Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| [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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| [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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| analysis of a multicomponent thermostable dna polymerase iii replicase from an extreme thermophile. | this report takes a proteomic/genomic approach to characterize the dna polymerase iii replication apparatus of the extreme thermophile, aquifex aeolicus. genes (dnax, hola, and holb) encoding the subunits required for clamp loading activity (tau, delta, and delta') were identified. the dnax gene produces only the full-length product, tau, and therefore differs from escherichia coli dnax that produces two proteins (gamma and tau). nonetheless, the a. aeolicus proteins form a taudeltadelta' comple ... | 2002 | 11859073 |
| the proton-pumping nadh:ubiquinone oxidoreductase (complex i) of aquifex aeolicus. | the proton-pumping nadh:ubiquinone oxidoreductase, also called complex i, is the first energy-transducing complex of many respiratory chains. homologues of complex i are present in the three domains of life. here, we report the properties of complex i in membranes of the hyperthermophilic bacterium aquifex aeolicus. the complex reacted with nadh but not with nadph and f(420)h(2) as electron donors. short-chain analogues of ubiquinone like decyl-ubiquinone and ubiquinone-2 were suitable electron ... | 2002 | 11852056 |
| a dna repair system specific for thermophilic archaea and bacteria predicted by genomic context analysis. | during a systematic analysis of conserved gene context in prokaryotic genomes, a previously undetected, complex, partially conserved neighborhood consisting of more than 20 genes was discovered in most archaea (with the exception of thermoplasma acidophilum and halobacterium nrc-1) and some bacteria, including the hyperthermophiles thermotoga maritima and aquifex aeolicus. the gene composition and gene order in this neighborhood vary greatly between species, but all versions have a stable, conse ... | 2002 | 11788711 |
| cloning, expression and preliminary x-ray analysis of the dihydroorotase from the hyperthermophilic eubacterium aquifex aeolicus. | dihydroorotase (dhoase) catalyzes the formation of dihydroorotate in the de novo pyrimidine biosynthetic pathway. the gene encoding the type i dhoase from the hyperthermophilic bacterium aquifex aeolicus has been cloned in escherichia coli with a polyhistidine affinity tag appended to the amino-terminal end and sequenced. the recombinant protein was expressed at high levels and could be purified readily in a single step by ni(2+) affinity chromatography. both native and selenomethionine-labeled ... | 2002 | 11752797 |
| structures of aquifex aeolicus kdo8p synthase in complex with r5p and pep, and with a bisubstrate inhibitor: role of active site water in catalysis. | we have determined the crystal structures of the metalloenzyme 3-deoxy-d-manno-octulosonate 8-phosphate (kdo8p) synthase from aquifex aeolicus in complex with phosphoenolpyruvate (pep) and ribose 5-phosphate (r5p), and with a bisubstrate inhibitor that mimics the postulated linear reaction intermediate. r5p, which is not a substrate for kdo8p synthase, binds in a manner similar to that of arabinose 5-phosphate (a5p), which is the natural substrate. the lack of reactivity of r5p appears to be pri ... | 2001 | 11747443 |
| crystallographic and modeling studies of rnase iii suggest a mechanism for double-stranded rna cleavage. | aquifex aeolicus ribonuclease iii (aa-rnase iii) belongs to the family of mg(2+)-dependent endonucleases that show specificity for double-stranded rna (dsrna). rnase iii is conserved in all known bacteria and eukaryotes and has 1-2 copies of a 9-residue consensus sequence, known as the rnase iii signature motif. the bacterial rnase iii proteins are the simplest, consisting of two domains: an n-terminal endonuclease domain, followed by a double-stranded rna binding domain (dsrbd). the three-dimen ... | 2001 | 11738048 |
