus thermophilus, using biochemical and nmr methods. chemical footprinting analyses using full-length tmrna demonstrated that the sites protected upon smpb binding are located exclusively in the trna-like domain (tld) of tmrna. to clarify the smpb binding sites, we constructed several segments derived from tld. optical biosensor interaction analy ... | 2005 | 16428302 |
| a theoretical model of aquifex pyrophilus flagellin: implications for its thermostability. | aquifex pyrophilus is a flagellated hyperthermophilic eubacterial species that grows optimally at 85 degrees c. the thermostable a. pyrophilus flagellar filament is primarily composed of a single protein called flagellin (flaa). the n- and c-terminal sequence regions of flaa are important for self-assembly and share high sequence similarity with mesophilic bacterial flagellins. we have developed a predictive 3d-structure of flaa, using the published structure of mesophilic salmonella typhimurium ... | 2006 | 16411078 |
| molecular signatures in protein sequences that are characteristics of the phylum aquificae. | species of the phylum aquificae are of great interest due to their strict extreme thermophilic growth characteristics. presently, there is no known molecular characteristic which is unique to this group of bacteria. this work describes six conserved inserts and deletions (indels or signature sequences) in four widely distributed proteins that are distinctive features of species from the phylum aquificae. these include three signatures consisting of a 2 aa insert, a 5-6 aa insert and a 6 aa delet ... | 2006 | 16403873 |
| insights on a new pdi-like family: structural and functional analysis of a protein disulfide oxidoreductase from the bacterium aquifex aeolicus. | a potential role in disulfide bond formation in the intracellular proteins of thermophilic organisms has recently been attributed to a new family of protein disulfide isomerase (pdi)-like proteins. members of this family are characterized by a molecular mass of about 26kda and by two trx folds, each comprising a cxxc active site motif. we report on the functional and structural characterization of a new member of this family, which was isolated from the thermophilic bacterium aquifex aeolicus (a ... | 2006 | 16364362 |
| genetic transplantation: salmonella enterica serovar typhimurium as a host to study sigma factor and anti-sigma factor interactions in genetically intractable systems. | in salmonella enterica serovar typhimurium, sigma(28) and anti-sigma factor flgm are regulatory proteins crucial for flagellar biogenesis and motility. in this study, we used s. enterica serovar typhimurium as an in vivo heterologous system to study sigma(28) and anti-sigma(28) interactions in organisms where genetic manipulation poses a significant challenge due to special growth requirements. the chromosomal copy of the s. enterica serovar typhimurium sigma(28) structural gene flia was exchang ... | 2006 | 16352826 |
| a slow, tight-binding inhibitor of the zinc-dependent deacetylase lpxc of lipid a biosynthesis with antibiotic activity comparable to ciprofloxacin. | the zinc-dependent enzyme lpxc catalyzes the deacetylation of udp-3-o-acyl-glcnac, the first committed step of lipid a biosynthesis. lipid a is an essential component of the outer membranes of most gram-negative bacteria, including escherichia coli, salmonella enterica, and pseudomonas aeruginosa, making lpxc an attractive target for antibiotic design. the inhibition of lpxc by a novel n-aroyl-l-threonine hydroxamic acid (chir-090) from a recent patent application (international patent wo 2004/0 ... | 2005 | 16342948 |
| the crystal structure of aq_328 from the hyperthermophilic bacteria aquifex aeolicus shows an ancestral histone fold. | the structure of aq_328, an uncharacterized protein from hyperthermophilic bacteria aquifex aeolicus, has been determined to 1.9 a by using multi-wavelength anomalous diffraction (mad) phasing. although the amino acid sequence analysis shows that aq_328 has no significant similarity to proteins with a known structure and function, the structure comparison by using the dali server reveals that it: (1) assumes a histone-like fold, and (2) is similar to an ancestral nuclear histone protein (pdb cod ... | 2006 | 16287087 |
| role of the unique peptide tail in hyperthermostable aquifex aeolicus cochaperonin protein 10. | all known cochaperonin protein 10 (cpn10) molecules are heptamers of seven identical subunits noncovalently linked by beta-strand interactions. cpn10 from the deep-branching, hyperthermophilic bacterium aquifex aeolicus (aacpn10) shows high homology with mesophilic and other thermophilic cpn10 sequences, except for a 25-residue c-terminal extension not found in any other cpn10. prior to atomic structure information, we here address the role of the tail by biophysical means. a tail-lacking varian ... | 2005 | 16262239 |
| expression, purification, and characterization of a new heterotetramer structure of leucyl-trna synthetase from aquifex aeolicus in escherichia coli. | aminoacyl-trna synthetases are key players in the interpretation of the genetic code. they constitute a textbook example of multi-domain proteins including insertion and terminal functional modules appended to one of the two class-specific active site domains. the non-catalytic domains usually have distinct roles in the aminoacylation reaction. aquifex aeolicus leucyl-trna synthetase (leurs) is composed of a separated catalytic site and trna anticodon-binding site, which would represent one of t ... | 2006 | 16256368 |
| a membrane-bound multienzyme, hydrogen-oxidizing, and sulfur-reducing complex from the hyperthermophilic bacterium aquifex aeolicus. | aquifex aeolicus is a hyperthermophilic, chemolithoautotrophic, hydrogen-oxidizing, and microaerophilic bacterium growing at 85 degrees c. we have shown that it can grow on an h2/s degrees medium and produce h2s from sulfur in the later exponential phase. the complex carrying the sulfur reducing activity (electron transport from h2 to s degrees ) has been purified and characterized. it is a membrane-bound multiprotein complex containing a [nife] hydrogenase and a sulfur reductase connected via q ... | 2005 | 16236714 |
| evolutionary relationships among photosynthetic bacteria. | to understand the evolution of photosynthetic bacteria it is necessary to understand how the main groups within bacteria have evolved from a common ancestor, a critical issue that has not been resolved in the past. recent analysis of shared conserved inserts or deletions (indels) in protein sequences has provided a powerful means to resolve this long-standing problem in microbiology. based on a set of 25 indels in highly conserved and widely distributed proteins, all main groups within bacteria ... | 2003 | 16228576 |
| the c-terminal rpon domain of sigma54 forms an unpredicted helix-turn-helix motif similar to domains of sigma70. | the "sigma" subunit of prokaryotic rna polymerase allows gene-specific transcription initiation. two sigma families have been identified, sigma70 and sigma54, which use distinct mechanisms to initiate transcription and share no detectable sequence homology. although the sigma70-type factors have been well characterized structurally by x-ray crystallography, no high resolution structural information is available for the sigma54-type factors. here we present the nmr-derived structure of the c-term ... | 2005 | 16210314 |
