Publications

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
the slc6 orphans are forming a family of amino acid transporters.	transporters in the human genome are grouped in solute carrier families (slc). the slc6 family is one of the biggest transporter families in the human genome comprising 20 members. it is usually referred to as the neurotransmitter transporter family because its founding members encode transporters for the neurotransmitters gaba, noradrenaline, serotonin and dopamine. the family also includes a number of 'orphan' transporters, the function of which has remained elusive until recently. identificat ...	2006	16540203
getting the message across: a recent transporter structure shows the way.	efforts to define the mechanisms governing neurotransmitter uptake and drug action have moved into high gear with the publication of a high-resolution structure of a leucine transporter from aquifex aeolicus, a bacterial member of the slc6 transporter family. solved with the substrate leucine bound, the new structure corroborates extensive biochemical and mutagenesis studies performed with related mammalian neurotransmitter transporters and provides exciting suggestions as to how coupling arises ...	2006	16543127
a simple tagging system for protein encapsulation.	molecular containers that encapsulate specific cargo can be useful for many natural and non-natural processes. we report a simple system, based on charge complementarity, for the encapsulation of appropriately tagged proteins within an engineered, proteinaceous capsid. four negative charges per monomer were added to the lumazine synthase from aquifex aeolicus (aals). the capsids formed by the engineered aals associate with green fluorescent protein bearing a positively charged deca-arginine tag ...	2006	16594656
nmr structure of the aquifex aeolicus tmrna pseudoknot pk1: new insights into the recoding event of the ribosomal trans-translation.	the transfer-messenger rna (tmrna) pseudoknot pk1 is essential for bacterial trans-translation, a ribosomal rescue mechanism. we report the solution structure of pk1 from aquifex aeolicus, which despite an unprecedented small number of nucleotides and thus an unprecented compact size, displays a very high thermal stability. several unusual structural features account for these properties and indicate that pk1 belongs to the class of ribosomal frameshift pseudoknots. this suggests a similarity be ...	2006	16595798
structural and functional studies of the response regulator hupr.	hupr is a response regulator that controls the synthesis of the membrane-bound [nife]hydrogenase of the photosynthetic bacterium rhodobacter capsulatus. the protein belongs to the ntrc subfamily of response regulators and is the second protein of a two-component system. we have crystallized the full-length protein hupr in the unphosphorylated state in two dimensions using the lipid monolayer technique. the 3d structure of negatively stained hupr was calculated to a resolution of approximately 23 ...	2006	16631791
flgm anti-sigma factors: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships.	flgm proteins, also known as anti-sigma-28 factor (sigma28), are negative regulators of flagellin synthesis. recently, a three-dimensional structure of the aquifex aeolicus sigma28/flgm complex (pdb code: 1rp3) was determined by x-ray crystallography at 2.3 a resolution. furthermore, experimental data on bacterial flgm, including site-directed mutagenesis and structural characterization by nmr are also available. however, an interpretation of the sequence-structure-function relationships combini ...	2006	16673084
the structure of the exopolyphosphatase (ppx) from escherichia coli o157:h7 suggests a binding mode for long polyphosphate chains.	polyphosphate (polyp) is a linear polymer consisting of tens to hundreds of phosphate molecules joined together by high-energy anhydride bonds. these polymers are found in virtually all prokaryotic and eukaryotic cells and perform many functions; prominent among them are the responses to many stresses. polyphosphate is synthesized by polyp kinase (ppk), using the terminal phosphate of atp as the substrate, and degraded to inorganic phosphate by both endo- and exopolyphosphatases. here we report ...	2006	16678853