| prokaryotic structural maintenance of chromosomes (smc) proteins: distribution, phylogeny, and comparison with mukbs and additional prokaryotic and eukaryotic coiled-coil proteins. | structural maintenance of chromosomes (smc) proteins are known to be essential for chromosome segregation in some prokaryotes and in eukaryotes. a systematic search for the distribution of smc proteins in prokaryotes with fully or partially sequenced genomes showed that they form a larger family than previously anticipated and raised the number of known prokaryotic homologs to 54. secondary structure predictions revealed that the length of the globular n-terminal and c-terminal domains is extrem ... | 2001 | 11707343 |
| collaboration between cc- and a-adding enzymes to build and repair the 3'-terminal cca of trna in aquifex aeolicus. | the universal 3'-terminal cca sequence of all transfer rnas (trnas) is repaired, and sometimes constructed de novo, by the cca-adding enzyme [atp(ctp):trna nucleotidyltransferase]. this rna polymerase has no nucleic acid template, yet faithfully builds the cca sequence one nucleotide at a time using cytidine triphosphate (ctp) and adenosine triphosphate (atp) as substrates. all previously characterized cca-adding enzymes from all three kingdoms are single polypeptides with cca-adding activity. h ... | 2001 | 11701927 |
| isolation and characterisation of the ylme homologue of thermus thermophilus. | screening of a thermus thermophilus genomic library led to the identification of a homologue of the ylme gene. ylme is highly conserved in widely divergent organisms from prokaryotes to mammals, suggesting an important, albeit currently unknown, cellular function. the 633 bp gene has a gc content of 69.2% overall and 90% in the third nucleotide position, while the gene product is predicted to be a soluble cytoplasmic protein of 23,441 da. it belongs to a family of conserved proteins of unknown f ... | 2001 | 11696977 |
| cytochromes c555 from the hyperthermophilic bacterium aquifex aeolicus. 2. heterologous production of soluble cytochrome c555s and investigation of the role of methionine residues. | the cycb2 gene encoding the soluble cytochrome c555s from aquifex aeolicus, an hyperthermophilic organism, has been cloned and expressed using escherichia coli as the host organism. the cytochrome was successfully produced in the periplasm of an e. coli strain coexpressing the ccmabcdefgh genes involved in the cytochrome c maturation process. comparison of native and recombinant cytochrome c555s shows that both proteins are indistinguishable in terms of spectroscopic and physicochemical properti ... | 2001 | 11695918 |
| cytochromes c555 from the hyperthermophilic bacterium aquifex aeolicus (vf5). 1. characterization of two highly homologous, soluble and membranous, cytochromes c555. | two distinct class i (monoheme) c-type cytochromes from the hyperthermophilic bacterium aquifex aeolicus were studied by biochemical and biophysical methods (i.e., optical and epr spectroscopy, electrochemistry). the sequences of these two heme proteins (encoded by the cycb1 and cycb2 genes) are close to identical (85% identity in the common part of the protein) apart from the presence of an n-terminal stretch of 62 amino acid residues present only in the cycb1 gene. a soluble cytochrome was pur ... | 2001 | 11695917 |
| signature lipids and stable carbon isotope analyses of octopus spring hyperthermophilic communities compared with those of aquificales representatives. | the molecular and isotopic compositions of lipid biomarkers of cultured aquificales genera have been used to study the community and trophic structure of the hyperthermophilic pink streamers and vent biofilm from octopus spring. thermocrinis ruber, thermocrinis sp. strain hi 11/12, hydrogenobacter thermophilus tk-6, aquifex pyrophilus, and aquifex aeolicus all contained glycerol-ether phospholipids as well as acyl glycerides. the n-c(20:1) and cy-c(21) fatty acids dominated all of the aquificale ... | 2001 | 11679343 |
| expression in escherichia coli of the thermostable inorganic pyrophosphatase from the aquifex aeolicus and purification and characterization of the recombinant enzyme. | the gene encoding the inorganic pyrophosphatase from a hyperthermophilic bacterium, aquifex aeolicus (aae), was amplified by pcr. then, the gene was overexpressed in escherichia coli using a pjr-based expression plasmid, paipd. the recombinant aae pyrophosphatase was purified 16.2-fold with a 53.4% yield and a specific activity of 34 u/mg protein by a combination of heating (to denature e. coli proteins) and two steps of deae-sephacel column chromatography (nonabsorbed enzyme at ph 7.3 and absor ... | 2001 | 11676598 |