| negative regulation of aaa + atpase assembly by two component receiver domains: a transcription activation mechanism that is conserved in mesophilic and extremely hyperthermophilic bacteria. | only a few transcriptional regulatory proteins have been characterized in extremely hyperthermophilic organisms, and most function as repressors. structural features of the ntrc1 protein from the hyperthermophilic bacterium aquifex aeolicus suggested that this protein functions similarly to the sigma(54)-polymerase activator dctd of sinorhizobium meliloti. here, we demonstrate that ntrc1 is an enzyme that hydrolyzes atp to activate initiation of transcription by sigma(54)-holoenzyme. new structu ... | 2005 | 16169010 |
| dichotomy of major bacterial phyla inferred from gene arrangement comparisons. | a computer search for gene arrangements that are present in gram-positive bacteria but are absent from proteobacteria and vice versa was carried out. four such arrangements were detected, based on which major bacterial phyla were divided into two groups; thermotoga, deinococcus-thermus, chloroflexi (green non-sulfur bacteria), and fusobacteria, represent gram-positive bacterial gene arrangements, while aquifex, spirochetes, planctomycetes, chlorobi (green sulfur bacteria), bacteroides show prote ... | 2006 | 16159660 |
| the catalytic and conformational cycle of aquifex aeolicus kdo8p synthase: role of the l7 loop. | kdo8p synthase catalyzes the condensation of arabinose 5-phosphate (a5p) and phosphoenolpyruvate (pep) to form the 8-carbon sugar kdo8p and inorganic phosphate (p(i)). the x-ray structure of the wild-type enzyme shows that when both pep and a5p bind, the active site becomes isolated from the environment due to a conformational change of the l7 loop. the structures of the r106g mutant, without substrates, and with pep and pep plus a5p bound, were determined and reveal that in r106g closure of the ... | 2005 | 16156656 |
| biochemical and structural studies of a-to-i editing by trna:a34 deaminases at the wobble position of transfer rna. | initial rna transcription produces several trnas (one in prokaryotes and plant chloroplasts and seven or eight in eukaryotes) that contain an adenosine (a) at the wobble position (position 34). however, in all cases, adenosine at position 34 is post-transcriptionally converted to inosine (i), producing mature trnas without adenosine at the wobble position. the enzymes responsible for this a-to-i conversion in trna are tada (acting as a homodimer) in prokaryotes and the heterodimeric adat2-adat3 ... | 2005 | 16142903 |
| thermoglobin, oxygen-avid hemoglobin in a bacterial hyperthermophile. | the hemoglobin family of proteins, ubiquitous in all domains of life, evolved from an ancestral protein of primordial function to extant hemoglobins that perform a myriad of functions with diverged biochemical properties. study of homologs in bacterial hyperthermophiles may shed light on both mechanisms of adaptation to extreme conditions and the nature of the ancestral protein. a hemoglobin was identified in aquifex aeolicus, cloned, recombinantly expressed, purified, and characterized. this he ... | 2005 | 16135523 |
| dissecting homo-heptamer thermodynamics by isothermal titration calorimetry: entropy-driven assembly of co-chaperonin protein 10. | normally, isothermal titration calorimetry (itc) is used to study binding reactions between two different biomolecules. self-association processes leading to homo-oligomeric complexes have usually not been studied by itc; instead, methods such as spectroscopy and analytical ultracentrifugation, which only provide affinity and gibbs-free energy (i.e., k(d) and deltag), are employed. we here demonstrate that complete thermodynamic descriptions (i.e., k(d), deltag, deltah, and deltas) for self-asso ... | 2005 | 16100270 |
| crystal structure of a. aeolicus argonaute, a site-specific dna-guided endoribonuclease, provides insights into risc-mediated mrna cleavage. | argonaute (ago) proteins constitute a key component of the rna-induced silencing complex (risc). we report the crystal structure of aquifex aeolicus ago (aa-ago) together with binding and cleavage studies, which establish this eubacterial ago as a bona fide guide dna strand-mediated site-specific rna endonuclease. we have generated a stereochemically robust model of the complex, where the guide dna-mrna duplex is positioned within a basic channel spanning the bilobal interface, such that the 5' ... | 2005 | 16061186 |
| crystal structure of a bacterial homologue of na+/cl--dependent neurotransmitter transporters. | na+/cl--dependent transporters terminate synaptic transmission by using electrochemical gradients to drive the uptake of neurotransmitters, including the biogenic amines, from the synapse to the cytoplasm of neurons and glia. these transporters are the targets of therapeutic and illicit compounds, and their dysfunction has been implicated in multiple diseases of the nervous system. here we present the crystal structure of a bacterial homologue of these transporters from aquifex aeolicus, in comp ... | 2005 | 16041361 |
| unexpected elevated production of aquifex aeolicus cytochrome c555 in escherichia coli cells lacking disulfide oxidoreductases. | mutant strains of escherichia coli lacking dsba, dsbb, or dsbd (proteins required for disulfide bond formation in the periplasm) did not produce mitochondrial or chloroplast cytochromes c, as previously observed for bacterial ones. unexpectedly, however, cytochrome c(555) (aa c(555)) from a hyperthermophile, aquifex aeolicus, was produced in the e. coli periplasm without dsb proteins, three times more than with them. these results indicate that the dsb proteins are not necessarily required for a ... | 2005 | 16041151 |
| a continuous fluorimetric assay for protoporphyrinogen oxidase by monitoring porphyrin accumulation. | a continuous spectrofluorimetric assay for protoporphyrinogen oxidase (ppo, ec 1.3.3.4) activity has been developed using a 96-well plate reader. protoporphyrinogen ix, the tetrapyrrole substrate, is a colorless nonfluorescent compound. the evolution of the fluorescent tetrapyrrole product, protoporphyrin ix, was detected using a fluorescence plate reader. the apparent km (kapp) values for protoporphyrinogen ix were measured as 3.8+/-0.3, 3.6+/-0.5, and 1.0+/-0.1 microm for the enzymes from huma ... | 2005 | 16039600 |
| crystal structure of the central and c-terminal domain of the sigma(54)-activator zrar. | the sigma(54)-dependent transcription in bacteria is associated with various stress and growth conditions. activators of the sigma(54) protein contain a central domain belonging to the aaa+ superfamily of atpases, members of which function in diverse cellular processes in both prokaryotic and eukaryotic cells. we describe the x-ray structure of an n-terminal domain deletion of the zrar protein from salmonella typhimurium, which is a homologue of the general nitrogen regulatory protein ntrc, at 3 ... | 2005 | 16005641 |
| adaptation to extreme environments: macromolecular dynamics in complex systems. | what we previously thought of as insurmountable physical and chemical barriers to life, we now see as yet another niche harbouring 'extremophiles'. extremophiles and their macromolecules had to develop molecular mechanisms of adaptation to extreme physico-chemical conditions. using neutron spectroscopy, we have demonstrated that molecular dynamics represents one of these molecular mechanisms of adaptation. to which extent do hyper-saline conditions and extreme temperatures influence molecular dy ... | 2005 | 15951115 |
