Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| a hyperthermophilic plant-type [2fe-2s] ferredoxin from aquifex aeolicus is stabilized by a disulfide bond. | a [2fe-2s] ferredoxin (fd1) from the hyperthermophilic bacterium aquifex aeolicus has been obtained by heterologous expression of the encoding gene in escherichia coli. sequence comparisons show that this protein belongs to the extended family of plant- and mammalian-type [2fe-2s] ferredoxins but also indicate that it is not closely similar to either the plant-type or mammalian-type subfamilies. instead, it appears to bear some similarity to novel members of this family, in particular the isc-ty ... | 2002 | 11863449 |
| helicobacter pylori 3-deoxy-d-manno-octulosonate-8-phosphate (kdo-8-p) synthase is a zinc-metalloenzyme. | 3-deoxy-d-manno-2-octulosonate-8-phosphate (kdo-8-p) synthase catalyzes the aldol-type condensation of phosphoenolpyruvate and d-arabinose-5-phosphate (a-5-p) to produce kdo-8-p and inorganic phosphate. all kdo-8-p synthases, as exemplified by the enzyme from escherichia coli, were believed not to require a metal cofactor for catalytic activity. however, recent studies have demonstrated that the kdo-8-p synthase from aquifex aeolicus is a metalloenzyme. moreover, sequence alignments and phylogen ... | 2002 | 11904225 |
| structure of small protein b: the protein component of the tmrna-smpb system for ribosome rescue. | small protein b (smpb) is an essential component of the highly conserved tmrna-smpb system that has the dual function of releasing stalled ribosomes from damaged messenger rnas and targeting incompletely synthesized protein fragments for degradation. nuclear magnetic resonance (nmr) analysis of smpb from aquifex aeolicus revealed an antiparallel beta-barrel structure, with three helices packed outside the core of the barrel. while the overall structure of smpb appears to be unique, the structure ... | 2002 | 11927568 |
| rusa proteins from the extreme thermophile aquifex aeolicus and lactococcal phage r1t resolve holliday junctions. | the rusa protein of escherichia coli is a dna structure-specific endonuclease that resolves holliday junction intermediates formed during dna replication, recombination and repair by introducing symmetrically paired incisions 5' to cc dinucleotides. it is encoded by the defective prophage dlp12, which raises the possibility that it may be of bacteriophage origin. we show that rusa-like sequences are indeed often associated with prophage sequences in the genomes of several bacterial species. they ... | 2002 | 11972790 |
| leucyl-trna synthetase from the extreme thermophile aquifex aeolicus has a heterodimeric quaternary structure. | class i aminoacyl-trna synthetases have been thought to be single polypeptide enzymes. however, the complete genome sequence of a hyper thermophile aquifex aeolicus suggests that the gene for leucyl-trna synthetases (leurs) is probably split into two pieces (leus and leus'). in this research, each gene was separately cloned and overexpressed in escherichia coli and the protein products were examined for leurs activity. leucylation activity was detected only when both gene products coexisted. gel ... | 2002 | 11997034 |
| cloning, analysis, and expression of the gene for inorganic pyrophosphatase of aquifex pyrophilus and properties of the enzyme. | the gene encoding aquifex pyrophilus (apy) pyrophosphatase was cloned and sequenced. the deduced amino acid sequence of apy pyrophosphatase showed a 94.2% homology to aquifex aeolicus (aae) pyrophosphatase. the gene exhibits a difference in the codon usage at the third position from aae pyrophosphatase. the gene was expressed under the control of a tac promoter in e. coli. the recombinant apy pyrophosphatase was purified 18.7-fold with a 52.8% yield and a specific activity of 26.2 u mg(-1) prote ... | 2002 | 12018853 |
| gas channels for nh(3): proteins from hyperthermophiles complement an escherichia coli mutant. | ammonium transport (amt) proteins appear to be bidirectional channels for nh(3). the amt genes of the hyperthermophiles aquifex aeolicus and methanococcus jannaschii complement enteric amtb mutants for growth at 25 nm nh(3) at 37 degrees c. to our knowledge, amt proteins are the first hyperthermophilic membrane transport proteins shown to be active in a mesophilic bacterium. despite low expression levels, his-tagged aquifex amt could be purified by heating and nickel chelate affinity chromatogra ... | 2002 | 12029058 |