| differential effects of replacing escherichia coli ribosomal protein l27 with its homologue from aquifex aeolicus. | the rpma gene, which encodes 50s ribosomal subunit protein l27, was cloned from the extreme thermophile aquifex aeolicus, and the protein was overexpressed and purified. comparison of the a. aeolicus protein with its homologue from escherichia coli by circular dichroism analysis and proton nuclear magnetic resonance spectroscopy showed that it readily adopts some structure in solution that is very stable, whereas the e. coli protein is unstructured under the same conditions. a mutant of e. coli ... | 2001 | 11673426 |
| central domain assembly: thermodynamics and kinetics of s6 and s18 binding to an s15-rna complex. | the 30 s ribosomal subunit assembles in vitro through the hierarchical binding of 21 ribosomal proteins to 16 s rrna. the central domain of 16 s rrna becomes the platform of the 30 s subunit upon binding of ribosomal proteins s6, s8, s11, s15, s18 and s21. the assembly of the platform is nucleated by binding of s15 to 16 s rrna, followed by the cooperative binding of s6 and s18. the prior binding of s6 and s18 is required for binding of s11 and s21. we have studied the mechanism of the cooperati ... | 2001 | 11601845 |
| mutational effects on thermostable superoxide dismutase from aquifex pyrophilus: understanding the molecular basis of protein thermostability. | we designed two mutants of superoxide dismutase (sod), one is thermostable and the other is thermolabile, which provide valuable insight to identify amino acid residues essential for the thermostability of the sod from aquifex pyrophilus (apsod). the mutant k12a, in which lys12 was replaced by ala, had increased thermostability compared to that of the wild type. the t(1/2) value of k12a was 210 min and that of the wild type was 175 min at 95 degrees c. however, the thermostability of the mutant ... | 2001 | 11594783 |
| hydrogenothermus marinus gen. nov., sp. nov., a novel thermophilic hydrogen-oxidizing bacterium, recognition of calderobacterium hydrogenophilum as a member of the genus hydrogenobacter and proposal of the reclassification of hydrogenobacter acidophilus as hydrogenobaculum acidophilum gen. nov., comb. nov., in the phylum 'hydrogenobacter/aquifex'. | a novel thermophilic, hydrogen-oxidizing bacterium, vm1t, has been isolated from a marine hydrothermal area of vulcano island, italy. cells of the strain were gram-negative rods, 2-4 microm long and 1-1.5 microm wide with four to seven monopolarly inserted flagella. cells grew chemolithoautotrophically under an atmosphere of h2/co2 (80:20) in the presence of low concentrations of o2 (optimum 1-2%). carbohydrates and peptide substrates were not utilized, neither for energy generation nor as a sou ... | 2001 | 11594618 |
| a novel carbamoyl-phosphate synthetase from aquifex aeolicus. | aquifex aeolicus, an extreme hyperthermophile, has neither a full-length carbamoyl-phosphate synthetase (cpsase) resembling the enzyme found in all mesophilic organisms nor a carbamate kinase-like cpsase such as those present in several hyperthermophilic archaea. however, the genome has open reading frames encoding putative proteins that are homologous to the major cpsase domains. the glutaminase, cps.a, and cps.b homologs from a. aeolicus were cloned, overexpressed in escherichia coli, and puri ... | 2001 | 11574542 |
| mapping the interaction of the [2fe-2s] clostridium pasteurianum ferredoxin with nitrogenase mofe protein. | the [2fe-2s] ferredoxin from clostridium pasteurianum had previously been shown to interact specifically with the nitrogenase mofe protein, and electrostatic forces were found to be important contributors to the interaction. this phenomenon has now been analyzed in detail by using ferredoxin variants in which charge inversions or cancellations were introduced on all charged residues. the mutated forms of the ferredoxin were covalently cross-linked to the mofe protein. the reaction products were ... | 2001 | 11566366 |
| a phylogenetic analysis of aquifex pyrophilus. | the 16s rrna of the bacterion aquifex pyrophilus, a microaerophilic, oxygen-reducing hyperthermophile, has been sequenced directly from the the pcr amplified gene. phylogenetic analyses show the aq. pyrophilus lineage to be probably the deepest (earliest) in the (eu)bacterial tree. the addition of this deep branching to the bacterial tree further supports the argument that the bacteria are of thermophilic ancestry. | 1992 | 11540077 |