| crystal structure of the "phou-like" phosphate uptake regulator from aquifex aeolicus. | the phou gene of aquifex aeolicus encodes a protein called phou_aquae with sequence similarity to the phou protein of escherichia coli. despite the fact that there is a large number of family members (more than 300) attributed to almost all known bacteria and despite phou_aquae's association with the regulation of genes for phosphate metabolism, the nature of its regulatory function is not well understood. nearly one-half of these phou-like proteins, including both phou_aquae and the one from e. ... | 2005 | 15937186 |
| the plastidic dna replication enzyme complex of plasmodium falciparum. | the replication and repair of organellar genomes in the malaria parasite plasmodium falciparum is poorly understood. we have assessed the properties of an open reading frame pfprex (formerly known as pom1) and confirm that it specifies a multi-domain polypeptide with dna primase, dna helicase, dna polymerase and 3'-5' exonuclease activities. the sequence of the primase/helicase domain is phylogenetically related to the t7-bacteriophage gene 4 product and mammalian mitochondrial helicase, twinkle ... | 2005 | 15926203 |
| structural basis for lysidine formation by atp pyrophosphatase accompanied by a lysine-specific loop and a trna-recognition domain. | lysidine, a lysine-combined modified cytidine, is exclusively located at the anticodon wobble position (position 34) of eubacterial trna(ile)(2) and not only converts the codon specificity from aug to aua, but also converts the aminoacylation specificity from recognition by methionyl-trna synthetase to that by isoleucyl-trna synthetase (ilers). here, we report the crystal structure of lysidine synthetase (tils) from aquifex aeolicus at 2.42-a resolution. tils forms a homodimer, and each subunit ... | 2005 | 15894617 |
| the use of (e)- and (z)-phosphoenol-3-fluoropyruvate as mechanistic probes reveals significant differences between the active sites of kdo8p and dahp synthases. | the enzymes 3-deoxy-d-manno-2-octulosonate-8-phosphate (kdo8p) synthase and 3-deoxy-d-arabino-2-heptulosonate-7-phosphate (dahp) synthase catalyze a similar aldol-type condensation between phosphoenolpyruvate (pep) and the corresponding aldose: arabinose 5-phosphate (a5p) and erythrose 4-phosphate (e4p), respectively. while kdo8p synthase is metal-dependent in one class of organisms and metal-independent in another, only a metal-dependent class of dahp synthases has thus far been identified in n ... | 2005 | 15882071 |
| the crystal structure of a novel, latent dihydroorotase from aquifex aeolicus at 1.7a resolution. | dihydroorotases (ec 3.5.2.3) catalyze the reversible cyclization of carbamoyl aspartate to form dihydroorotate in de novo pyrimidine biosynthesis. the x-ray structures of aquifex aeolicus dihydroorotase in two space groups, c222(1) and c2, were determined at a resolution of 1.7a. these are the first structures of a type i dihydroorotase, a class of molecules that includes the dihydroorotase domain of mammalian cad. the type i enzymes are more ancient and larger, at 45 kda, than the type ii enzym ... | 2005 | 15826652 |
| experimental rnomics in aquifex aeolicus: identification of small non-coding rnas and the putative 6s rna homolog. | by an experimental rnomics approach, we have generated a cdna library from small rnas expressed from the genome of the hyperthermophilic bacterium aquifex aeolicus. the library included rnas that were antisense to mrnas and trnas as well as rnas encoded in intergenic regions. substantial steady-state levels in a.aeolicus cells were confirmed for several of the cloned rnas by northern blot analysis. the most abundant intergenic rna of the library was identified as the 6s rna homolog of a.aeolicus ... | 2005 | 15814812 |
| construction of new forms of pyruvate carboxylase to assess the allosteric regulation by acetyl-coa. | the single polypeptide chain of bacillus thermodenitrificans pyruvate carboxylase (pc) is composed of the biotin carboxylase (bc), carboxyl transferase (ct) and biotin carboxyl carrier protein (bccp) domains from the amino terminus. this polypeptide chain was divided into two between the ct and bccp domains. the resulting proteins, pc-(bc + ct) and pc-(bccp), were expressed in escherichia coli separately, purified to homogeneity and characterized. pc-(bc + ct) was 4% as active as native pc in th ... | 2005 | 15788420 |
| crystal structure of thep1 from the hyperthermophile aquifex aeolicus: a variation of the reca fold. | aathep1, the gene product of aq_1292 from aquifex aeolicus, shows sequence homology to proteins from most thermophiles, hyperthermophiles, and higher organisms such as man, mouse, and fly. in contrast, there are almost no homologous proteins in mesophilic unicellular microorganisms. aathep1 is a thermophilic enzyme exhibiting both atpase and gtpase activity in vitro. although annotated as a nucleotide kinase, such an activity could not be confirmed for aathep1 experimentally and the in vivo func ... | 2005 | 15777481 |
| leucyl-trna synthetase from the ancestral bacterium aquifex aeolicus contains relics of synthetase evolution. | the editing reactions catalyzed by aminoacyl-trna synthetases are critical for the faithful protein synthesis by correcting misactivated amino acids and misaminoacylated trnas. we report that the isolated editing domain of leucyl-trna synthetase from the deep-rooted bacterium aquifex aeolicus (alphabeta-leurs) catalyzes the hydrolytic editing of both mischarged trna(leu) and minihelix(leu). within the domain, we have identified a crucial 20-amino-acid peptide that confers editing capacity when t ... | 2005 | 15775966 |
| polyamine analysis for chemotaxonomy of thermophilic eubacteria: polyamine distribution profiles within the orders aquificales, thermotogales, thermodesulfobacteriales, thermales, thermoanaerobacteriales, clostridiales and bacillales. | cellular polyamines of 45 thermophilic and 8 related mesophilic eubacteria were investigated by hplc and gc analyses for the thermophilic and chemotaxonomic significance of polyamine distribution profiles. spermidine and a quaternary branched penta-amine, n4-bis(aminopropyl)norspermidine, were the major polyamine in thermocrinis, hydrogenobacter, hydrogenobaculum, aquifex, persephonella, sulfurihydrogenibium, hydrogenothermus, balnearium and thermovibrio, located in the order aquificales. thermo ... | 2004 | 15747232 |
| statistical criteria for the identification of protein active sites using theoretical microscopic titration curves. | theoretical microscopic titration curves (thematics) may be used to identify chemically important residues in active sites of enzymes by characteristic deviations from the normal, sigmoidal henderson-hasselbalch titration behavior. clusters of such deviant residues in physical proximity constitute reliable predictors of the location of the active site. originally the residues with deviant predicted behavior were identified by human observation of the computed titration curves. however, it is pre ... | 2005 | 15739204 |