| expression, refolding and crystallization of aquifex aeolicus elongation factor p. | elongation factor p is a universally conserved protein stimulating peptidyltransferase activity during protein synthesis. the factor is sensitive to classical inhibitors of the ribosomal peptidyltransferase activity and is possibly involved in alignment of the substrate trnas in the catalytic centre of 70s ribosomes. elongation factor p from the thermophilic aquifex aeolicus was overexpressed as a soluble protein in escherichia coli and crystallized. a fast generally applicable refolding protoco ... | 2002 | 12037310 |
| the branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. | the presence of shared conserved inserts and deletions (indels or signature sequences) in proteins provides a powerful means for understanding the evolutionary relationships among the bacteria. using such indels, all of the main groups within the bacteria can be defined in clear molecular terms and it has become possible to deduce that they branched from a common ancestor in the following order: low g + c gram-positive --> high g+c gram-positive --> deinococcus thermus --> cyanobacteria --> spir ... | 2001 | 12051562 |
| crystal structure of conserved hypothetical protein aq1575 from aquifex aeolicus. | the crystal structure of a conserved hypothetical protein, aq1575, from aquifex aeolicus has been determined by using x-ray crystallography. the protein belongs to the domain of unknown function duf28 in the pfam and pali databases for which there was no structural information available until now. a structural homology search with the dali algorithm indicates that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. the protein r ... | 2002 | 12060744 |
| crystallization of a stringent response factor from aquifex aeolicus. | the crystallization of a key enzyme from aquifex aeolicus with suggested bifunctional activity, acting as an exopolyphosphatase and a guanosine pentaphosphate phosphohydrolase, is reported. native data were collected to below 2 a resolution from an orthorhombic crystal with unit-cell parameters a = 50.8, b = 70.3, c = 90.9 a. methionine residues were introduced by mutation and deliberate oxidation of the protein allowed us to produce additional crystal forms with reproducible diffraction ability ... | 2002 | 12077442 |
| high resolution crystal structures of the wild type and cys-55-->ser and cys-59-->ser variants of the thioredoxin-like [2fe-2s] ferredoxin from aquifex aeolicus. | the [2fe-2s] ferredoxin (fd4) from aquifex aeolicus adopts a thioredoxin-like polypeptide fold that is distinct from other [2fe-2s] ferredoxins. crystal structures of the cys-55 --> ser (c55s) and cys-59 --> ser (c59s) variants of this protein have been determined to 1.25 a and 1.05 a resolution, respectively, whereas the resolution of the wild type (wt) has been extended to 1.5 a. the improved wt structure provides a detailed description of the [2fe-2s] cluster, including two features that have ... | 2002 | 12089152 |
| smpb: a protein that binds to double-stranded segments in tmrna and trna. | binding of the smpb protein to tmrna is essential for trans-translation, a process that facilitates peptide tagging of incompletely synthesized proteins. we have used three experimental approaches to study these interactions in vitro. gel mobility shift assays demonstrated that tmrna(delta90-299), a truncated tmrna derivative lacking pseudoknots 2-4, has the same affinity for the escherichia coli and aquifex aeolicus smpb proteins as the intact e. coli tmrna. these interactions can be challenged ... | 2002 | 12102625 |
| cysteine activation is an inherent in vitro property of prolyl-trna synthetases. | aminoacyl-trna synthetases are well known for their remarkable precision in substrate selection during aminoacyl-trna formation. some synthetases enhance the accuracy of this process by editing mechanisms that lead to hydrolysis of incorrectly activated and/or charged amino acids. prolyl-trna synthetases (prorss) can be divided into two structurally divergent groups, archaeal-type and bacterial-type enzymes. a striking difference between these groups is the presence of an insertion domain (appro ... | 2002 | 12130657 |
| persephonella marina gen. nov., sp. nov. and persephonella guaymasensis sp. nov., two novel, thermophilic, hydrogen-oxidizing microaerophiles from deep-sea hydrothermal vents. | two thermophilic, strictly chemolithoautotrophic, microaerophilic, hydrogen-oxidizing members of the bacteria designated strain ex-h1t and strain ex-h2t were isolated from two separate deep-sea hydrothermal vent sites at 9 degrees n 104 degrees w in the pacific ocean and guaymas basin. the motile 2-4-microm-long rods were gram-negative and non-sporulating. the temperature range for growth was between 55 and 80 degrees c for ex- h1t (optimum at 73 degrees c) and 55-75 c for ex-h2t (optimum at 70 ... | 2002 | 12148650 |