| expression and characterization of the terminal heme synthetic enzymes from the hyperthermophile aquifex aeolicus. | the terminal two heme biosynthetic pathway enzymes, protoporphyrinogen oxidase and ferrochelatase, of the hyperthermophilic bacterium aquifex aeolicus have been expressed in escherichia coli, purified to homogeneity, and biochemically characterized. ferrochelatase and protoporphyrinogen oxidase of this organism are both monomeric, as was found for the corresponding enzymes of bacillus subtilis. however, unlike the b. subtilis proteins, both a. aeolicus enzymes are membrane-associated. both prote ... | 2001 | 11506917 |
| molecular cloning and characterization of thermostable dna ligase from aquifex pyrophilus, a hyperthermophilic bacterium. | a dna ligase gene from the hyperthermophilic bacterium aquifex pyrophilus (ap) was cloned and sequenced. an open reading frame of 2,157 bp that codes for a 82-kda protein showed 40%-60% homology with a series of nad+-dependent dna ligases from different organisms. the recombinant enzyme ap dna ligase expressed in escherichia coli was purified to homogeneity and characterized. the activity of ap dna ligase gradually increased in proportion to the concentration of monovalent salt up to 200 mm nacl ... | 2001 | 11453459 |
| purification and properties of aquifex aeolicus dna polymerase expressed in escherichia coli. | the gene encoding aquifex aeolicus (aae) dna polymerase was expressed under the control of the trp promoter on a high-copy plasmid, ptrpns, in escherichia coli. the expressed enzyme was purified 11-fold with a 13.8% yield and a specific activity of 2268.3 u mg(-1). the optimum ph of the enzyme was 6.8-7.2. the optimal concentrations of kcl and mg(2+) were 20-30 mm and 4-5 mm, respectively. aae dna polymerase contained a double-strand-dependent 3'-->5' proofreading exonuclease activity but lacked ... | 2001 | 11445170 |
| mutational analyses of aquifex pyrophilus dna ligase define essential domains for self-adenylation and dna binding activity. | we constructed nine deletion mutants of nad+-dependent dna ligase from aquifex pyrophilus to characterize the functional domains. all of dna ligase deletion mutants were analyzed in biochemical assays for nad+-dependent self-adenylation, dna binding, and nick-closing activity. although the mutant lsub1 (91-362) included the active site lysine (kxdg), self-adenylation was not shown. however, the mutants lsub6 (1-362), lsub7 (1-516), and lsub9 (1-635) showed the same adenylation activity as that o ... | 2001 | 11368162 |
| solution structure of the ribosome recycling factor from aquifex aeolicus. | the solution structure of ribosome recycling factor (rrf) from hyperthermophilic bacterium, aquifex aeolicus, was determined by heteronuclear multidimensional nmr spectroscopy. fifteen structures were calculated using restraints derived from noe, j-coupling, and t1/t2 anisotropies. the resulting structure has an overall l-shaped conformation with two domains and is similar to that of a trna molecule. the domain i (corresponding to the anticodon stem of trna) is a rigid three alpha-helix bundle. ... | 2001 | 11327859 |
| analysis of codon usage patterns of bacterial genomes using the self-organizing map. | codon usage varies both between organisms and between different genes in the same organism. this observation has been used as a basis for earlier work in identifying highly expressed and horizontally transferred genes in escherichia coli. in this work, we applied kohonen's self-organizing map to analysis of the codon usage pattern of the escherichia coli, aquifex aeolicus, archaeoglobus fulgidus, haemophilus influenzae rd:, methanococcus jannaschii, methanobacterium thermoautotrophicum, and pyro ... | 2001 | 11319263 |
| simultaneous binding of two proteins to opposite sides of a single transfer rna. | transfer rna (trna) is a small nucleic acid (typically 76 nucleotides) that forms binary complexes with proteins, such as aminoacyl trna synthetases (rs) and trbp111. the latter is a widely distributed structure-specific trna-binding protein that is incorporated into cell signaling molecules. the structure of trbp111 was modeled onto to the outer, convex side of the l-shaped trna. here we present rna footprints that are consistent with this model. this binding mode is in contrast to that of trna ... | 2001 | 11276256 |