| histone deacetylase 1: a target of 9-hydroxystearic acid in the inhibition of cell growth in human colon cancer. | recent studies have shown that an endogenous lipoperoxidation product, 9-hydroxystearic acid (9-hsa), acts in colon carcinoma cells (ht29) as a growth inhibitor by inducing p21(waf1) in an immediate-early, p53-independent manner and that p21(waf1) is required for 9-hsa-mediated growth arrest in ht29 cells. it is conceivable, therefore, to hypothesize that the cytostatic effect induced by this agent is at least partially associated with a molecular mechanism that involves histone deacetylase 1 (h ... | 2005 | 15716589 |
| udp-3-o-((r)-3-hydroxymyristoyl)-n-acetylglucosamine deacetylase functions through a general acid-base catalyst pair mechanism. | udp-3-o-((r)-3-hydroxymyristoyl)-n-acetylglucosamine deacetylase (lpxc) is a zinc-dependent enzyme that catalyzes the deacetylation of udp-3-o-((r)-3-hydroxymyristoyl)-n-acetylglucosamine to form udp-3-o-(r-hydroxymyristoyl)glucosamine and acetate. the structural similarity of the active site of lpxc to metalloproteases led to the proposal that lpxc functions via a metalloprotease-like mechanism. the ph dependence of k(cat)/km catalyzed by escherichia coli and aquifex aeolicus lpxc displayed a b ... | 2005 | 15705580 |
| crystal structure of trna adenosine deaminase (tada) from aquifex aeolicus. | the bacterial trna adenosine deaminase (tada) generates inosine by deaminating the adenosine residue at the wobble position of trna(arg-2). this modification is essential for the decoding system. in this study, we determined the crystal structure of aquifex aeolicus tada at a 1.8-a resolution. this is the first structure of a deaminase acting on trna. a. aeolicus tada has an alpha/beta/alpha three-layered fold and forms a homodimer. the a. aeolicus tada dimeric structure is completely different ... | 2005 | 15677468 |
| hydrogen metabolism in the hyperthermophilic bacterium aquifex aeolicus. | aquifex aeolicus is a microaerophilic, hydrogen-oxidizing, hyperthermophilic bacterium containing three [nife] hydrogenases. two of these three enzymes (one membrane-bound and one soluble) have been purified and characterized. the aquifex hydrogenases are thermostable and tolerant to oxygen. a cellular function for the three hydrogenases has been proposed. the two membrane-bound periplasmic hydrogenases may function in energy conservation, whereas the soluble cytoplasmic hydrogenase is probably ... | 2005 | 15667254 |
| refined solution structure of the lpxc-tu-514 complex and pka analysis of an active site histidine: insights into the mechanism and inhibitor design. | lipopolysaccharide, the major constituent of the outer monolayer of the outer membrane of gram-negative bacteria, is anchored into the membrane through the hydrophobic moiety lipid a, a hexaacylated disaccharide. the zinc-dependent metalloamidase udp-3-o-acyl-n-acetylglucosamine deacetylase (lpxc) catalyzes the second and committed step in the biosynthesis of lipid a. lpxc shows no homology to mammalian metalloamidases and is essential for cell viability, making it an important target for the de ... | 2005 | 15667205 |
| kinetic analysis of the zinc-dependent deacetylase in the lipid a biosynthetic pathway. | the first committed step of lipid a biosynthesis in gram-negative bacteria is catalyzed by the zinc-dependent hydrolase lpxc that removes an acetate from the nitrogen at the 2' '-position of udp-3-o-acyl-n-acetylglucosamine. recent structural characterization by both nmr and x-ray crystallography provides many important details about the active site environment of lpxc from aquifex aeolicus, a heat-stable orthologue that displays 32% sequence identity to lpxc from escherichia coli. the detailed ... | 2005 | 15667204 |
| breaking sieve for steric exclusion of a noncognate amino acid from active site of a trna synthetase. | the genetic code is fixed in aminoacylation reactions catalyzed by aminoacyl-trna synthetases. amino acid discrimination occurs at two sites: one for amino acid activation and aminoacylation and one for editing misactivated amino acids. although the active site sieves out bulkier amino acids, misactivation occurs with substrates whose side chains are smaller than the cognate one. paradoxically, although alanyl-trna synthetase activates glycine as well as alanine, the sterically larger (than alan ... | 2005 | 15657145 |
| nmr structure of hi0004, a putative essential gene product from haemophilus influenzae, and comparison with the x-ray structure of an aquifex aeolicus homolog. | the solution structure of the 154-residue conserved hypothetical protein hi0004 has been determined using multidimensional heteronuclear nmr spectroscopy. hi0004 has sequence homologs in many organisms ranging from bacteria to humans and is believed to be essential in haemophilus influenzae, although an exact function has yet to be defined. it has a alpha-beta-alpha sandwich architecture consisting of a central four-stranded beta-sheet with the alpha2-helix packed against one side of the beta-sh ... | 2005 | 15632286 |
| functional dissection of a conserved motif within the pilus retraction protein pilt. | pilt is a hexameric atpase required for type iv pilus retraction in gram-negative bacteria. retraction of type iv pili mediates intimate attachment to and signaling in host cells, surface motility, biofilm formation, natural transformation, and phage sensitivity. we investigated the in vivo and in vitro roles of each amino acid of the distinct, highly conserved c-terminal airnlire motif in pilt. substitution of amino acids a288, i289, l292, and i293 as well as a double substitution of r290 and r ... | 2005 | 15629932 |
| characterization of aquifex aeolicus rnase e/g. | the rnase e/g homologue from the thermophilic eubacterium aquifex aeolicus has been overexpressed in escherichia coli, purified, and characterized in vitro. we show that a. aeolicus rnase e/g has a temperature-dependent, endoribonucleolytic activity. the enzyme site-specifically cleaves oligonucleotides and structured rnas at locations that are partly overlapping or completely different when compared to the positions of e. coli rnase e and rnase g cleavage sites. the efficiency of cleavage by a. ... | 2005 | 15629127 |
| heterologous expression of aquifex aeolicus ribosome recycling factor in escherichia coli is dominant lethal by forming a complex that lacks functional co-ordination for ribosome disassembly. | recycling the post-termination ribosomal complex requires the co-ordinated effort of the ribosome, ribosome recycling factor (rrf) and elongation factor ef-g. although aquifex aeolicus rrf (aarrf) binds escherichia coli ribosomes as efficiently as e. coli rrf, the resulting complex is non-functional and dominant lethal in e. coli, even in the presence of homologous a. aeolicus ef-g. these findings suggest that the e. coli post-termination ribosomal complex with aarrf lacks functional co-ordinati ... | 2005 | 15612924 |
| mitochondrial cytochrome c1 is a collapsed di-heme cytochrome. | cytochrome c(1) from mitochondrial complex iii and the di-heme cytochromes c in the corresponding enzyme from epsilon-proteobacteria have so far been considered to represent unrelated cytochromes. a missing link protein discovered in the genome of the hyperthermophilic bacterium aquifex aeolicus, however, provides evidence for a close evolutionary relationship between these two cytochromes. the mono-heme cytochrome c(1) from a. aeolicus contains stretches of strong sequence homology toward the e ... | 2004 | 15591339 |