| critical issues in bacterial phylogeny. | to understand bacterial phylogeny, it is essential that the following two critical issues be resolved: (i) development of well-defined (molecular) criteria for identifying the main groups within bacteria, and (ii) to understand how the different main groups are related to each other and how they branched off from a common ancestor. these issues are not resolved at present. we have recently described a new approach, based on shared conserved inserts and deletions (indels or signature sequences) f ... | 2002 | 12167362 |
| leucyl-trna synthetase consisting of two subunits from hyperthermophilic bacteria aquifex aeolicus. | in a hyperthermophilic bacterium, aquifex aeolicus, leucyl-trna synthetase (leurs) consists of two non-identical polypeptide subunits (alpha and beta), different from the canonical leurs, which has a single polypeptide chain. by pcr, using genome dna of a. aeolicus as a template, genes encoding the alpha and beta subunits were amplified and cloned in escherichia coli. the alpha subunit could not be expressed stably in vivo, whereas the beta subunit was overproduced and purified by a simple proce ... | 2002 | 12196521 |
| crystal structures of transcription factor nusg in light of its nucleic acid- and protein-binding activities. | microbial transcription modulator nusg interacts with rna polymerase and termination factor rho, displaying striking functional homology to eukaryotic spt5. the protein is also a translational regulator. we have determined crystal structures of aquifex aeolicus nusg showing a modular design: an n-terminal rnp-like domain, a c-terminal element with a kow sequence motif and a species-specific immunoglobulin-like fold. the structures reveal bona fide nucleic acid binding sites, and nucleic acid bin ... | 2002 | 12198166 |
| cloning, expression, and characterization of the gsda gene encoding thermophilic glucose-6-phosphate dehydrogenase from aquifex aeolicus. | the gsda gene of the extreme thermophilic bacterium aquifex aeolicus, encoding glucose-6-phosphate dehydrogenase (g6pdh), was cloned into a high-expression vector and overexpressed as a fusion protein in escherichia coli. here we report the characterization of this recombinant thermostable g6pdh. g6pdh was purified to homogeneity by heat precipitation followed by immobilized metal affinity chromatography on a nickel-chelate column. the data obtained indicate that the enzyme is a homodimer with a ... | 2002 | 12215813 |
| new isolates and physiological properties of the aquificales and description of thermocrinis albus sp. nov. | the ecology of the aquificales was studied using a combination of phylogenetic and cultivation approaches. enrichment cultures were prepared from low-salt and marine samples of geothermally and volcanically heated environments of the united states (yellowstone national park), russia (kamchatka), italy, germany, djibouti, iceland, and africa (lake tanganyika). isolation of single cells using the selected cell cultivation technique resulted in 15 different pure cultures. comparisons of their 16s r ... | 2002 | 12215816 |
| the structure of bacterial dnaa: implications for general mechanisms underlying dna replication initiation. | the initiation of dna replication is a key event in the cell cycle of all organisms. in bacteria, replication initiation occurs at specific origin sequences that are recognized and processed by an oligomeric complex of the initiator protein dnaa. we have determined the structure of the conserved core of the aquifex aeolicus dnaa protein to 2.7 a resolution. the protein comprises an aaa+ nucleotide-binding fold linked through a long, helical connector to an all-helical dna-binding domain. the str ... | 2002 | 12234917 |
| the beta subunit of aquifex aeolicus leucyl-trna synthetase is responsible for cognate trna recognition. | the active form of the leucyl-trna synthetase from an extreme thermophile aquifex aeolicus has a heterodimeric (alpha/beta type) quaternary structure that is unique among class i aminoacyl-trna synthetases. in an attempt to clarify the individual roles of each subunit in the function of leucyl-trna synthetase, several elementary activities were separately measured using each of the subunits alone or the reconstructed alpha/beta complex. it was found that the beta subunit alone is capable of reco ... | 2002 | 12359246 |