| aquifex aeolicus 3-deoxy-d-manno-2-octulosonic acid 8-phosphate synthase: a new class of kdo 8-p synthase? | the relationship between 3-deoxy-d-manno-2-octulosonic acid 8-phosphate (kdo 8-p) synthase and 3-deoxy-d-arabino-2-heptulosonic acid 7-phosphate (dah 7-p) synthase has not been adequately addressed in the literature. based on recent reports of a metal requiring kdo 8-p synthase and the newly solved x-ray crystal structures of both escherichia coli kdo 8-p synthase and dah 7-p synthase, we begin to address the evolutionary kinship between these catalytically similar enzymes. using a maximum likel ... | 2001 | 11244581 |
| molecular cloning, expression, purification, and characterization of fructose-1,6-bisphosphate aldolase from thermus aquaticus. | fructose-1,6-bisphosphate aldolase from the thermophilic eubacteria, thermus aquaticus yt-1, was cloned and sequenced. nucleotide-sequence analysis revealed an open reading frame coding for a 33-kda protein of 305 amino acids having amino acid sequence typical of thermophilic adaptation. multiple sequence alignment classifies the enzyme as a class ii b aldolase that shares similarity with aldolases from other extremophiles: thermotoga maritima, aquifex aeolicus, and helicobacter pylori (49--54% ... | 2001 | 11237691 |
| x-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile aquifex aeolicus at 1.6 a resolution: determinants of thermostability revealed from structural comparisons. | an open reading frame optimized for expression of 6,7-dimethyl-8-ribityl-lumazine synthase of the hyperthermophilic bacterium aquifex aeolicus in escherichia coli was synthesized and expressed in a recombinant e. coli strain to a level of around 15 %. the recombinant protein was purified by heat-treatment and gel-filtration. the protein was crystallized in the cubic space group i23 with the cell dimensions a = b = c = 180.8 a, and diffraction data were collected to 1.6 a resolution. the structur ... | 2001 | 11237620 |
| phylogenetic analyses of two "archaeal" genes in thermotoga maritima reveal multiple transfers between archaea and bacteria. | the genome sequence of thermotoga maritima revealed that 24% of its open reading frames (orfs) showed the highest similarity scores to archaeal genes in blast analyses. here we screened 16 strains from the genus thermotoga and other related thermotogales for the occurrence of two of these "archaeal" genes: the gene encoding the large subunit of glutamate synthase (gltb) and the myo-inositol 1p synthase gene (ino1). both genes were restricted to the thermotoga species within the thermotogales. th ... | 2001 | 11230537 |
| genome of aquifex aeolicus. | 2001 | 11210496 | |
| site-directed mutagenesis of the bacterial metalloamidase udp-(3-o-acyl)-n-acetylglucosamine deacetylase (lpxc). identification of the zinc binding site. | udp-3-o-(acyl)-n-acetylglucosamine deacetylase (lpxc) catalyzes the second step in the biosynthesis of lipid a in gram-negative bacteria. compounds targeting this enzyme are proposed to chelate the single, essential zinc ion bound to lpxc and have been demonstrated to stop the growth of escherichia coli. a comparison of lpxc sequences from diverse bacteria identified 10 conserved his, asp, and glu residues that might play catalytic roles. each amino acid was altered in both e. coli and aquifex a ... | 2001 | 11148046 |
| cloning and characterization of thermostable endoglucanase (cel8y) from the hyperthermophilic aquifex aeolicus vf5. | aquifex aeolicus is the hyperthermophilic bacterium known, with growth-temperature maxima near 95 degrees c. the cel8y gene, encoding a thermostable endoglucanase (cel8y) from aquifex aeolicus vf5, was cloned into a vector for expression and expressed in escherichia coli xl1-blue. a clone of 1.7 kb fragment containing endoglucanase activity, designated pkycy100, was sequenced and found to contain an orf of 978 bp encoding a protein of 325 amino acid residues, with a calculated molecular mass of ... | 2000 | 11118302 |