| direct demonstration of carbamoyl phosphate formation on the c-terminal domain of carbamoyl phosphate synthetase. | carbamoyl phosphate synthetase synchronizes the utilization of two atp molecules at duplicated atp-grasp folds to catalyze carbamoyl phosphate formation. to define the dedicated functional role played by each of the two atp sites, we have carried out pulse/labeling studies using the synthetases from aquifex aeolicus and methanococcus jannaschii, hyperthermophilic organisms that encode the two atp-grasp folds on separate subunits. these studies allowed us to differentially label each active site ... | 2004 | 15576558 |
| conservation of recg activity from pathogens to hyperthermophiles. | maintaining the integrity of the genome is essential for the survival of all organisms. recg helicase plays an important part in this process in escherichia coli, promoting recombination and dna repair, and providing ways to rescue stalled replication forks by way of a holliday junction intermediate. we purified recg proteins from three other species: two gram-positive mesophiles, bacillus subtilis and streptococcus pneumoniae, and one extreme thermophile, aquifex aeolicus. all three proteins bi ... | 2005 | 15533834 |
| crystallization and preliminary x-ray diffraction studies of a protein disulfide oxidoreductase from aquifex aeolicus. | a protein disulfide oxidoreductase from the thermophilic bacterium aquifex aeolicus has been overexpressed in escherichia coli and crystallized at 298 k using the hanging-drop vapour-diffusion method. crystals belong to space group r32, with unit-cell parameters a = b = 161.1, c = 153.1 a. a complete data set has been collected to 2.4 a using synchrotron radiation. packing-density considerations agree with the presence of 2-4 monomers in the asymmetric unit, with a corresponding solvent content ... | 2004 | 15502332 |
| cloning, expression, purification, crystallization and preliminary x-ray characterization of the full-length single-stranded dna-binding protein from the hyperthermophilic bacterium aquifex aeolicus. | single-stranded dna-binding (ssb) proteins stabilize single-stranded dna, which is exposed by separation of the duplex during dna replication, recombination and repair. the ssb protein from the hyperthermophile aquifex aeolicus has been overexpressed in escherichia coli, purified and characterized and crystals of the full-length protein (147 amino acids; m(r) 17 131.20) have been grown by vapour diffusion from ammonium sulfate ph 7.5 in both the absence and presence of ssdna [dt(pt)(68)]. all cr ... | 2004 | 15502311 |
| mutational analysis of the nuclease domain of escherichia coli ribonuclease iii. identification of conserved acidic residues that are important for catalytic function in vitro. | the ribonuclease iii superfamily represents a structurally distinct group of double-strand-specific endonucleases with essential roles in rna maturation, rna decay, and gene silencing. bacterial rnase iii orthologs exhibit the simplest structures, with an n-terminal nuclease domain and a c-terminal double-stranded rna-binding domain (dsrbd), and are active as homodimers. the nuclease domain contains conserved acidic amino acids, which in escherichia coli rnase iii are e38, e41, d45, e65, e100, d ... | 2004 | 15476399 |
| a challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy? | we assess the use to which bioinformatics in the form of bacterial genome sequences, functional gene probes and the protein sequence databases can be applied to hypotheses about obligate autotrophy in eubacteria. obligate methanotrophy and obligate autotrophy among the chemo- and photo-lithotrophic bacteria lack satisfactory explanation a century or more after their discovery. various causes of these phenomena have been suggested, which we review in the light of the information currently availab ... | 2004 | 15449607 |
| aquifex aeolicus dihydroorotase: association with aspartate transcarbamoylase switches on catalytic activity. | dihydroorotase (dhoase) catalyzes the reversible condensation of carbamoyl aspartate to form dihydroorotate in de novo pyrimidine biosynthesis. the enzyme from aquifex aeolicus, a hyperthermophilic organism of ancient lineage, was cloned and expressed in escherichia coli. the purified protein was found to be a 45-kda monomer containing a single zinc ion. although there is no other dhoase gene in the a. aeolicus genome, the recombinant protein completely lacked catalytic activity at any temperatu ... | 2004 | 15381710 |
| unique biosynthesis of dehydroquinic acid? | a search of the genomic sequences of the thermophilic microorganisms aquifex aeolicus, archaeoglobus fulgidus, methanobacterium thermoautotrophicum, and methanococcus jannaschii for the first seven enzymes (arog, b, d, e, k, a, and c ) involved in the shikimic acid biosynthetic pathway reveal two key enzymes are missing. the first enzyme in the pathway, 3-deoxy-d-arabino-heptulosonic acid 7-phosphate synthase (arog) and the second enzyme in the pathway, 5-dehydroquinic acid synthase (arob) are " ... | 2004 | 15381397 |
| the box vii motif of escherichia coli dnaa protein is required for dnaa oligomerization at the e. coli replication origin. | escherichia coli dnaa protein initiates dna replication from the chromosomal origin, oric, and regulates the frequency of this process. structure-function studies indicate that the replication initiator comprises four domains. based on the structural similarity of aquifex aeolicus dnaa to other aaa+ proteins that are oligomeric, it was proposed that domain iii functions in oligomerization at oric (erzberger, j. p., pirruccello, m. m., and berger, j. m. (2002) embo j. 21, 4763-4773). because the ... | 2004 | 15371441 |
| substrate trna recognition mechanism of trna (m7g46) methyltransferase from aquifex aeolicus. | transfer rna (m7g46) methyltransferase catalyzes the methyl transfer from s-adenosylmethionine to n7 atom of the guanine 46 residue in trna. analysis of the aquifex aeolicus genome revealed one candidate open reading frame, aq065, encoding this gene. the aq065 protein was expressed in escherichia coli and purified to homogeneity on 15% sds-polyacrylamide gel electrophoresis. although the overall amino acid sequence of the aq065 protein differs considerably from that of e. coli yggh, the purified ... | 2004 | 15358762 |
| investigation on the causes of codon and amino acid usages variation between thermophilic aquifex aeolicus and mesophilic bacillus subtilis. | base composition, codon usages and amino acid usages have been analyzed by taking 529 orthologous sequences of aquifex aeolicus and bacillus subtilis, having different optimal growth temperatures. these two bacteria do not have significant difference in overall gc composition, but gc(1+2) and gc3 levels were found to vary significantly. significant increments in purine content and gc3 composition have been observed in the coding sequences of aquifex aeolicus than its bacillus subtilis counterpar ... | 2004 | 15317481 |
| a reciprocal single mutation affects the metal requirement of 3-deoxy-d-manno-2-octulosonate-8-phosphate (kdo8p) synthases from aquifex pyrophilus and escherichia coli. | the enzyme 3-deoxy-d-manno-2-octulosonate-8-phosphate (kdo8p) synthase is metal-dependent in one class of organisms and metal-independent in another. we have used a rapid transient kinetic approach combined with site-directed mutagenesis to characterize the role of the metal ion as well as to explore the catalytic mechanisms of the two classes of enzymes. in the metal-dependent aquifex pyrophilus kdo8p synthase, cys11 was replaced by asn (apc11n), and in the metal-independent escherichia coli kd ... | 2004 | 15308670 |