| atp sulfurylase from the hyperthermophilic chemolithotroph aquifex aeolicus. | atp sulfurylase from the hyperthermophilic chemolithotroph aquifex aeolicus is a bacterial ortholog of the enzyme from filamentous fungi. (the subunit contains an adenosine 5'-phosphosulfate (aps) kinase-like, c-terminal domain.) the enzyme is highly heat stable with a half-life >1h at 90 degrees c. steady-state kinetics are consistent with a random a-b, ordered p-q mechanism where a=mgatp, b=so4(2-), p=pp(i), and q=aps. the kinetic constants suggest that the enzyme is optimized to act in the di ... | 2002 | 12361716 |
| nmr structure of bacterial ribosomal protein l20: implications for ribosome assembly and translational control. | l20 is a specific protein of the bacterial ribosome, which is involved in the early assembly steps of the 50s subunit and in the feedback control of the expression of its own gene. this dual function involves specific interactions with either the 23s rrna or its messenger rna. the solution structure of the free aquifex aeolicus l20 has been solved. it is composed of an unstructured n-terminal domain comprising residues 1-58 and a c-terminal alpha-helical domain. this is in contrast with what is ... | 2002 | 12368106 |
| closely related cc- and a-adding enzymes collaborate to construct and repair the 3'-terminal cca of trna in synechocystis sp. and deinococcus radiodurans. | the 3'-terminal cca sequence of trna is faithfully constructed and repaired by the cca-adding enzyme (atp(ctp):trna nucleotidyltransferase) using ctp and atp as substrates but no nucleic acid template. until recently, all cca-adding enzymes from all three kingdoms appeared to be composed of a single kind of polypeptide with dual specificity for adding both ctp and atp; however, we recently found that in aquifex aeolicus, which lies near the deepest root of the eubacterial 16 s rrna-based phyloge ... | 2002 | 12370185 |
| aquifex aeolicus pilt, homologue of a surface motility protein, is a thermostable oligomeric ntpase. | bacterial surface motility works by retraction of surface-attached type iv pili. this retraction requires the pilt protein, a member of a large family of putative ntpases from type ii and iv secretion systems. in this study, the pilt homologue from the thermophilic eubacterium aquifex aeolicus was cloned, overexpressed, and purified. a. aeolicus pilt was shown to be a thermostable atpase with a specific activity of 15.7 nmol of atp hydrolyzed/min/mg of protein. this activity was abolished when a ... | 2002 | 12426333 |
| function of his185 in aquifex aeolicus 3-deoxy-d-manno-octulosonate 8-phosphate synthase. | aquifex aeolicus 3-deoxy-d-manno-octulosonate 8-phosphate synthase (kdo8ps) catalyzes the condensation of arabinose 5-phosphate (a5p) and phosphoenolpyruvate (pep) by favoring the activation of a water molecule coordinated to the active-site metal ion. cys11, his185, glu222 and asp233 are the other metal ligands. wild-type kdo8ps is purified with zn(2+) or fe(2+) in the active site, but maximal activity in vitro is achieved when the endogenous metal is replaced with cd(2+). the h185g enzyme reta ... | 2002 | 12441100 |
| crystallization and preliminary x-ray diffraction studies of nusg, a protein shared by the transcription and translation machines. | n-utilization factor g (nusg) from aquifex aeolicus (aa) was overexpressed in escherichia coli, purified and crystallized using the hanging-drop vapor-diffusion technique. the drops consisted of 2.5 microl protein solution (approximately 30 mg ml(-1) in 20 mm tris-hcl ph 8.0, 200 mm nacl, 2 mm edta and 10 mm dtt) and 2.5 microl reservoir solution (0.085 m na hepes ph 7.5, 15% glycerol, 11% 2-propanol and 20% peg 4000) derived from condition number 41 of the hampton cryo screen. the crystals grew ... | 2002 | 12454485 |
| trna maturation in aquifex aeolicus. | several trnas in the hyperthermophilic bacterium aquifex aeolicus are encoded in clusters and as part of ribosomal rna operons, implying the requirement for trna processing by ribonuclease p (rnase p). intriguingly, neither a gene for the rna nor the protein component of this ubiquitous ribonucleoprotein enzyme has been hitherto identified in the sequenced genome of a. aeolicus, despite extensive data mining. as a result of the present study, primer extension analysis revealed that trnas in a. a ... | 2002 | 12457559 |
| exceptional stability of a [2fe-2s] ferredoxin from hyperthermophilic bacterium aquifex aeolicus. | aquifex aeolicus is the only hyperthermophile that is known to contain a plant- and mammalian-type [2fe-2s] ferredoxin (aae fd1). this unique protein contains two cysteines, in addition to the four that act as ligands of the [2fe-2s] cluster, which form a disulfide bridge. we have investigated the stability of aae fd1 with (wild-type) and without (c87a variant) the disulfide bond, with respect to ph, thermal and chemical perturbation, and compared the results to those for the mesophilic [2fe-2s] ... | 2002 | 12479408 |