| substrate and metal complexes of 3-deoxy-d-manno-octulosonate-8-phosphate synthase from aquifex aeolicus at 1.9-a resolution. implications for the condensation mechanism. | 3-deoxy-d-manno-octulosonate-8-phosphate synthase (kdo8ps) from the hyperthermophilic bacterium aquifex aeolicus differs from its escherichia coli counterpart in the requirement of a divalent metal for activity (duewel, h. s., and woodard, r. w. (2000) j. biol. chem. 275, 22824-22831). here we report the crystal structure of the a. aeolicus enzyme, which was determined by molecular replacement using e. coli kdo8ps as a model. the structures of the metal-free and cd(2+) forms of the enzyme were d ... | 2001 | 11115499 |
| crystal structure of trbp111: a structure-specific trna-binding protein. | trbp111 is a 111 amino acid aquifex aeolicus structure-specific trna-binding protein that has homologous counterparts distributed throughout evolution. a dimer is the functional unit for binding a single trna. here we report the 3d structures of the a.aeolicus protein and its escherichia coli homolog at resolutions of 2.50 and 1.87 a, respectively. the structure shows a symmetrical dimer of two core domains and a central dimerization domain where the n- and c-terminal regions of trbp111 form an ... | 2000 | 11101501 |
| genomic analysis of the genes encoding ribosomal proteins in eight eubacterial species and saccharomyces cerevisiae. | the complete genomic nucleotide sequence data of more than 10 unicellular organisms have become available. during the past years, we have been focusing our attention to the analysis of the structure and function of the ribosome and its protein components. by making use of the genomic sequence data, our work can now be extended to comparative analysis of the ribosomal components at the genomic level. such analysis will contribute to our understanding of the structure-function relationship of the ... | 1998 | 11072316 |
| the alternative sigma factor sigma(28) of the extreme thermophile aquifex aeolicus restores motility to an escherichia coli flia mutant. | sigma factor sigma(28) (sigma(f), flia, sigd) directs rna polymerase to transcribe the genes required for flagellar biosynthesis and chemotaxis in many bacteria, including bacillus subtilis, legionella pneumophila, salmonella typhimurium, escherichia coli, yersinia enterolytica, treponema maltophilum and pseudomonas aeruginosa. remarkably the flia gene from the extreme thermophile aquifex aeolicus restored motility to the e. coli mutant at relatively low temperature, albeit partially. this clear ... | 2000 | 11004406 |
| survey and summary: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. | holliday junction resolvases (hjrs) are key enzymes of dna recombination. a detailed computer analysis of the structural and evolutionary relationships of hjrs and related nucleases suggests that the hjr function has evolved independently from at least four distinct structural folds, namely rnase h, endonuclease, endonuclease vii-colicin e and rusa. the endonuclease fold, whose structural prototypes are the phage lambda exonuclease, the very short patch repair nuclease (vsr) and type ii restrict ... | 2000 | 10982859 |
| the phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. | the evolutionary relationships of proteobacteria, which comprise the largest and phenotypically most diverse division among prokaryotes, are examined based on the analyses of available molecular sequence data. sequence alignments of different proteins have led to the identification of numerous conserved inserts and deletions (referred to as signature sequences), which either are unique characteristics of various proteobacterial species or are shared by only members from certain subdivisions of p ... | 2000 | 10978543 |
| letter to the editor: 1h, 13c and 15n resonance assignments of aquifex aeolicus shikimate kinase in complex with the substrate shikimate. | 2000 | 10959638 | |
| structural and genomic correlates of hyperthermostability. | while most organisms grow at temperatures ranging between 20 and 50 degrees c, many archaea and a few bacteria have been found capable of withstanding temperatures close to 100 degrees c, or beyond, such as pyrococcus or aquifex. here we report the results of two independent large scale unbiased approaches to identify global protein properties correlating with an extreme thermophile lifestyle. first, we performed a comparative proteome analyses using 30 complete genome sequences from the three k ... | 2000 | 10940293 |