| structural basis for template-independent rna polymerization. | the 3'-terminal cca nucleotide sequence (positions 74-76) of transfer rna is essential for amino acid attachment and interaction with the ribosome during protein synthesis. the cca sequence is synthesized de novo and/or repaired by a template-independent rna polymerase, 'cca-adding enzyme', using ctp and atp as substrates. despite structural and biochemical studies, the mechanism by which the cca-adding enzyme synthesizes the defined sequence without a nucleic acid template remains elusive. here ... | 2004 | 15295603 |
| multiple substrate binding states and chiral recognition in cofactor-independent glutamate racemase: a molecular dynamics study. | glutamate racemase (muri) catalyzes the racemization of glutamate; two cysteine residues serve as catalytic acid and base. on the basis of the crystal structure of muri from the hyperthermophilic bacterium aquifex pyrophilus, we performed molecular dynamics (md) simulations of six different systems to investigate stereochemistry, substrate ligation, and active site protonation state. the catalytic competence of individual systems was assessed by the abundance of reactive conformers. only systems ... | 2004 | 15274623 |
| structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family. | exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (ppx/gppa) enzymes play central roles in the bacterial stringent response induced by starvation. the high-resolution crystal structure of the putative aquifex aeolicus ppx/gppa phosphatase from the actin-like atpase domain superfamily has been determined, providing the first insights to features of the common catalytic core of the ppx/gppa family. the protein has a two-domain structure with an active site located in the interdomain cle ... | 2004 | 15248747 |
| single processing center models for human dicer and bacterial rnase iii. | dicer is a multidomain ribonuclease that processes double-stranded rnas (dsrnas) to 21 nt small interfering rnas (sirnas) during rna interference, and excises micrornas from precursor hairpins. dicer contains two domains related to the bacterial dsrna-specific endonuclease, rnase iii, which is known to function as a homodimer. based on an x-ray structure of the aquifex aeolicus rnase iii, models of the enzyme interaction with dsrna, and its cleavage at two composite catalytic centers, have been ... | 2004 | 15242644 |
| general stress protein ctc from bacillus subtilis specifically binds to ribosomal 5s rna. | two recombinant proteins of the ctc family were prepared: the general stress protein ctc from bacillus subtilis and its homolog from aquifex aeolicus. the general stress protein ctc from b. subtilis forms a specific complex with 5s rrna and its stable fragment of 60 nucleotides, which contains internal loop e. the ribosomal protein tl5 from thermus thermophilus, which binds with high affinity to 5s rrna in the loop e region, was also shown to replace the ctc protein from b. subtilis in its compl ... | 2004 | 15236599 |
| a genomic perspective on the relationship between the aquificales and the epsilon-proteobacteria. | the goal of this study was to determine to what extent the aquificales are related to the epsilon-proteobacteria. the genome sequence of several members of this group as well as the genome sequence of aquifex aeolicus are available. in this study we used information extracted from those whole-genome sequences to gain further insights into the relationships between these organisms, including the fraction of shared putative orthologous protein-encoding genes, dinucleotide relative abundance values ... | 2004 | 15214637 |
| two distinct domains of the beta subunit of aquifex aeolicus leucyl-trna synthetase are involved in trna binding as revealed by a three-hybrid selection. | the aquifex aeolicus alphabeta-leurs is the only known heterodimeric class ia aminoacyl-trna synthetase. in this study, we investigated the function of the beta subunit which is believed to bind trna(leu). a yeast three-hybrid system was constructed on the basis of the interaction of the beta subunit with its cognate trna(leu). then, seven mutated beta subunits exhibiting impaired trna binding capacities were selected out from a randomly mutated library. two mutations were identified in the clas ... | 2004 | 15208367 |
| conversion of aquifex aeolicus 3-deoxy-d-manno-octulosonate 8-phosphate synthase, a metalloenzyme, into a nonmetalloenzyme. | the aquifex aeolicus 3-deoxy-d-manno-octulosonate 8-phosphate synthase (kdo8ps), a class ii metalloenzyme, is converted into an active nonmetalloenzyme by a single amino acid mutation, namely, c11n. the result may provide insight into the evolutionary link between the two kdo8ps classes as well as the potential role of the metal and/or asparagine in the catalytic mechanism. | 2004 | 15198585 |
| formation of linear three-iron clusters in aquifex aeolicus two-iron ferredoxins: effect of protein-unfolding speed. | the presence of a linear [3fe-4s] cluster in a protein was first observed in beef-heart aconitase. here, we report the formation of linear [3fe-4s] clusters upon guanidine hydrochloride (guhcl)-induced unfolding of aquifex aeolicus [2fe-2s] ferredoxins (fd) (aaefd1, aaefd4, and aaefd5) at alkaline conditions (ph 10, 20 degrees c). we find the mechanism of linear [3fe-4s] cluster formation to depend critically on the speed of polypeptide unfolding. in similarity to seven-iron fds, polypeptide unf ... | 2004 | 15196989 |
| evolution of bacterial rna polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. | comparative analysis of the domain architectures of the beta, beta', and sigma(70) subunits of bacterial dna-dependent rna polymerases (ddrp), combined with sequence-based phylogenetic analysis, revealed a fundamental split among bacteria. dna-dependent rna polymerase subunits of group i, which includes proteobacteria, aquifex, chlamydia, spirochaetes, cytophaga-chlorobium, and planctomycetes, are characterized by three distinct inserts, namely a sandwich barrel hybrid motif domain in the beta s ... | 2004 | 15194191 |
| high-level expression and single-step purification of leucyl-trna synthetase from aquifex aeolicus. | aquifex aeolicus leucyl-trna synthetase is the only known heterodimeric leurs, consisting of two subunits with molecular masses of 74.0 and 33.5 kda, and named alphabeta-leurs. the gene encoding alpha subunit was cloned into psbet-b vector. synthetic oligonucleotide encoding six histidine residues was also inserted in front of alpha subunit. psbet-b vector contains argu gene, which encodes a rare escherichia coli trna(arg)(aga/agg). the argu gene helps a. aeolicus leurs, which contains aga/agg c ... | 2004 | 15177296 |
| designing a metal-binding site in the scaffold of escherichia coli kdo8ps. | kdo8ps (3-deoxy-d-manno-octulosonate-8-phosphate synthase) and dah7ps (3-deoxy-d-arabino-heptulosonic acid-7-phosphate synthase) enzymes catalyse analogous condensation reactions between phosphoenolpyruvate and arabinose 5-phosphate or erythrose 4-phosphate, respectively. all known dah7ps and some of kdo8ps enzymes (aquifex aeolicus kdo8ps) require a metal ion for activity whereas another class of kdo8ps (including escherichia coli kdo8ps) does not. based on sequence alignment of all known kdo8p ... | 2004 | 15166313 |
| leucyl-trna synthetase from the hyperthermophilic bacterium aquifex aeolicus recognizes minihelices. | aminoacylation of the minihelix mimicking the amino acid acceptor arm of trna has been demonstrated in more than 10 aminoacyl-trna synthetase systems. although escherichia coli or homo sapiens cytoplasmic leucyl-trna synthetase (leurs) is unable to charge the cognate minihelix or microhelix, we show here that minihelix(leu) is efficiently charged by aquifex aeolicus synthetase, the only known heterodimeric leurs (alpha beta-leurs). aminoacylation of minihelices is strongly dependent on the prese ... | 2004 | 15161932 |
| evaluation of the phylogenetic position of the planctomycete 'rhodopirellula baltica' sh 1 by means of concatenated ribosomal protein sequences, dna-directed rna polymerase subunit sequences and whole genome trees. | in recent years, the planctomycetes have been recognized as a phylum of environmentally important bacteria with habitats ranging from soil and freshwater to marine ecosystems. the planctomycetes form an independent phylum within the bacterial domain, whose exact phylogenetic position remains controversial. with the completion of sequencing of the genome of 'rhodopirellula baltica' sh 1, it is now possible to re-evaluate the phylogeny of the planctomycetes based on multiple genes and genome trees ... | 2004 | 15143026 |
| the pilus-retraction protein pilt: ultrastructure of the biological assembly. | pilt is a biological motor required for the retraction of bacterial type iv pili. nesseria gonorrhoeae pilt has been purified and its ultrastructure has been examined by freeze-etch electron microscopy, revealing a 115 a outer diameter, 15-35 a inner diameter ring. aquifex aeolicus pilt crystals were obtained in a primitive hexagonal space group (unit-cell parameters a = b = 107.3, c = 68.5 a) and diffract to a minimum bragg spacing of 2.8 a when pilt is co-crystallized with adenine nucleotides. ... | 2004 | 15103158 |
| positional recognition of a trna determinant dependent on a peptide insertion. | the crystal structure of a catalytic fragment of aquifex aeolicus alars and additional data suggest how the critical g3:u70 identity element of its cognate trna acceptor stem is recognized. though this identity element is conserved from bacteria to the cytoplasm of eukaryotes, drosophila melanogaster mitochondrial (dm mt) trna(ala) contains a g:u base pair that has been translocated to the adjacent 2:71 position. this g2:u71 is the major determinant for identity of dm mt trna(ala). sequence alig ... | 2004 | 15053877 |
| alanyl-trna synthetase crystal structure and design for acceptor-stem recognition. | early work on aminoacylation of alanine-specific trna (trna(ala)) by alanyl-trna synthetase (alars) gave rise to the concept of an early "second genetic code" imbedded in the acceptor stems of trnas. a single conserved and position-specific g:u base pair in the trna acceptor stem is the key identity determinant. further understanding has been limited due to lack of a crystal structure of the enzyme. we determined a 2.14 a crystal structure of the 453 amino acid catalytic fragment of aquifex aeol ... | 2004 | 15053876 |
| first characterization of co-chaperonin protein 10 from hyper-thermophilic aquifex aeolicus. | all known co-chaperonin protein 10 (cpn10) molecules are heptamers of seven identical subunits that are linked together by beta-strand interactions. here, we report the first characterization of a cpn10 protein from a thermophilic organism: aquifex aeolicus. primary-structure alignment of a. aeolicus cpn10 (aaecpn10) shows high homology with mesophilic cpn10 sequences, except for a unique 25-residue c-terminal extension not found in any other cpn10. recombinant aaecpn10 adopts a heptameric struc ... | 2004 | 15047164 |
| noncatalytic assembly of ribonuclease iii with double-stranded rna. | ribonuclease iii (rnase iii) represents a family of double-stranded rna (dsrna) endonucleases. the simplest bacterial enzyme contains an endonuclease domain (endond) and a dsrna binding domain (dsrbd). rnase iii can affect rna structure and gene expression in either of two ways: as a dsrna-processing enzyme that cleaves dsrna, or as a dsrna binding protein that binds but does not cleave dsrna. we previously determined the endond structure of aquifex aeolicus rnase iii (aa-rnase iii) and modeled ... | 2004 | 15016361 |
| nmr structure of the hypothetical protein aq-1857 encoded by the y157 gene from aquifex aeolicus reveals a novel protein fold. | 2004 | 14997575 | |
| structure of the biotin carboxylase subunit of pyruvate carboxylase from aquifex aeolicus at 2.2 a resolution. | pyruvate carboxylase (pc) is distributed in many eukaryotes as well as in some prokaryotes. pc catalyzes the atp-dependent carboxylation of pyruvate to form oxalacetate. pc has three functional domains, one of which is a biotin carboxylase (bc) domain. the bc subunit of pc from aquifex aeolicus (pc-beta) was crystallized in an orthorhombic form with space group p2(1)2(1)2, unit-cell parameters a = 92.4, b = 122.1, c = 59.0 a and one molecule in the asymmetric unit. diffraction data were collecte ... | 2004 | 14993673 |
| assignment of the 1h, 13c and 15n resonances of the lpxc deacetylase from aquifex aeolicus in complex with the substrate-analog inhibitor tu-514. | 2004 | 14755169 | |
| crystal structure of chorismate synthase from aquifex aeolicus reveals a novel beta alpha beta sandwich topology. | 2004 | 14705034 | |
| probing the role of metal ions in the catalysis of helicobacter pylori 3-deoxy-d-manno-octulosonate-8-phosphate synthase using a transient kinetic analysis. | 3-deoxy-d-manno-2-octulosonate-8-phosphate (kdo8p) synthase catalyzes the net condensation of phosphoenolpyruvate and d-arabinose 5-phosphate to form kdo8p and inorganic phosphate (pi). two classes of kdo8p synthases have been identified. the class i kdo8p synthases (e.g. escherchia coli kdo8p synthase) catalyze the condensation reaction in a metal-independent fashion, whereas the class ii enzymes (e.g. aquifex aeolicus) require metal ions for catalysis. helicobacter pylori (h. pylori) kdo8p syn ... | 2004 | 14701842 |
| molecular characterization of community structures and sulfur metabolism within microbial streamers in japanese hot springs. | community structures of submerged microbial slime streamers (smss) in sulfide-containing hot springs at 72 to 80 degrees c at nakabusa and yumata, japan, were investigated by molecular analysis based on the 16s rrna gene. the smss were classified into two consortia; consortium i occurred at lower levels of sulfide in the hot springs (less than 0.1 mm), and consortium ii dominated when the sulfide levels were higher (more than 0.1 mm). the dominant cell morphotypes in consortium i were filamentou ... | 2003 | 14660348 |
| amperometric sensing at high temperature with a "wired" thermostable glucose-6-phosphate dehydrogenase from aquifex aeolicus. | an amperometric enzyme sensor capable of operating at high temperatures was developed by utilizing a "wired" thermostable glucose-6-phosphate dehydrogenase (tg6pdh) from the hyperthermophilic bacterium aquifex aeolicus. the response of the system was monitored through detection of the product of the enzymatic reaction, nadh, which was electrocatalytically reoxidized to nad by a thermostable redox mediator, osmium (1,10-phenanthroline-5,6-dione)2-poly(4-vinylpyridine), at eapp = +150 mvvs ag/agcl ... | 2003 | 14572059 |