| trbp111 selectively binds a noncovalently assembled trna-like structure. | transfer rnas are key components of the genetic code by virtue of aminoacylation reactions whereby each amino acid is linked to the trna that bears the anticodon for the attached amino acid. the l-shaped trna structure contains two domains connected at right angles through a corner formed from tertiary interactions involving loops of each domain. some evidence suggests that the domains arose separately and eventually were fused into a single covalent structure. in this scenario, the present-day ... | 2002 | 12481025 |
| lytb protein catalyzes the terminal step of the 2-c-methyl-d-erythritol-4-phosphate pathway of isoprenoid biosynthesis. | recombinant lytb protein from the thermophilic eubacterium aquifex aeolicus produced in escherichia coli was purified to apparent homogeneity. the purified lytb protein catalyzed the reduction of (e)-4-hydroxy-3-methyl-but-2-enyl diphosphate (hmbpp) in a defined in vitro system. the reaction products were identified as isopentenyl diphosphate and dimethylallyl diphosphate. a spectrophotometric assay was established to determine the steady-state kinetic parameters of lytb protein. the maximal spe ... | 2002 | 12482608 |
| the processing of human mitochondrial leucyl-trna synthetase in the insect cells. | a his-tagged full-length cdna of human mitochondrial leucyl-trna synthetase was expressed in a baculovirus system. the n-terminal sequence of the enzyme isolated from the mitochondria of insect cells was found to be iysatgkwtkeytl, indicating that the mitochondrial targeting signal peptide was cleaved between ser39 and ile40 after the enzyme precursor was translocated into mitochondria. the enzyme purified from mitochondria catalyzed the leucylation of escherichia coli trna(1)(leu)(cag) and aqui ... | 2003 | 12527375 |
| [identification and cloning of partial mbh2 gene cluster of hyperthermophile aquifex pyrophilus]. | a 0.8 kb fragment of mbhs2 gene of aquifex pyrophilus was obtained by pcr with designed primers basing mbhs2 gene of a. aeolicus. it showed 85% homology with the corresponding region of a. aeolicus. using it as probe, a 5.0 kb nco i fragment was fished out from the partial genomic library of a. pyrophilus. then this fragment was cloned, subcloned and sequenced. the result revealed that the fragment contains the full length gene for the mbhs2, the gene orf1 and the first 366 bp of orf2. compariso ... | 2001 | 12552822 |
| an isc-type extremely thermostable [2fe-2s] ferredoxin from aquifex aeolicus. biochemical, spectroscopic, and unfolding studies. | analysis of the genome of the hyperthermophilic bacterium aquifex aeolicus has revealed the presence of a previously undetected gene potentially encoding a plant- and mammalian-type [2fe-2s] ferredoxin. expression of that gene in escherichia coli has yielded a novel thermostable [2fe-2s] ferredoxin (designated ferredoxin 5) whose sequence is most similar to those of ferredoxins involved in the assembly of iron-sulfur clusters (isc-fd). it nevertheless differs from the latter proteins by having d ... | 2003 | 12564939 |
| a spring-loaded state of nusg in its functional cycle is suggested by x-ray crystallography and supported by site-directed mutants. | transcription factor nusg is present in all prokaryotes, and orthologous proteins have also been identified in yeast and humans. nusg contains a 27-residue kow motif, found in ribosomal protein l24 where it interacts with rrna. nusg in escherichia coli (ecnusg) is an essential protein and functions as a regulator of rho-dependent transcription termination, phage lambda n and rrna transcription antitermination, and phage hk022 nun termination. relative to ecnusg, aquifex aeolicus nusg (aanusg) an ... | 2003 | 12600194 |
| laccases and their occurrence in prokaryotes. | laccases are copper-containing proteins that require o(2) to oxidize phenols, polyphenols, aromatic amines, and different non-phenolic substrates by one-electron transfer, resulting in the formation of reactive radicals. although their specific physiological functions are not completely understood, there are several indications that laccases are involved in the morphogenesis of microorganisms (e.g., fungal spore development, melanization) and in the formation and/or degradation of complex organi ... | 2003 | 12610719 |