intersubunit disulfide interactions play a critical role in maintaining the thermostability of glucose-6-phosphate dehydrogenase from the hyperthermophilic bacterium aquifex aeolicus.	proteins from thermophilic microorganisms are stabilized by various mechanisms to preserve their native folded states at higher temperatures. a thermostable glucose-6-phosphate dehydrogenase (tg6pdh) from the hyperthermophilic bacterium aquifex aeolicus was expressed as a recombinant protein in escherichia coli. the a. aeolicus g6pdh is a homodimer exhibiting remarkable thermostability (t1/2 = 24 hr at 90 degrees c). based on homology modeling and upon comparison of its structure with human g6pd ...	2006	16721657
biochemical characterization of prephenate dehydrogenase from the hyperthermophilic bacterium aquifex aeolicus.	a monofunctional prephenate dehydrogenase (pd) from aquifex aeolicus was expressed as a his-tagged protein in escherichia coli and was purified by nickel affinity chromatography allowing the first biochemical and biophysical characterization of a thermostable pd. a. aeolicus pd is susceptible to proteolysis. in this report, the properties of the full-length pd are compared with one of these products, an n-terminally truncated protein variant (delta19pd) also expressed recombinantly in e. coli. b ...	2006	16731976
formation of functional tat translocases from heterologous components.	the tat pathway transports folded proteins across the cytoplasmic membrane of bacteria and the thylakoid membrane of plants. in eschericha coli, tat transport requires the integral membrane proteins tata, tatb and tatc. in this study we have tested the ability of tat genes from the eubacterial species pseudomonas syringae, streptomyces coelicolor and aquifex aeolicus, to compensate for the absence of the cognate e. coli tat gene, and thus to form functional tat translocases with e. coli tat comp ...	2006	16854235
a comprehensive structure-based alignment of prokaryotic and eukaryotic neurotransmitter/na+ symporters (nss) aids in the use of the leut structure to probe nss structure and function.	the recently elucidated crystal structure of a prokaryotic member of the neurotransmitter/sodium symporter (nss) family (yamashita et al., 2005) is a major advance toward understanding structure-function relationships in this important class of transporters. to aid in the generalization of these results, we present here a comprehensive sequence alignment of all known prokaryotic and eukaryotic nss proteins, based on the crystal structure of the leucine transporter from aquifex aeolicus (leut). r ...	2006	16880288
a homology model of sert based on the leut(aa) template.	a human serotonin transporter (sert) model has been constructed based on the crystal structure of the bacterial homologue of na(+)/cl(-)-dependent neurotransmitter transporters from aquifex aeolicus (leut(aa)). amino acids in the ligand binding area predicted by icm pocket finder included tyr95, ala96, asp98, gly100 (transmembrane helix (tmh) 1), ala169, ile172, ala173, tyr176 (tmh3), phe335, ser336, gly338, phe341, val343 (tmh6), thr439, ala441, and gly442 (tmh8). the present model is an update ...	2006	16919451
multiple assembly states of lumazine synthase: a model relating catalytic function and molecular assembly.	lumazine synthases have been observed in the form of pentamers, dimers of pentamers, icosahedral capsids consisting of 60 subunits and larger capsids with unknown molecular structure. here we describe the analysis of the assembly of native and mutant forms of lumazine synthases from bacillus subtilis and aquifex aeolicus at various ph values and in the presence of different buffers using small angle x-ray scattering and electron microscopy. both wild-type lumazine synthases are able to form caps ...	2006	16935304
comparative analysis and "expression space" coverage of the production of prokaryotic membrane proteins for structural genomics.	membrane proteins comprise up to one-third of prokaryotic and eukaryotic genomes, but only a very small number of membrane protein structures are known. membrane proteins are challenging targets for structural biology, primarily due to the difficulty in producing and purifying milligram quantities of these proteins. we are evaluating different methods to produce and purify large numbers of prokaryotic membrane proteins for subsequent structural and functional analysis. here, we present the compa ...	2006	16943447
occurrence of 1-glyceryl-1-myo-inosityl phosphate in hyperthermophiles.	the accumulation of compatible solutes was studied in the hyperthermophilic bacterium aquifex pyrophilus as a function of the temperature and the nacl concentration of the growth medium. nuclear magnetic resonance analysis of cell extracts revealed the presence of alpha- and beta-glutamate, di-mannosyl-di-myo-inositol phosphate, di-myo-inositol phosphate, and an additional compound here identified as 1-glyceryl-1-myo-inosityl phosphate. all solutes accumulated by a. pyrophilus are negatively cha ...	2006	16957243
molecular determinants of dihydrouridine synthase activity.	dihydrouridine is one of the most abundant modified bases in trna. however, little is known concerning the biochemistry of dihydrouridine synthase (dus) enzymes. to identify molecular determinants that are necessary for dus activity, we have developed a dus-complementation assay in escherichia coli. using this assay, we have identified amino-acid residues that are critical for the activity of yjbn, an e. coli dus. we also show that the aq1598 gene product, a putative dus from aquifex aeolicus, c ...	2006	16962594
kinetic folding and assembly mechanisms differ for two homologous heptamers.	here we investigate the time-resolved folding and assembly mechanism of the heptameric co-chaperonin protein 10 (cpn10) in vitro. the structure of cpn10 is conserved throughout nature: seven beta-barrel subunits are non-covalently assembled through beta-strand pairings in an overall doughnut-like shape. kinetic folding/assembly experiments of chemically denatured cpn10 from homo sapiens (hmcpn10) and aquifex aeolicus (aacpn10) were monitored by far-uv circular dichroism and fluorescence. we find ...	2006	16979655
thermostable rnase p rnas lacking p18 identified in the aquificales.	the rnase p rna (rnpb) and protein (rnpa) genes were identified in the two aquificales sulfurihydrogenibium azorense and persephonella marina. in contrast, neither of the two genes has been found in the sequenced genome of their close relative, aquifex aeolicus. as in most bacteria, the rnpa genes of s. azorense and p. marina are preceded by the rpmh gene coding for ribosomal protein l34. this genetic region, including several genes up- and downstream of rpmh, is uniquely conserved among all thr ...	2006	17005927
engineered zinc-binding sites confirm proximity and orientation of transmembrane helices i and iii in the human serotonin transporter.	the human serotonin transporter (hsert) regulates neurotransmission by removing released serotonin (5-ht) from the synapse. previous studies identified residues in sert transmembrane helices (tmhs) i and iii as interaction sites for substrates and antagonists. despite an abundance of data supporting a 12-tmh topology, the arrangement of the tmhs in sert and other biogenic amine transporters remains undetermined. a high-resolution structure of a bacterial leucine transporter that demonstrates hom ...	2006	17008722
a potential protein-rna recognition event along the risc-loading pathway from the structure of a. aeolicus argonaute with externally bound sirna.	argonaute proteins are key components of the rna-induced silencing complex (risc). they provide both architectural and catalytic functionalities associated with small interfering rna (sirna) guide strand recognition and subsequent guide strand-mediated cleavage of complementary mrnas. we report on the 3.0 a crystal structures of 22-mer and 26-mer sirnas bound to aquifex aeolicus argonaute (aa-ago), where one 2 nt 3' overhang of the sirna inserts into a cavity positioned on the outer surface of t ...	2006	17027504
biochemical and electron microscopic characterization of the f1f0 atp synthase from the hyperthermophilic eubacterium aquifex aeolicus.	the f(1)f(0) atp synthase has been purified from the hyperthermophilic eubacterium aquifex aeolicus and characterized. its subunits have been identified by maldi-mass spectrometry through peptide mass fingerprinting and ms/ms. it contains the canonical subunits alpha, beta, gamma, delta and epsilon of f(1) and subunits a and c of f(0). two versions of the b subunit were found, which show a low sequence homology to each other. most likely they form a heterodimer. an electron microscopic single pa ...	2006	17045990
folding of s6 structures with divergent amino acid composition: pathway flexibility within partly overlapping foldons.	studies of circular permutants have demonstrated that the folding reaction of s6 from thermus thermophilus (s6(t)) is malleable and responds in an ordered manner to changes of the sequence separation between interacting residues: the s6(t) permutants retain a common nucleation pattern in the form of a two-strand-helix motif that can be recruited from different parts of the structure. to further test the robustness of the two-strand-helix nucleus we have here determined the crystal structure and ...	2007	17056063
the nucleotide-binding site of aquifex aeolicus lpxc.	the structure of recombinant aquifex aeolicus udp-3-o-acyl-n-acetylglucosamine deacetylase (lpxc) in complex with udp has been determined to a resolution of 2.2 a. previous studies have characterized the binding sites of the fatty-acid and sugar moieties of the substrate, udp-(3-o-hydroxymyristoyl)-n-acetylglucosamine, but not that of the nucleotide. the uracil-binding site is constructed from amino acids that are highly conserved across species. hydrophobic associations with the phe155 and arg2 ...	2006	17077484
folding and assembly pathways of co-chaperonin proteins 10: origin of bacterial thermostability.	to compare folding/assembly processes of heptameric co-chaperonin proteins 10 (cpn10) from different species and search for the origin of thermostability in hyper-thermostable aquifex aeolicus cpn10 (aacpn10), we have studied two bacterial variants-aacpn10 and escherichia coli cpn10 (groes)-and compared the results to data on homo sapiens cpn10 (hmcpn10). equilibrium denaturation of groes by urea, guanidine hydrochloride (guhcl) and temperature results in coupled heptamer-to-monomer transitions ...	2006	17084377
crystal structure of the bifunctional atp sulfurylase-aps kinase from the chemolithotrophic thermophile aquifex aeolicus.	the thermophilic chemolithotroph, aquifex aeolicus, expresses a gene product that exhibits both atp sulfurylase and adenosine-5'-phosphosulfate (aps) kinase activities. these enzymes are usually segregated on two separate proteins in most bacteria, fungi, and plants. the domain arrangement in the aquifex enzyme is reminiscent of the fungal atp sulfurylase, which contains a c-terminal domain that is homologous to aps kinase yet displays no kinase activity. rather, in the fungal enzyme, the motif ...	2007	17095009
a present-day aminoacyl-trna synthetase with ancestral editing properties.	leucyl-, isoleucyl-, and valyl-trna synthetases form a subgroup of related aminoacyl-trna synthetases that attach similar amino acids to their cognate trnas. to prevent amino acid misincorporation during translation, these enzymes also hydrolyze mischarged trnas through a post-transfer editing mechanism. here we show that leurs from the deep-branching bacterium aquifex aeolicus edits the complete set of aminoacylated trnas generated by the three enzymes: ile-trna(ile), val-trna(ile), val-trna(va ...	2007	17095543
the substrate specificity of trna (m1g37) methyltransferase (trmd) from aquifex aeolicus.	transfer rna (m(1)g37) methyltransferase (trmd) catalyzes methyl-transfer from s-adenosyl-l-methionine to the n(1) atom of g37 in trna. in escherichia coli cells, trmd methylates trna species possessing a g36g37 sequence. it was previously believed that g36 was the positive determinant of trmd recognition. in the current study, we demonstrate that trmd from aquifex aeolicus methylates trna transcripts possessing an a36g37 sequence as well as trna transcripts possessing a g36g37 sequence. in cont ...	2006	17121543
structure of aquifex aeolicus argonaute highlights conformational flexibility of the paz domain as a potential regulator of rna-induced silencing complex function.	gene silencing mediated by rna interference requires the sequence-specific recognition of target mrna by the endonuclease argonaute, the primary enzymatic component of the rna-induced silencing complex. we report the crystal structure of aquifex aeolicus argonaute, refined at 3.2a resolution. relative to recent argonaute structures, a 24 degrees reorientation of the paz domain in our structure opens a basic cleft between the n-terminal and paz domains, exposing the guide strand binding pocket of ...	2007	17130125
split leucine-specific domain of leucyl-trna synthetase from the hyperthermophilic bacterium aquifex aeolicus.	leucyl-trna synthetase (leurs) from aquifex aeolicus is the only known heterodimer synthetase. it is named leurs alphabeta;, and its alpha and beta subunits contain 634 and 289 residues, respectively. like thermus thermophilus leurs, leurs alphabeta has a large extra domain, the leucine-specific domain, inserted into the catalytic domain. the subunit split site is exactly in the middle of the leucine-specific domain and may have a unique function. here, a series of mutants of leurs alphabeta con ...	2006	17144674
aquifex aeolicus trm1[trna (m2(2)g26) methyltransferase] has a novel recognition mechanism of the substrate rna.	aquifex aeolicus is a hyper-thermophilic eubacterium, which probably diverged at the earliest period from the other bacteria on the evolution of life. therefore, analyses of rna modification enzymes of this bacterium may supply important information in relation to the establishment of the early protein synthesis. in the previous meeting, we have reported that aquifex aeolicus trm1 gene product possesses a trna (m2(2)g26) methyltransferase activity. this enzyme catalyzes the methyl-transfer from ...	2005	17150754
the core domain of aquifex aeolicus trna (m7g46) methyltransferase has the methyl-transfer activity to trna.	transfer rna (m(7)g46) methyltransferase [trmb] catalyses the transfer of methyl groups from s-adenosyl-l-methionine to the n(7)-atom of guanine at position 46 in trna. trmb proteins from thermophilic bacteria such as aquifex aeolicus have a long c-terminal region as compared to those from mesophilic bacteria. further, n-terminal region observed in trmb proteins from mesophiles is missing in a. aeolicus trmb. therefore, we considered that this distinct c-terminal region in a. aeolicus trmb might ...	2006	17150909
binding of uridine 5'-diphosphate in the "basic patch" of the zinc deacetylase lpxc and implications for substrate binding.	lpxc is a zinc metalloenzyme that catalyzes the first committed step in the biosynthesis of lipid a, a vital component of the outer membrane of gram-negative bacteria. accordingly, the inhibition of lpxc is an attractive strategy for the treatment of gram-negative bacterial infections. here, we report the 2.7 a resolution x-ray crystal structure of lpxc from aquifex aeolicus complexed with uridine 5'-diphosphate (udp), and the 3.1 a resolution structure of lpxc complexed with pyrophosphate. the ...	2006	17176043
reengineering cca-adding enzymes to function as (u,g)- or dcdcda-adding enzymes or poly(c,a) and poly(u,g) polymerases.	cca-adding enzymes build and repair the 3'-terminal cca sequence of trna. these unusual rna polymerases use either a ribonucleoprotein template (class i) or pure protein template (class ii) to form mock base pairs with the watson-crick edges of incoming ctp and atp. guided by the class ii bacillus stearothermophilus cca-adding enzyme structure, we introduced mutations designed to reverse the polarity of hydrogen bonds between the nucleobases and protein template. we were able to transform the cc ...	2007	17179213
localization of cocaine analog [125i]rti 82 irreversible binding to transmembrane domain 6 of the dopamine transporter.	the site of cocaine binding on the dopamine transporter (dat) was investigated using the photoactivatable irreversible cocaine analog [125i]3beta-(p-chlorophenyl)tropane-2beta-carboxylic acid, 4'-azido-3'-iodophenylethyl ester ([125i]rti 82). the incorporation site of this compound was mapped to transmembrane domains (tms) 4-6 using epitope-specific immunoprecipitation of trypsin fragments and further localized using cyanogen bromide (cnbr), which hydrolyzes proteins on the c-terminal side of me ...	2007	17255098
crystallization and x-ray diffraction analysis of the beta-ketoacyl-acyl carrier protein reductase fabg from aquifex aeolicus vf5.	the gene product of fabg from aquifex aeolicus has been heterologously expressed in escherichia coli. purification of the protein took place using anion-exchange and size-exclusion chromatography and the protein was then crystallized. diffraction data were collected to a maximum resolution of 1.8 a and the initial phases were determined by molecular replacement. the a. aeolicus fabg protein is a putative beta-ketoacyl-acyl carrier protein reductase. structure-function studies of this protein are ...	2007	17277451
inhibition of lipid a biosynthesis as the primary mechanism of chir-090 antibiotic activity in escherichia coli.	the deacetylation of udp-3-o-[(r)-3-hydroxymyristoyl]-n-acetylglucosamine (udp-3-o-acyl-glcnac) by lpxc is the committed reaction of lipid a biosynthesis. chir-090, a novel n-aroyl-l-threonine hydroxamic acid, is a potent, slow, tight-binding inhibitor of the lpxc deacetylase from the hyperthermophile aquifex aeolicus, and it has excellent antibiotic activity against pseudomonas aeruginosa and escherichia coli, as judged by disk diffusion assays. we now report that chir-090 is also a two-step sl ...	2007	17335290
crystal structures of the pilus retraction motor pilt suggest large domain movements and subunit cooperation drive motility.	pilt is a hexameric atpase required for bacterial type iv pilus retraction and surface motility. crystal structures of adp- and atp-bound aquifex aeolicus pilt at 2.8 and 3.2 a resolution show n-terminal pas-like and c-terminal reca-like atpase domains followed by a set of short c-terminal helices. the hexamer is formed by extensive polar subunit interactions between the atpase core of one monomer and the n-terminal domain of the next. an additional structure captures a nonsymmetric pilt hexamer ...	2007	17355871
crystal structure of a peptidoglycan glycosyltransferase suggests a model for processive glycan chain synthesis.	peptidoglycan is an essential polymer that forms a protective shell around bacterial cell membranes. peptidoglycan biosynthesis is the target of many clinically used antibiotics, including the beta-lactams, imipenems, cephalosporins, and glycopeptides. resistance to these and other antibiotics has prompted interest in an atomic-level understanding of the enzymes that make peptidoglycan. representative structures have been reported for most of the enzymes in the pathway. until now, however, there ...	2007	17360321
structural and mechanistic changes along an engineered path from metallo to nonmetallo 3-deoxy-d-manno-octulosonate 8-phosphate synthases.	there are two classes of kdo8p synthases characterized respectively by the presence or absence of a metal in the active site. the nonmetallo kdo8ps from escherichia coli and the metallo kdo8ps from aquifex aeolicus are the best characterized members of each class. all amino acid residues that make important contacts with the substrates are conserved in both enzymes with the exception of pro-10, cys-11, ser-235, and gln-237 of the a. aeolicus enzyme, which correspond respectively to met-25, asn-2 ...	2007	17381075
homology modeling of the serotonin transporter: insights into the primary escitalopram-binding site.	the serotonin transporter (sert) is one of the neurotransmitter transporters that plays a critical role in the regulation of endogenous amine concentrations and therefore is an important target for therapeutic agents affecting the central nervous system. the recently published, high resolution x-ray structure of the closely related amino acid transporter, aquifex aeolicus leucine transporter (leut), provides an opportunity to develop a three-dimensional model of the structure of sert. we present ...	2007	17405130
mechanism and putative structure of b(0)-like neutral amino acid transporters.	the na(+)-dependent transport of neutral amino acids in epithelial cells and neurons is mediated by b(0)-type neutral amino acid transporters. two b(0)-type amino acid transporters have been identified in the neurotransmitter transporter family slc6, namely b(0)at1 (slc6a19) and b(0)at2 (slc6a15). in contrast to other members of this family, b(0)-like transporters are chloride-independent. b(0)at1 and b(0)at2 preferentially bind the substrate prior to the na(+)-ion. the na(+)-concentration affec ...	2007	17417702
molecular dynamics simulations of na+/cl(-)-dependent neurotransmitter transporters in a membrane-aqueous system.	we have performed molecular dynamics simulations of a homology model of the human serotonin transporter (hsert) in a membrane environment and in complex with either the natural substrate 5-ht or the selective serotonin reuptake inhibitor escitalopram. we have also included a transporter homologue, the aquifex aeolicus leucine transporter (leut), in our study to evaluate the applicability of a simple and computationally attractive membrane system. fluctuations in leut extracted from simulations a ...	2007	17436258