| regulation of the transcriptional activator ntrc1: structural studies of the regulatory and aaa+ atpase domains. | transcription by sigma54 rna polymerase depends on activators that contain atpase domains of the aaa+ class. these activators, which are often response regulators of two-component signal transduction systems, remodel the polymerase so that it can form open complexes at promoters. here, we report the first crystal structures of the atpase domain of an activator, the ntrc1 protein from the extreme thermophile aquifex aeolicus. this domain alone, which is active, crystallized as a ring-shaped hepta ... | 2003 | 14561776 |
| aquifex aeolicus aspartate transcarbamoylase, an enzyme specialized for the efficient utilization of unstable carbamoyl phosphate at elevated temperature. | aquifex aeolicus, an organism that flourishes at 95 degrees c, is one of the most thermophilic eubacteria thus far described. the a. aeolicus pyrb gene encoding aspartate transcarbamoylase (atcase) was cloned, overexpressed in escherichia coli, and purified by affinity chromatography to a homogeneous form that could be crystallized. chemical cross-linking and size exclusion chromatography showed that the protein was a homotrimer of 34-kda catalytic chains. the activity of a. aeolicus atcase incr ... | 2003 | 14534296 |
| crystal structure of trna (m1g37) methyltransferase from aquifex aeolicus at 2.6 a resolution: a novel methyltransferase fold. | 2003 | 14517984 | |
| thermophile-specific proteins: the gene product of aq_1292 from aquifex aeolicus is an ntpase. | to identify thermophile-specific proteins, we performed phylogenetic patterns searches of 66 completely sequenced microbial genomes. this analysis revealed a cluster of orthologous groups (cog1618) which contains a protein from every thermophile and no sequence from 52 out of 53 mesophilic genomes. thus, cog1618 proteins belong to the group of thermophile-specific proteins (theps) and therefore we here designate cog1618 proteins as thep1s. since no thep1 had been analyzed biochemically thus far, ... | 2003 | 14503925 |
| ab initio study of the binding of trichostatin a (tsa) in the active site of histone deacetylase like protein (hdlp). | histone deacetylase (hdac) inhibitors have recently attracted considerable interest because of their therapeutic potential for the treatment of cell proliferative diseases. an x-ray structure of a very potent inhibitor, trichostatin a (tsa), bound to hdlp (an hdac analogue isolated from aquifex aeolicus), is available. from this structure, an active site model (322 atoms), relevant for the binding of tsa and structural analogues, has been derived, and tsa has been minimized in this active site a ... | 2003 | 12968347 |
| the naphthoquinol oxidizing cytochrome bc1 complex of the hyperthermophilic knallgasbacterium aquifex aeolicus: properties and phylogenetic relationships. | phylogenetic analysis of constituent proteins of rieske/cytochrome b complexes [schütz et al. (2000) j. mol. biol. 300, 663-675] indicated that the respective enzyme from the hyperthermophile aquifex (a.) aeolicus is closely related to proteobacterial counterparts, in disagreement with positioning of its parent species on small subunit rrna trees. an assessment of the details and possible reasons for this discrepancy necessitates a thorough understanding of the biochemical and biophysical proper ... | 2003 | 12962505 |
| similar modes of polypeptide recognition by export chaperones in flagellar biosynthesis and type iii secretion. | assembly of the bacterial flagellum and type iii secretion in pathogenic bacteria require cytosolic export chaperones that interact with mobile components to facilitate their secretion. although their amino acid sequences are not conserved, the structures of several type iii secretion chaperones revealed striking similarities between their folds and modes of substrate recognition. here, we report the first crystallographic structure of a flagellar export chaperone, aquifex aeolicus flis. flis ad ... | 2003 | 12958592 |
| cloning, expression, and biochemical characterization of 3-deoxy-d-manno-2-octulosonate-8-phosphate (kdo8p) synthase from the hyperthermophilic bacterium aquifex pyrophilus. | 3-deoxy-d-manno-2-octulosonate-8-phosphate (kdo8p) synthase, catalyzes the aldol-type condensation between phosphoenolpyruvate (pep) and d-arabinose-5-phosphate (a5p) to produce the unusual 8-carbon sugar kdo8p, and inorganic phosphate. a 15.5-kb segment containing the kdsa gene from the hyperthermophilic bacterium aquifex pyrophilus was cloned from a genomic library and sequenced. the native kdsa gene lacks a typical ribosome binding site, but contains a conserved u,a-rich sequence upstream to ... | 2003 | 12955602 |
| identification of aquifex aeolicus trna (m2(2g26) methyltransferase gene. | the modifications of n2,n2-dimethylguanine (m2(2)g) are found in trnas and rrnas from eukarya and archaea. in trnas, modification at position g26 is generated by trna (m2(2)g26) methyltransferase, which is encoded by the corresponding gene, trm1. this enzyme catalyzes the methyl-transfer from s-adenosyl-l-methionine to the semi-conserved residue, g26, via the intermediate modified base, m2g26. recent genome sequencing project has been reported that the putative trm1 is encoded in the genome of a ... | 2002 | 12903189 |
| alkylation damage repair protein o6-alkylguanine-dna alkyltransferase from the hyperthermophiles aquifex aeolicus and archaeoglobus fulgidus. | agt (o6-alkylguanine dna alkyltransferase) is an important dna-repair protein that protects cells from killing and mutagenesis by alkylating agents. the agt genes from two extremely thermophilic organisms, the bacterium aquifex aeolicus and the archaeon archaeoglobus fulgidus were pcr-derived and cloned into an expression vector. the nucleotide sequence of the aq. aeolicus agt encodes a 201-amino-acid protein with a molecular mass of 23000 da and ar. fulgidus agt codes for a 147-amino-acid prote ... | 2003 | 12892560 |
| the trna-like domains of e coli and a.aeolicus transfer-messenger rna: structural and functional studies. | transfer-messenger rna (tmrna, 10sa rna or ssra) acts to rescue stalled bacterial ribosomes while encoding a peptide tag added trans-translationally to the nascent peptide, targeting it for proteolysis. the understanding at molecular level of this ubiquitous quality control system in eubacteria requires structural information. here, we describe the purification and structural analysis of a functional fragment of both aquifex aeolicus and escherichia coli tmrna, recapitulating their trna-like dom ... | 2003 | 12888352 |
| temperature-dependent presteady state kinetics of lumazine synthase from the hyperthermophilic eubacterium aquifex aeolicus. | 6,7-dimethyl-8-ribityllumazine synthase (lumazine synthase) catalyzes the condensation of 5-amino-6-ribitylamino-2,4(1h,3h)-pyrimidinedione and 3,4-dihydroxy-2-butanone 4-phosphate. presteady state kinetic experiments using the enzyme from the hyperthermophilic bacterium aquifex aeolicus were monitored by multiwavelength photometry. an early optical transient absorbing around 330 nm is interpreted as a schiff base intermediate obtained by reaction of the position 5 amino group of the heterocycli ... | 2003 | 12867427 |