| exafs studies of the zinc sites of udp-(3-o-acyl)-n-acetylglucosamine deacetylase (lpxc). | extended x-ray absorption fine structure (exafs) spectroscopy has been used to determine the structure of the zn(ii) sites in udp-(3-o-acyl)-n-acetylglucosamine deacetylase (lpxc) from aquifex aeolicus and pseudomonas aeruginosa. the active site zn(ii) is four coordinate, with exclusively low-z (nitrogen and oxygen) ligation in both enzymes. the amplitude of the outer-shell scattering from the histidine ligands is best fit using two histidine ligands, suggesting a zno(2)(his)(2) site, where o mo ... | 2003 | 12620676 |
| isolation, characterization and electron microscopic single particle analysis of the nadh:ubiquinone oxidoreductase (complex i) from the hyperthermophilic eubacterium aquifex aeolicus. | the proton-translocating nadh:ubiquinone oxidoreductase (complex i) has been purified from aquifex aeolicus, a hyperthermophilic eubacterium of known genome sequence. the purified detergent solubilized enzyme is highly active above 50 degrees c. the specific activity for electron transfer from nadh to decylubiquinone is 29 u/mg at 80 degrees c. the a. aeolicus complex i is completely sensitive to rotenone and 2-n-decyl-quinazoline-4-yl-amine. sds polyacrylamide gel electrophoresis shows that it ... | 2003 | 12627969 |
| biotinylation in the hyperthermophile aquifex aeolicus. | biotin protein ligase (bpl) catalyses the biotinylation of the biotin carboxyl carrier protein (bccp) subunit of acetyl coa carboxylase and this post-translational modification of a single lysine residue is exceptionally specific. the exact details of the protein-protein interactions involved are unclear as a bpl:bccp complex has not yet been isolated. moreover, detailed information is lacking on the composition, biosynthesis and role of fatty acids in hyperthermophilic organisms. we have cloned ... | 2003 | 12631286 |
| voltammetry of a "protein on a rope". | a periplasmic electron-transfer protein, cytochrome c(555)(m) from aquifex aeolicus contains a 62-residue n-terminal extension by which it is anchored to the membrane--most probably via a thioester bond to its n-terminal cysteine. this linker can act as a "rope" to tether the protein close to its reaction partners. mimicking this principle, a recombinant cytochrome c(555)(m), expressed in escherichia coli, has been attached covalently to a gold electrode modified with 6-mercaptohexan-1-ol. the " ... | 2003 | 12650932 |
| [nife] hydrogenases from the hyperthermophilic bacterium aquifex aeolicus: properties, function, and phylogenetics. | genes potentially coding for three distinct [nife] hydrogenases are present in the genome of aquifex aeolicus. we have demonstrated that all three hydrogenases are expressed under standard growth conditions of the organism. two hydrogenases were further purified to homogeneity. a periplasmically oriented hydrogenase was obtained in two forms, i.e., as a soluble enzyme containing only the two essential subunits and as a detergent-solubilized complex additionally containing a membrane-integral b-t ... | 2003 | 12664267 |
| a novel uracil-dna glycosylase family related to the helix-hairpin-helix dna glycosylase superfamily. | cytosine bases can be deaminated spontaneously to uracil, causing dna damage. uracil-dna glycosylase (udg), a ubiquitous uracil-excising enzyme found in bacteria and eukaryotes, is one of the enzymes that repair this kind of dna damage. to date, no udg-coding gene has been identified in methanococcus jannaschii, although its entire genome was deciphered. here, we have identified and characterized a novel udg from m.jannaschii designated as mjudg. it efficiently removed uracil from both single- a ... | 2003 | 12682355 |
| a structure-based model of the reaction catalyzed by lumazine synthase from aquifex aeolicus. | 6,7-dimethyl-8-ribityllumazine is the biosynthetic precursor of riboflavin, which, as a coenzyme, plays a vital role in the electron transfer process for energy production in all cellular organisms. the enzymes involved in lumazine biosynthesis have been studied in considerable detail. however, the conclusive mechanism of the reaction catalyzed by lumazine synthase has remained unclear. here, we report four crystal structures of the enzyme from the hyperthermophilic bacterium aquifex aeolicus in ... | 2003 | 12684006 |
| aquifex aeolicus trna (gm18) methyltransferase has unique substrate specificity. trna recognition mechanism of the enzyme. | transfer rna (guanosine-2')-methyltransferase (gm-methylase) catalyzes the transfer of a methyl group from s-adenosyl-l-methionine to 2'-oh of g18 in the d-loop of trna. based on their mode of trna recognition, gm-methylases can be divided into the following two types: type i having broad specificity toward the substrate trna, and type ii that methylates only limited trna species. protein synthesized by in vitro cell-free translation revealed that gm-methylase encoded in the aquifex aeolicus gen ... | 2003 | 12704200 |