atp ground- and transition states of bacterial enhancer binding aaa+ atpases support complex formation with their target protein, sigma54.	transcription initiation by the sigma54 form of bacterial rna polymerase requires hydrolysis of atp by an enhancer binding protein (ebp). we present sas-based solution structures of the atpase domain of the ebp ntrc1 from aquifex aeolicus in different nucleotide states. structures of apo protein and that bound to amppnp or adp-bef(x) (ground-state mimics), adp-alf(x) (a transition-state mimic), or adp (product) show substantial changes in the position of the gaftga loops that contact polymerase, ...	2007	17437715
a robust metallo-oxidase from the hyperthermophilic bacterium aquifex aeolicus.	the gene, aquifex aeolicus aac07157.1, encoding a multicopper oxidase (mcoa) and localized in the genome as part of a putative copper-resistance determinant, has been cloned, over-expressed in escherichia coli and the recombinant enzyme purified to homogeneity. the purified enzyme shows spectroscopic and biochemical characteristics typical of the well-characterized multicopper oxidase family of enzymes. mcoa presents higher specificity (k(cat)/k(m)) for cuprous and ferrous ions than for aromatic ...	2007	17451433
bifunctional ctp:inositol-1-phosphate cytidylyltransferase/cdp-inositol:inositol-1-phosphate transferase, the key enzyme for di-myo-inositol-phosphate synthesis in several (hyper)thermophiles.	the pathway for the synthesis of di-myo-inositol-phosphate (dip) was recently elucidated on the basis of the detection of the relevant activities in cell extracts of archaeoglobus fulgidus and structural characterization of products by nuclear magnetic resonance (nmr) (n. borges, l. g. gonçalves, m. v. rodrigues, f. siopa, r. ventura, c. maycock, p. lamosa, and h. santos, j. bacteriol. 188:8128-8135, 2006). here, a genomic approach was used to identify the genes involved in the synthesis of dip. ...	2007	17526717
structure of o67745_aquae, a hypothetical protein from aquifex aeolicus.	using single-wavelength anomalous dispersion data obtained from a gold-derivatized crystal, the x-ray crystal structure of the protein 067745_aquae from the prokaryotic organism aquifex aeolicus has been determined to a resolution of 2.0 a. amino-acid residues 1-371 of the 44 kda protein were identified by pfam as an hd domain and a member of the metal-dependent phosphohydrolase superfamily (accession no. pf01966). although three families from this large and diverse group of enzymatic proteins a ...	2007	17565173
protein aq_1862 from the hyperthermophilic bacterium aquifex aeolicus is a porin and contains two conductance pathways of different selectivity.	the "hypothetical protein" aq_1862 was isolated from the membrane fraction of aquifex aeolicus and identified as the major porin. in experiments with one conducting unit (molecule) a conductance of 1.4 ns was observed in 0.1 m kcl at ph 7.5. this stable (basic) conductance was superimposed by conductance fluctuations of approximately 0.25 ns. because both events were always observed simultaneously, it is suggested that they are caused by the same molecular entity. nonetheless they show very diff ...	2007	17586565
structural and functional analysis of two glutamate racemase isozymes from bacillus anthracis and implications for inhibitor design.	glutamate racemase (race) is responsible for converting l-glutamate to d-glutamate, which is an essential component of peptidoglycan biosynthesis, and the primary constituent of the poly-gamma-d-glutamate capsule of the pathogen bacillus anthracis. race enzymes are essential for bacterial growth and lack a human homolog, making them attractive targets for the design and development of antibacterial therapeutics. we have cloned, expressed and purified the two glutamate racemase isozymes, race1 an ...	2007	17610893
phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases.	the beta/alpha-barrel fold type basic amino acid decarboxylases include eukaryotic ornithine decarboxylases (odc) and bacterial and plant enzymes with activity on l-arginine and meso-diaminopimelate. these enzymes catalyze essential steps in polyamine and lysine biosynthesis. phylogenetic analysis suggests that diverse bacterial species also contain odc-like enzymes from this fold type. however, in comparison with the eukaryotic odcs, amino acid differences were identified in the sequence of the ...	2007	17626020