| recombinant superoxide dismutase from a hyperthermophilic archaeon, pyrobaculum aerophilium. | superoxide dismutase (sod) from the hyperthermophilic archaeon pyrobaculum aerophilum (a facultative aerobe) has been cloned and expressed in a mesophilic host (escherichia coli) as a soluble tetrameric apoprotein. the purified apoprotein can be reconstituted with either mn or fe by heating the protein with the appropriate metal salt at an elevated temperature (95 degrees c). both mn- and fe-reconstituted p. aerophilum sod exhibit superoxide dismutase activity, with the mn-containing enzyme havi ... | 2000 | 10907751 |
| a soxa gene, encoding a diheme cytochrome c, and a sox locus, essential for sulfur oxidation in a new sulfur lithotrophic bacterium. | a mobilizable suicide vector, psup5011, was used to introduce tn5-mob in a new facultative sulfur lithotrophic bacterium, kct001, to generate mutants defective in sulfur oxidation (sox(-)). the sox(-) mutants were unable to oxidize thiosulfate while grown mixotrophically in the presence of thiosulfate and succinate. the mutants were also impaired in oxidizing other reduced sulfur compounds and elemental sulfur as evident from the study of substrate oxidation by the whole cells. sulfite oxidase a ... | 2000 | 10894738 |
| three-dimensional model of human tip30, a coactivator for hiv-1 tat-activated transcription, and cc3, a protein associated with metastasis suppression. | human tip30 is a cofactor that specifically enhances human immunodeficiency virus-1 (hiv-1) tat-activated transcription. the sequence of tip30 is identical to that of cc3, a protein associated with metastasis suppression. tip30/cc3 is a member of the short-chain dehydrogenases/reductases (sdr) family. of the several experimentally determined sdr structures, escherichia coli uridine diphosphate (udp) galactose-4 epimerase is most similar to tip30/cc3. because the direct sequence similarity betwee ... | 2000 | 10892349 |
| structure of a thioredoxin-like [2fe-2s] ferredoxin from aquifex aeolicus. | the 2.3 a resolution crystal structure of a [2fe-2s] cluster containing ferredoxin from aquifex aeolicus reveals a thioredoxin-like fold that is novel among iron-sulfur proteins. the [2fe-2s] cluster is located near the surface of the protein, at a site corresponding to that of the active-site disulfide bridge in thioredoxin. the four cysteine ligands are located near the ends of two surface loops. two of these ligands can be substituted by non-native cysteine residues introduced throughout a st ... | 2000 | 10884354 |
| characterization of a solvent resistant and thermostable aminopeptidase from the hyperthermophillic bacterium, aquifex aeolicus. | a leucine aminopeptidase gene of aquifex aeolicus, a hyperthermophilic bacterium, was cloned and expressed in escherichia coli, and its expression product was purified and characterized. the expressed protein was purified to homogeneity by using heat to denature contaminating proteins followed by ion-exchange chromatography to purify the heat-stable product. the purified enzyme gave a single band on sds-page with a molecular weight of 54 kda. kinetic studies on the purified enzyme confirmed that ... | 2000 | 10862905 |
| cyanobacterial sulfide-quinone reductase: cloning and heterologous expression. | the gene encoding sulfide-quinone reductase (sqr; e.c.1.8.5.'), the enzyme catalyzing the first step of anoxygenic photosynthesis in the filamentous cyanobacterium oscillatoria limnetica, was cloned by use of amino acid sequences of tryptic peptides as well as sequences conserved in the rhodobacter capsulatus sqr and in an open reading frame found in the genome of aquifex aeolicus. sqr activity was also detected in the unicellular cyanobacterium aphanothece halophytica following sulfide inductio ... | 2000 | 10852862 |
| temperature-dependent function of the glutamine phosphoribosylpyrophosphate amidotransferase ammonia channel and coupling with glycinamide ribonucleotide synthetase in a hyperthermophile. | genes encoding glutamine phosphoribosylpyrophosphate amidotransferase (gpat) and glycinamide ribonucleotide synthetase (gars) from aquifex aeolicus were expressed in escherichia coli, and the enzymes were purified to near homogeneity. both enzymes were maximally active at a temperature of at least 90 degrees c, with half-lives of 65 min for gpat and 60 h for gars at 80 degrees c. gpat activity is known to depend upon channeling of nh(3) from a site in an n-terminal glutaminase domain to a distal ... | 2000 | 10850988 |