| crystal structure of the trna processing enzyme rnase ph from aquifex aeolicus. | rnase ph is one of the exoribonucleases that catalyze the 3' end processing of trna in bacteria. rnase ph removes nucleotides following the cca sequence of trna precursors by phosphorolysis and generates mature trnas with amino acid acceptor activity. in this study, we determined the crystal structure of aquifex aeolicus rnase ph bound with a phosphate, a co-substrate, in the active site at 2.3-a resolution. rnase ph has the typical alpha/beta fold, which forms a hexameric ring structure as a tr ... | 2003 | 12746447 |
| sulfurihydrogenibium subterraneum gen. nov., sp. nov., from a subsurface hot aquifer. | a polyphasic taxonomic study was performed on a novel facultatively anaerobic, hydrogen- or sulfur/thiosulfate-oxidizing, thermophilic chemolithoautotroph recently isolated from subsurface hot aquifer water in a japanese gold mine. the cells were straight to slightly curved rods, with a single polar flagellum. growth was observed at 40-70 degrees c (optimum 60-65 degrees c; 80 min doubling time) and at ph 6.4-8.8 (optimum ph 7.5). the isolate was unable to use complex organic compounds, carbohyd ... | 2003 | 12807207 |
| crystal structure of lpxc, a zinc-dependent deacetylase essential for endotoxin biosynthesis. | the outer leaflet of the outer membrane of the gram-negative bacterium serves as a permeability barrier and is composed of lipopolysaccharide, also known as endotoxin. the membrane anchor of lipopolysaccharide is lipid a, the biosynthesis of which is essential for cell viability. the first committed step in lipid a biosynthesis is catalyzed by udp-(3-o-(r-3-hydroxymyristoyl))-n-acetylglucosamine deacetylase (lpxc), a zinc-dependent deacetylase. here we report the crystal structure of lpxc from a ... | 2003 | 12819349 |
| enzymes assembled from aquifex aeolicus and escherichia coli leucyl-trna synthetases. | aquifex aeolicus alphabeta-leurs is the only known heterodimeric leurs, while escherichia coli leurs is a canonical monomeric enzyme. by using the genes encoding a. aeolicus and e. coli leurs as pcr templates, the genes encoding the alpha and beta subunits from a. aeolicus alphabeta-leurs and the equivalent amino- and carboxy-terminal parts of e. coli leurs (identified as alpha' and beta') were amplified and recombined using suitable plasmids. these recombinant plasmids were transformed or cotra ... | 2003 | 12820878 |
| structure of the hypothetical protein aq_1354 from aquifex aeolicus. | the crystal structure of a hypothetical protein aq_1354 (gi 2983779) from the hyperthermophilic bacteria aquifex aeolicus has been determined using x-ray crystallography. as found in many structural genomics studies, this protein is not associated with any known function based on its amino-acid sequence. psi-blast analysis against a non-redundant sequence database gave 68 similar sequences referred to as 'conserved hypothetical proteins' from the uncharacterized protein family upf0054 (accession ... | 2003 | 12832766 |
| structure of the lpxc deacetylase with a bound substrate-analog inhibitor. | the zinc-dependent udp-3-o-acyl-n-acetylglucosamine deacetylase (lpxc) catalyzes the first committed step in the biosynthesis of lipid a, the hydrophobic anchor of lipopolysaccharide (lps) that constitutes the outermost monolayer of gram-negative bacteria. as lpxc is crucial for the survival of gram-negative organisms and has no sequence homology to known mammalian deacetylases or amidases, it is an excellent target for the design of new antibiotics. the solution structure of lpxc from aquifex a ... | 2003 | 12833153 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| crystal structure of trna (m1g37) methyltransferase from aquifex aeolicus at 2.6 a resolution: a novel methyltransferase fold. | 2003 | 14517984 | |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| crystal structure of chorismate synthase from aquifex aeolicus reveals a novel beta alpha beta sandwich topology. | 2004 | 14705034 | |
| 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 | |
| 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 |
| nmr structure of the hypothetical protein aq-1857 encoded by the y157 gene from aquifex aeolicus reveals a novel protein fold. | 2004 | 14997575 | |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |